# HG changeset patch
# User galaxyp
# Date 1759357254 0
# Node ID b4f6df8fa89b98f8969320a7260db3f9ed2c25b5
# Parent  59fec1e2a6c368040015dd3f7255a1fab151a80f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4

diff -r 59fec1e2a6c3 -r b4f6df8fa89b fragpipe
--- a/fragpipe	Sun Mar 30 23:00:45 2025 +0000
+++ b/fragpipe	Wed Oct 01 22:20:54 2025 +0000
@@ -22,6 +22,10 @@
             shift
             ionquant_key=$1
             ;;
+        --diatracer_key)
+            shift
+            diatracer_key=$1
+            ;;
         --workflow)
             fragpipe_args+=("$1")
             shift
@@ -35,16 +39,7 @@
     shift
 done
 
-if [[ ! -z "$workflow_file" ]]; then
-    # Because the DIA-NN license is incompatible with bioconda, we remove the feature.
-    grep 'diann.run-dia-nn=true' "$workflow_file" >/dev/null
-    if [[ $? -eq 0 ]]; then
-        echo "Error: DIA-NN is disabled in the FragPipe bioconda package."
-        exit 1
-    fi
-fi
-
-if [[ -z $msfragger_key || -z $ionquant_key ]]; then
+if [[ -z $msfragger_key || -z $ionquant_key || -z $diatracer_key ]]; then
     echo "$license_agreement_text"
     exit 1
 else
@@ -60,6 +55,12 @@
         echo "$license_agreement_text"
         exit 1
     fi
+    diatracer --key $diatracer_key --help | grep 'License key verified' >/dev/null 2>&1
+    if [[ $? -ne 0 ]]; then
+        echo "Error: Invalid diaTracer license key"
+        echo "$license_agreement_text"
+        exit 1
+    fi
 fi
 
 sh fragpipe_local/bin/fragpipe "${fragpipe_args[@]}"
diff -r 59fec1e2a6c3 -r b4f6df8fa89b fragpipe.xml
--- a/fragpipe.xml	Sun Mar 30 23:00:45 2025 +0000
+++ b/fragpipe.xml	Wed Oct 01 22:20:54 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="fragpipe" name="FragPipe -  Academic Research and Education User License (Non-Commercial)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+<tool id="fragpipe" name="FragPipe -  Academic Research and Education User License (Non-Commercial)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
     <description>Data analysis for mass spectrometry-based proteomics</description>
     <macros>
         <import>macros.xml</import>
@@ -12,8 +12,9 @@
                level="fatal"
                description="A FragPipe pipeline process returned non-zero exit code."/>
     </stdio>
-
-    <version_command>fragpipe --help | grep 'FragPipe v'</version_command>
+    <version_command>
+        fragpipe --msfragger_key @MSFRAGGER_ACADEMIC_USE_KEY@ --ionquant_key @IONQUANT_ACADEMIC_USE_KEY@ --help | grep 'FragPipe v'
+    </version_command>
 
     <!--
         FragPipe wrapper command:
@@ -32,19 +33,24 @@
             @PREPARE_INPUTS@
             @PREPARE_DATABASE@
 
+            mkdir tools &&
+            ln -s \${env_location}/share/diatracer-*/diaTracer-*/diaTracer-*.jar tools/ &&
+            ln -s \${env_location}/share/ionquant-*/IonQuant-*/IonQuant-*.jar tools/ &&
+            ln -s \${env_location}/share/msfragger-*/MSFragger-*/MSFragger-*.jar tools/ &&
+            ln -s \${env_location}/share/msfragger-*/MSFragger-*/ext tools/ &&
+
             ## Run FragPipe
             '$__tool_directory__/fragpipe'
-                --msfragger_key f28c4be2-759b0a11-6c1ea652-1240565a
-                --ionquant_key 47cb2953-b4bf7726-2c96f5fe-8f1013aa
+                --msfragger_key @MSFRAGGER_ACADEMIC_USE_KEY@
+                --ionquant_key @IONQUANT_ACADEMIC_USE_KEY@
+                --diatracer_key @DIATRACER_ACADEMIC_USE_KEY@
                 --headless
                 --threads \${GALAXY_SLOTS:-8}
                 --ram \$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]
                 --workflow fp.workflow --manifest fp.manifest
                 --workdir outputs
-                --config-msfragger \${env_location}/share/msfragger-*/MSFragger-*/MSFragger-*.jar
-                --config-philosopher \$(which philosopher)
-                --config-python \$(which python)
-                --config-ionquant \${env_location}/share/ionquant-*/IonQuant.jar &&
+                --config-tools-folder tools
+                --config-python \$(which python) &&
 
             @PREPARE_OUTPUTS@
         #end if
@@ -76,65 +82,96 @@
             <option value="log">FragPipe Log</option>
             <option value="combined_outputs">FragPipe Combined Outputs</option>
             <option value="concatenated_outputs">TSV Outputs Concatenated</option>
+            <option value="individual_outputs">Individual Experiment Outputs</option>
         </param>
     </inputs>
 
     <outputs>
         <!-- Workflow file used by FragPipe -->
-        <data name="output_workflow" format="txt" label="${tool.name} on ${on_string}: workflow" from_work_dir="fp.workflow">
+        <data name="output_workflow" format="txt" label="FragPipe workflow" from_work_dir="fp.workflow">
             <filter>workflow_only or (output_options and 'workflow' in output_options)</filter>
         </data>
         <!-- FragPipe log -->
-        <data name="log" format="txt" label="${tool.name} on ${on_string}: log.txt" from_work_dir="outputs/log_*.txt">
+        <data name="log" format="txt" label="FragPipe log.txt" from_work_dir="outputs/log_*.txt">
             <filter>not workflow_only and output_options and 'log' in output_options</filter>
         </data>
 
+        <!-- DIA-NN Quant -->
+        <data name="diaquant_msstats_csv" format="csv" label="FragPipe DIA-NN Quant msstats.csv" from_work_dir="outputs/dia-quant-output/msstats.csv">
+            <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
+        </data>
+        <data name="diaquant_msstats_ptm_csv" format="csv" label="FragPipe DIA-NN Quant msstats_ptm.csv" from_work_dir="outputs/dia-quant-output/msstats_ptm.csv">
+            <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
+        </data>
+        <data name="diaquant_report_tsv_speclib" format="txt" label="FragPipe DIA-NN Quant report-tsv.speclib" from_work_dir="outputs/dia-quant-output/report-tsv.speclib">
+            <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
+        </data>
+        <data name="diaquant_report_gg_matrix_tsv" format="tsv" label="FragPipe DIA-NN Quant report.gg_matrix.tsv" from_work_dir="outputs/dia-quant-output/report.gg_matrix.tsv">
+            <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
+        </data>
+        <data name="diaquant_report_log_txt" format="txt" label="FragPipe DIA-NN Quant report.log.txt" from_work_dir="outputs/dia-quant-output/report.log.txt">
+            <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
+        </data>
+        <data name="diaquant_report_pg_matrix_tsv" format="tsv" label="FragPipe DIA-NN Quant report.pg_matrix.tsv" from_work_dir="outputs/dia-quant-output/report.pg_matrix.tsv">
+            <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
+        </data>
+        <data name="diaquant_report_pr_matrix_tsv" format="tsv" label="FragPipe DIA-NN Quant report.pr_matrix.tsv" from_work_dir="outputs/dia-quant-output/report.pr_matrix.tsv">
+            <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
+        </data>
+        <data name="diaquant_report_stats_tsv" format="tsv" label="FragPipe DIA-NN Quant report.stats.tsv" from_work_dir="outputs/dia-quant-output/report.stats.tsv">
+            <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
+        </data>
+        <data name="diaquant_report_tsv" format="tsv" label="FragPipe DIA-NN Quant report.tsv" from_work_dir="outputs/dia-quant-output/report.tsv">
+            <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
+        </data>
+        <data name="diaquant_report_unique_genes_matrix_tsv" format="tsv" label="FragPipe DIA-NN Quant report.unique_genes_matrix.tsv" from_work_dir="outputs/dia-quant-output/report.unique_genes_matrix.tsv">
+            <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
+        </data>
+
+
         <!-- Collection outputs comprised of separate results for different experiments -->
-        <collection name="output_psm" type="list" label="${tool.name} - ${on_string}: psm.tsv" >
-            <filter>not workflow_only</filter>
+        <collection name="output_psm" type="list" label="FragPipe psm.tsv" >
+            <filter>not workflow_only and 'individual_outputs' in output_options</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+\.psm.tsv)" ext="tabular" directory="outputs"/>
         </collection>
-        <collection name="output_ion" type="list" label="${tool.name} - ${on_string}: ion.tsv" >
-            <filter>not workflow_only</filter>
+        <collection name="output_ion" type="list" label="FragPipe ion.tsv" >
+            <filter>not workflow_only and 'individual_outputs' in output_options</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+\.ion.tsv)" ext="tabular" directory="outputs"/>
         </collection>
-        <collection name="output_peptide" type="list" label="${tool.name} - ${on_string}: peptide.tsv" >
-            <filter>not workflow_only</filter>
+        <collection name="output_peptide" type="list" label="FragPipe peptide.tsv" >
+            <filter>not workflow_only and 'individual_outputs' in output_options</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+\.peptide.tsv)" ext="tabular" directory="outputs"/>
         </collection>
-        <collection name="output_protein" type="list" label="${tool.name} - ${on_string}: protein.tsv" >
-            <filter>not workflow_only</filter>
+        <collection name="output_protein" type="list" label="FragPipe protein.tsv" >
+            <filter>not workflow_only and 'individual_outputs' in output_options</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+\.protein.tsv)" ext="tabular" directory="outputs"/>
         </collection>
 
         <!-- Combined results from all experimental groups -->
-        <collection name="combined_outputs" type="list" label="${tool.name} - ${on_string}: Combined Outputs" >
+        <collection name="combined_outputs" type="list" label="FragPipe Combined Outputs" >
             <filter>not workflow_only and output_options and 'combined_outputs' in output_options</filter>
             <discover_datasets pattern="__designation__" ext="tabular" directory="outputs/combined_outputs"/>
         </collection>
 
         <!-- Galaxy-wrapper concatenated results -->
-        <data name="concat_psm_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated psm.tsv" from_work_dir="outputs/concat_psm.tsv">
+        <data name="concat_psm_tsv" format="tabular" label="FragPipe Concatenated psm.tsv" from_work_dir="outputs/concat_psm.tsv">
             <filter>not workflow_only and 'concatenated_outputs' in output_options</filter>
         </data>
-        <data name="concat_ion_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated ion.tsv" from_work_dir="outputs/concat_ion.tsv">
+        <data name="concat_ion_tsv" format="tabular" label="FragPipe Concatenated ion.tsv" from_work_dir="outputs/concat_ion.tsv">
             <filter>not workflow_only and 'concatenated_outputs' in output_options</filter>
         </data>
-        <data name="concat_peptide_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated peptide.tsv" from_work_dir="outputs/concat_peptide.tsv">
+        <data name="concat_peptide_tsv" format="tabular" label="FragPipe Concatenated peptide.tsv" from_work_dir="outputs/concat_peptide.tsv">
             <filter>not workflow_only and 'concatenated_outputs' in output_options</filter>
         </data>
-        <data name="concat_protein_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated protein.tsv" from_work_dir="outputs/concat_protein.tsv">
+        <data name="concat_protein_tsv" format="tabular" label="FragPipe Concatenated protein.tsv" from_work_dir="outputs/concat_protein.tsv">
             <filter>not workflow_only and 'concatenated_outputs' in output_options</filter>
         </data>
 
         <!-- PTM-Shepherd Results -->
-        <data name="global_profile_tsv" format="tabular" label="${tool.name} on ${on_string}: global.profile.tsv" from_work_dir="outputs/global.profile.tsv">
+        <data name="global_profile_tsv" format="tabular" label="FragPipe global.profile.tsv" from_work_dir="outputs/ptm-shepherd-output/global.profile.tsv">
                <filter>(not workflow_only) and ('Open' in  wf['workflow_name'])</filter>
         </data>
-        <data name="global_summary_tsv" format="tabular" label="${tool.name} on ${on_string}: global.modsummary.tsv" from_work_dir="outputs/global.modsummary.tsv">
-               <filter>(not workflow_only) and ('Open' in  wf['workflow_name'])</filter>
-        </data>
-        <data name="global_diagmine_tsv" format="tabular" label="${tool.name} on ${on_string}: global.diagmine.tsv" from_work_dir="outputs/global.diagmine.tsv">
+        <data name="global_summary_tsv" format="tabular" label="FragPipe global.modsummary.tsv" from_work_dir="outputs/ptm-shepherd-output/global.modsummary.tsv">
                <filter>(not workflow_only) and ('Open' in  wf['workflow_name'])</filter>
         </data>
 
@@ -142,7 +179,7 @@
             TMT/iTRAW Results
             Only produced by TMT, TRAQ, and SLC workflows
         -->
-        <collection name="tmt_results" type="list" label="${tool.name} - ${on_string}: TMT Results" >
+        <collection name="tmt_results" type="list" label="FragPipe TMT Results" >
             <discover_datasets pattern="__designation__" ext="tabular" directory="outputs/tmt-report"/>
             <filter>(not workflow_only) and ('TMT' in wf['workflow_name'])</filter>
         </collection>
@@ -150,67 +187,63 @@
 
     <tests>
       <test expect_num_outputs="11">
-        <param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/>
-        <param name="database_name" value="default/test.fasta" ftype="fasta"/>
-        <param name="manifest" value="default/test.manifest" ftype="tabular"/>
-        <param name="wf|workflow_name" value="Default"/>
-        <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/>
+        <param name="inputs" value="basic-search/test1.mzML,basic-search/test2.mzML" ftype="mzml"/>
+        <param name="database_name" value="basic-search/test.fasta" ftype="fasta"/>
+        <param name="manifest" value="basic-search/test.manifest" ftype="tabular"/>
+        <param name="wf|workflow_name" value="Basic-Search"/>
+        <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs,individual_outputs"/>
         <param name="license_agreements" value="true"/>
         <param name="wf|validation|validation_tab|psm_validation|run_psm_validation" value="percolator"/>
         <output name="concat_psm_tsv" ftype="tabular">
             <assert_contents>
-                <has_text text="Experiment&#x9;Spectrum&#x9;Spectrum File&#x9;Peptide&#x9;Modified Peptide&#x9;Extended Peptide&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Charge&#x9;Retention&#x9;Observed Mass&#x9;Calibrated Observed Mass&#x9;Observed M/Z&#x9;Calibrated Observed M/Z&#x9;Calculated Peptide Mass&#x9;Calculated M/Z&#x9;Delta Mass&#x9;Expectation&#x9;Hyperscore&#x9;Nextscore&#x9;PeptideProphet Probability&#x9;Number of Enzymatic Termini&#x9;Number of Missed Cleavages&#x9;Protein Start&#x9;Protein End&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Purity&#x9;Is Unique&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
+                <has_text text="Experiment&#x9;Spectrum&#x9;Spectrum File"/>
                 <has_text text="sample1"/>
+                <has_text text="sample2"/>
             </assert_contents>
         </output>
         <output name="concat_ion_tsv" ftype="tabular">
             <assert_contents>
-                <has_text text="Experiment&#x9;Peptide Sequence&#x9;Modified Sequence&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Protein Start&#x9;Protein End&#x9;M/Z&#x9;Charge&#x9;Observed Mass&#x9;Probability&#x9;Expectation&#x9;Spectral Count&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
+                <has_text text="Experiment&#x9;Peptide Sequence&#x9;Modified Sequence"/>
                 <has_text text="sample1"/>
+                <has_text text="sample2"/>
             </assert_contents>
         </output>
         <output name="concat_peptide_tsv" ftype="tabular">
             <assert_contents>
-                <has_text text="Experiment&#x9;Peptide&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Protein Start&#x9;Protein End&#x9;Charges&#x9;Probability&#x9;Spectral Count&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
+                <has_text text="Experiment&#x9;Peptide&#x9;Prev AA&#x9;"/>
                 <has_text text="sample1"/>
+                <has_text text="sample2"/>
             </assert_contents>
         </output>
         <output name="concat_protein_tsv" ftype="tabular">
             <assert_contents>
-                <has_text text="Experiment&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Length&#x9;Organism&#x9;Protein Description&#x9;Protein Existence&#x9;Coverage&#x9;Protein Probability&#x9;Top Peptide Probability&#x9;Total Peptides&#x9;Unique Peptides&#x9;Razor Peptides&#x9;Total Spectral Count&#x9;Unique Spectral Count&#x9;Razor Spectral Count&#x9;Total Intensity&#x9;Unique Intensity&#x9;Razor Intensity&#x9;Razor Assigned Modifications&#x9;Razor Observed Modifications&#x9;Indistinguishable Proteins"/>
+                <has_text text="Experiment&#x9;Protein&#x9;Protein ID&#x9;"/>
                 <has_text text="sample1"/>
+                <has_text text="sample2"/>
             </assert_contents>
         </output>
-        <output name="output_workflow" ftype="txt" file="default/outputs/workflow.txt" compare="contains">
-            <assert_contents>
-                <has_text text="crystalc.run-crystalc=false"/>
-            </assert_contents>
-        </output>
+        <output name="output_workflow" ftype="txt" file="basic-search/outputs/workflow.txt" compare="contains"/>
         <output name="log" ftype="txt">
             <assert_contents>
-                <has_text text="FragPipe version 20.0"/>
+                <has_text text="FragPipe version 23.0"/>
             </assert_contents>
         </output>
         <output_collection name="combined_outputs" type="list">
             <element name="combined_protein.tsv" ftype="tabular">
                 <assert_contents>
-                    <has_text text="Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Length&#x9;Organism&#x9;Protein Existence&#x9;Description&#x9;Protein Probability&#x9;Top Peptide Probability&#x9;Combined Total Peptides&#x9;Combined Spectral Count&#x9;Combined Unique Spectral Count&#x9;Combined Total Spectral Count&#x9;sample1 Spectral Count&#x9;sample2 Spectral Count&#x9;sample1 Intensity&#x9;sample2 Intensity&#x9;Indistinguishable Proteins"/>
+                    <has_text text="Protein&#x9;Protein ID&#x9;Entry Name"/>
                 </assert_contents>
             </element>
         </output_collection>
       </test>
-      <test expect_num_outputs="11">
-        <param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/>
-        <param name="database_name" value="default/test.fasta" ftype="fasta"/>
-        <param name="manifest" value="default/test.manifest" ftype="tabular"/>
+      <test expect_num_outputs="7">
+        <param name="inputs" value="basic-search/test1.mzML,basic-search/test2.mzML" ftype="mzml"/>
+        <param name="database_name" value="basic-search/test.fasta" ftype="fasta"/>
+        <param name="manifest" value="basic-search/test.manifest" ftype="tabular"/>
         <param name="wf|workflow_name" value="Nonspecific-HLA"/>
         <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/>
         <param name="license_agreements" value="true"/>
-        <output name="output_workflow" ftype="txt" file="nonspecific-hla/outputs/workflow.txt" compare="contains">
-            <assert_contents>
-                <has_text text="crystalc.run-crystalc=false"/>
-            </assert_contents>
-        </output>
+        <output name="output_workflow" ftype="txt" file="nonspecific-hla/outputs/workflow.txt" compare="contains"/>
         <output name="concat_protein_tsv" ftype="tabular">
             <assert_contents>
                 <has_text text="sample1"/>
@@ -219,110 +252,16 @@
             </assert_contents>
         </output>
       </test>
-      <test expect_num_outputs="11">
-        <param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/>
-        <param name="database_name" value="default/test.fasta" ftype="fasta"/>
-        <param name="manifest" value="default/test.manifest" ftype="tabular"/>
-        <param name="wf|workflow_name" value="Default"/>
-        <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/>
-        <param name="license_agreements" value="true"/>
-        <param name="wf|validation|validation_tab|psm_validation|run_psm_validation" value="msbooster_percolator"/>
-        <output name="concat_psm_tsv" ftype="tabular">
-            <assert_contents>
-                <has_text text="Experiment&#x9;Spectrum&#x9;Spectrum File&#x9;Peptide&#x9;Modified Peptide&#x9;Extended Peptide&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Charge&#x9;Retention&#x9;Observed Mass&#x9;Calibrated Observed Mass&#x9;Observed M/Z&#x9;Calibrated Observed M/Z&#x9;Calculated Peptide Mass&#x9;Calculated M/Z&#x9;Delta Mass&#x9;SpectralSim&#x9;RTScore&#x9;Expectation&#x9;Hyperscore&#x9;Nextscore&#x9;PeptideProphet Probability&#x9;Number of Enzymatic Termini&#x9;Number of Missed Cleavages&#x9;Protein Start&#x9;Protein End&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Purity&#x9;Is Unique&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
-                <has_text text="sample1"/>
-            </assert_contents>
-        </output>
-        <output name="concat_ion_tsv" ftype="tabular">
-            <assert_contents>
-                <has_text text="Experiment&#x9;Peptide Sequence&#x9;Modified Sequence&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Protein Start&#x9;Protein End&#x9;M/Z&#x9;Charge&#x9;Observed Mass&#x9;Probability&#x9;Expectation&#x9;Spectral Count&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
-                <has_text text="sample1"/>
-            </assert_contents>
-        </output>
-        <output name="concat_peptide_tsv" ftype="tabular">
-            <assert_contents>
-                <has_text text="Experiment&#x9;Peptide&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Protein Start&#x9;Protein End&#x9;Charges&#x9;Probability&#x9;Spectral Count&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
-                <has_text text="sample1"/>
-            </assert_contents>
-        </output>
-        <output name="concat_protein_tsv" ftype="tabular">
-            <assert_contents>
-                <has_text text="Experiment&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Length&#x9;Organism&#x9;Protein Description&#x9;Protein Existence&#x9;Coverage&#x9;Protein Probability&#x9;Top Peptide Probability&#x9;Total Peptides&#x9;Unique Peptides&#x9;Razor Peptides&#x9;Total Spectral Count&#x9;Unique Spectral Count&#x9;Razor Spectral Count&#x9;Total Intensity&#x9;Unique Intensity&#x9;Razor Intensity&#x9;Razor Assigned Modifications&#x9;Razor Observed Modifications&#x9;Indistinguishable Proteins"/>
-                <has_text text="sample1"/>
-            </assert_contents>
-        </output>
-        <output name="output_workflow" ftype="txt" file="default/outputs/workflow_msbooster_percolator.txt" compare="contains">
-            <assert_contents>
-                <has_text text="crystalc.run-crystalc=false"/>
-            </assert_contents>
-        </output>
-        <output name="log" ftype="txt">
-            <assert_contents>
-                <has_text text="FragPipe version 20.0"/>
-            </assert_contents>
-        </output>
-        <output_collection name="combined_outputs" type="list">
-            <element name="combined_protein.tsv" ftype="tabular">
-                <assert_contents>
-                    <has_text text="Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Length&#x9;Organism&#x9;Protein Existence&#x9;Description&#x9;Protein Probability&#x9;Top Peptide Probability&#x9;Combined Total Peptides&#x9;Combined Spectral Count&#x9;Combined Unique Spectral Count&#x9;Combined Total Spectral Count&#x9;sample1 Spectral Count&#x9;sample2 Spectral Count&#x9;sample1 Intensity&#x9;sample2 Intensity&#x9;Indistinguishable Proteins"/>
-                </assert_contents>
-            </element>
-        </output_collection>
-      </test>
-      <test expect_num_outputs="11">
+      <test expect_num_outputs="1">
         <param name="inputs" value="tmt11/test1.mzML,tmt11/test2.mzML" ftype="mzml"/>
         <param name="database_name" value="tmt11/test.fasta" ftype="fasta"/>
         <param name="manifest" value="tmt11/test.manifest" ftype="tabular"/>
         <param name="wf|annotation" value="tmt11/test.annotation" ftype="tabular"/>
         <param name="wf|workflow_name" value="TMT11"/>
-        <param name="output_options" value="workflow,log,concatenated_outputs"/>
+        <param name="output_options" value="workflow"/>
         <param name="license_agreements" value="true"/>
-        <output name="concat_psm_tsv" ftype="tabular">
-            <assert_contents>
-                <has_text text="Experiment&#x9;Spectrum&#x9;Spectrum File&#x9;Peptide&#x9;Modified Peptide&#x9;Extended Peptide&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Charge&#x9;Retention&#x9;Observed Mass&#x9;Calibrated Observed Mass&#x9;Observed M/Z&#x9;Calibrated Observed M/Z&#x9;Calculated Peptide Mass&#x9;Calculated M/Z&#x9;Delta Mass&#x9;SpectralSim&#x9;RTScore&#x9;Expectation&#x9;Hyperscore&#x9;Nextscore&#x9;PeptideProphet Probability&#x9;Number of Enzymatic Termini&#x9;Number of Missed Cleavages&#x9;Protein Start&#x9;Protein End&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Purity&#x9;Is Unique&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
-                <has_text text="sample1"/>
-            </assert_contents>
-        </output>
-        <output name="concat_ion_tsv" ftype="tabular">
-            <assert_contents>
-                <has_text text="Experiment&#x9;Peptide Sequence&#x9;Modified Sequence&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Protein Start&#x9;Protein End&#x9;M/Z&#x9;Charge&#x9;Observed Mass&#x9;Probability&#x9;Expectation&#x9;Spectral Count&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
-                <has_text text="sample1"/>
-            </assert_contents>
-        </output>
-        <output name="concat_peptide_tsv" ftype="tabular">
-            <assert_contents>
-                <has_text text="Experiment&#x9;Peptide&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Protein Start&#x9;Protein End&#x9;Charges&#x9;Probability&#x9;Spectral Count&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
-                <has_text text="sample1"/>
-            </assert_contents>
-        </output>
-        <output name="concat_protein_tsv" ftype="tabular">
-            <assert_contents>
-                <has_text text="Experiment&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Length&#x9;Organism&#x9;Protein Description&#x9;Protein Existence&#x9;Coverage&#x9;Protein Probability&#x9;Top Peptide Probability&#x9;Total Peptides&#x9;Unique Peptides&#x9;Razor Peptides&#x9;Total Spectral Count&#x9;Unique Spectral Count&#x9;Razor Spectral Count&#x9;Total Intensity&#x9;Unique Intensity&#x9;Razor Intensity&#x9;Razor Assigned Modifications&#x9;Razor Observed Modifications&#x9;Indistinguishable Proteins"/>
-                <has_text text="sample1"/>
-            </assert_contents>
-        </output>
-        <output name="output_workflow" ftype="txt" file="tmt11/outputs/workflow.txt" compare="contains">
-            <assert_contents>
-                <has_text text="crystalc.run-crystalc=false"/>
-            </assert_contents>
-        </output>
-        <output name="log" ftype="txt">
-            <assert_contents>
-                <has_text text="FragPipe version 20.0"/>
-            </assert_contents>
-        </output>
-        <output_collection name="tmt_results" type="list">
-            <element name="abundance_gene_MD.tsv" ftype="tabular">
-                <assert_contents>
-                    <has_text text="Index&#x9;NumberPSM&#x9;ProteinID&#x9;MaxPepProb&#x9;ReferenceIntensity&#x9;sample-01&#x9;sample-02&#x9;sample-03&#x9;sample-04&#x9;sample-05&#x9;sample-06&#x9;sample-07&#x9;sample-08&#x9;sample-09&#x9;sample-10&#x9;Bridge"/>
-                </assert_contents>
-            </element>
-            <element name="ratio_gene_MD.tsv" ftype="tabular">
-                <assert_contents>
-                    <has_text text="Index&#x9;NumberPSM&#x9;ProteinID&#x9;MaxPepProb&#x9;ReferenceIntensity&#x9;sample-01&#x9;sample-02&#x9;sample-03&#x9;sample-04&#x9;sample-05&#x9;sample-06&#x9;sample-07&#x9;sample-08&#x9;sample-09&#x9;sample-10&#x9;Bridge"/>
-                </assert_contents>
-            </element>
-        </output_collection>
+        <param name="workflow_only" value="true"/>
+        <output name="output_workflow" ftype="txt" file="tmt11/outputs/workflow.txt" compare="contains"/>
       </test>
     </tests>
 
@@ -332,7 +271,8 @@
 FragPipe_ is a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data.
 FragPipe uses MSFragger_ - an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification.
 
-FragPipe_ runs a user selected analysis workflow_
+Each FragPipe job is configured around a user-selected FragPipe _workflow.
+Blank optional parameters in the Galaxy tool will default to the settings in the selected FragPipe workflow file.
 
 **License Agreements**
 
diff -r 59fec1e2a6c3 -r b4f6df8fa89b macros.xml
--- a/macros.xml	Sun Mar 30 23:00:45 2025 +0000
+++ b/macros.xml	Wed Oct 01 22:20:54 2025 +0000
@@ -1,7 +1,15 @@
 <macros>
     <import>msfragger_macros.xml</import>
-    <token name="@TOOL_VERSION@">20.0</token>
-    <token name="@VERSION_SUFFIX@">6</token>
+    <token name="@TOOL_VERSION@">23.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+
+    <!--
+        These keys were generated ONLY for use by the Galaxy tool wrapper, and only after
+        the user has selected agreed to the academic-use only terms in the tool wrapper.
+    -->
+    <token name="@MSFRAGGER_ACADEMIC_USE_KEY@">f28c4be2-759b0a11-6c1ea652-1240565a</token>
+    <token name="@IONQUANT_ACADEMIC_USE_KEY@">b6c0ad83-9a4e8900-3e83d29c-aeba3bfb</token>
+    <token name="@DIATRACER_ACADEMIC_USE_KEY@">8de4daf3-a090ed0d-0acdb00a-1485d8a7</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement>
@@ -59,7 +67,14 @@
 
         #for $sf in $inputs
             #set $i_name = $ln_name($sf)
-            ln -s '$sf' 'scans/${i_name}' &&
+
+            ## speclib library does not follow links
+            #if $wf.workflow_name == "DIA_SpecLib_Quant"
+                cp '$sf' 'scans/${i_name}' &&
+            #else
+                ln -s '$sf' 'scans/${i_name}' &&
+            #end if
+
         #end for
     ]]></token>
 
@@ -117,7 +132,12 @@
                     awk 'NR==1{printf("Experiment\t%s\n",\$0);}' \$i > concat_\${f};
                 fi;
                 awk 'NR>1{printf("'"\${d}"'\t%s\n",\$0);}' \$i >> concat_\${f}; t=\$(echo \${i} | tr '/' '.');
-                mv \${i} \${t}; n=\$((n+1));
+                if [[ \${i} == \${t} ]]; then
+                    mv \${i} 1.\${i};
+                else
+                    mv \${i} \${t};
+                fi;
+                n=\$((n+1));
             done;
         done
     ]]></token>
@@ -151,16 +171,17 @@
     -->
     <xml name="workflow">
         <conditional name="wf">
-            <param name="workflow_name" type="select" label="Workflow"  help="Note: MSBooster is currently disabled in all Galaxy FragPipe workflows.">
-                <option value="Default">Default</option>
+            <param name="workflow_name" type="select" label="Workflow">
+                <option value="Basic-Search">Basic-Search</option>
                 <option value="Open">Open</option>
                 <option value="Nonspecific-HLA">Nonspecific-HLA</option>
                 <option value="LFQ-MBR">LFQ-MBR</option>
                 <option value="TMT10">TMT10</option>
                 <option value="TMT11">TMT11</option>
+                <option value="DIA_SpecLib_Quant">DIA_SpecLib_Quant</option>
             </param>
 
-            <when value="Default">
+            <when value="Basic-Search">
                 <section name="msfragger" expanded="false" title="MSFragger Options">
                     <expand macro="msfragger_default"/>
                 </section>
@@ -180,6 +201,8 @@
                 <expand macro="label_free_quantification" yes="false" no="true"/>
                 <expand macro="ptm_shepherd" yes="false" no="true" c="true" z="true"/>
                 <expand macro="isobaric_quantification" yes="false" no="true"/>
+                <expand macro="diann_quantification" yes="false" no="true"/>
+                <expand macro="dia_pseuedo_ms2"/>
             </when>
 
             <when value="Open">
@@ -204,6 +227,8 @@
                 <expand macro="label_free_quantification" yes="false" no="true"/>
                 <expand macro="ptm_shepherd" yes="true" no="false"/>
                 <expand macro="isobaric_quantification" yes="false" no="true" bridge="false" pool="true"/>
+                <expand macro="diann_quantification" yes="false" no="true"/>
+                <expand macro="dia_pseuedo_ms2"/>
             </when>
 
             <when value="Nonspecific-HLA">
@@ -226,6 +251,8 @@
                 <expand macro="label_free_quantification" yes="false" no="true"/>
                 <expand macro="ptm_shepherd" yes="false" no="true"/>
                 <expand macro="isobaric_quantification" yes="false" no="true"/>
+                <expand macro="diann_quantification" yes="false" no="true"/>
+                <expand macro="dia_pseuedo_ms2"/>
             </when>
 
             <when value="LFQ-MBR">
@@ -248,6 +275,34 @@
                 <expand macro="label_free_quantification" yes="true" no="false"/>
                 <expand macro="ptm_shepherd" yes="false" no="true"/>
                 <expand macro="isobaric_quantification" yes="false" no="true"/>
+                <expand macro="diann_quantification" yes="false" no="true"/>
+                <expand macro="dia_pseuedo_ms2"/>
+            </when>
+
+            <when value="DIA_SpecLib_Quant">
+                <section name="msfragger" expanded="false" title="MSFragger Options">
+                    <expand macro="msfragger_dia_speclib_quant"/>
+                </section>
+                <expand macro="validation"
+                  pep="false"
+                  perc="false"
+                  boost="true"
+                  no="false"
+                  masswidth="5"
+                  clevel="0"
+                  accmass="true"
+                  decoyprobs="true"
+                  nonparam="true"
+                  expectscore="true"
+                  ppm="true"
+                  combined_pepxml="false"
+                  protp_minprob="0.5"
+                  perc_minprob="0.7"/>
+                <expand macro="label_free_quantification" yes="false" no="true"/>
+                <expand macro="ptm_shepherd" yes="false" no="true" c="true" z="true"/>
+                <expand macro="isobaric_quantification" yes="false" no="true"/>
+                <expand macro="diann_quantification" yes="true" no="false"/>
+                <expand macro="dia_pseuedo_ms2"/>
             </when>
 
             <when value="TMT10">
@@ -284,6 +339,8 @@
         <expand macro="isobaric_quantification" yes="true" no="false" plex="@PLEX@" level="2" ref_tag="Bridge" mod_tag="none"/>
         <expand macro="label_free_quantification" yes="false" no="true"/>
         <expand macro="ptm_shepherd" yes="false" no="true" token_unimod="false" token_common="true"/>
+        <expand macro="diann_quantification" yes="false" no="true"/>
+        <expand macro="dia_pseuedo_ms2"/>
     </xml>
 
     <!-- Generates the FragPipe workflow-->
@@ -311,10 +368,55 @@
 
             ## Get the MSFragger Params (shared with the MSFragger tool)
             #set $prefix = $wf.msfragger
+
             @MSFRAGGER_PARAM_DICT@
             #if len($vmods) > 0
-              #set $msfragger_dict['table.var-mods'] = '; '.join([$re.sub('^(.*,)(\d)$','\\1True,\\2',m) for m in $vmods])
+              #set $msfragger_dict['table.var-mods'] = '; '.join([$re.sub('^(.*,)(\d)$','\\1true,\\2',m) for m in $vmods])
             #end if
+
+            #set $fmod_items = [
+                ("add_Cterm_peptide", "C-Term Peptide"),
+                ("add_Nterm_peptide", "N-Term Peptide"),
+                ("add_Cterm_protein", "C-Term Protein"),
+                ("add_Nterm_protein", "N-Term Protein"),
+                ("add_G_glycine","G (glycine)"),
+                ("add_A_alanine", "A (alanine)"),
+                ("add_S_serine", "S (serine)"),
+                ("add_P_proline", "P (proline)"),
+                ("add_V_valine", "V (valine)"),
+                ("add_T_threonine", "T (threonine)"),
+                ("add_C_cysteine", "C (cysteine)"),
+                ("add_L_leucine", "L (leucine)"),
+                ("add_I_isoleucine", "I (isoleucine)"),
+                ("add_N_asparagine", "N (asparagine)"),
+                ("add_D_aspartic_acid", "D (aspartic acid)"),
+                ("add_Q_glutamine", "Q (glutamine)"),
+                ("add_K_lysine", "K (lysine)"),
+                ("add_E_glutamic_acid", "E (glutamic acid)"),
+                ("add_M_methionine", "M (methionine)"),
+                ("add_H_histidine", "H (histidine)"),
+                ("add_F_phenylalanine", "F (phenylalanine)"),
+                ("add_R_arginine", "R (arginine)"),
+                ("add_Y_tyrosine", "Y (tyrosine)"),
+                ("add_W_tryptophan", "W (tryptophan)"),
+                ("add_B_user_amino_acid", "B "),
+                ("add_J_user_amino_acid", "J"),
+                ("add_O_user_amino_acid", "O"),
+                ("add_U_user_amino_acid", "U"),
+                ("add_X_user_amino_acid", "X"),
+                ("add_Z_user_amino_acid", "Z")
+            ]
+            #set $fmod_string = ""
+            #for $m in $fmod_items
+                #set fmod_var_name = $m[0]
+                #set fmod_wf_name = $m[1]
+                #set $fmod_bool = $fmod_bools.get($fmod_var_name + "_bool")
+                #set $fmod_val = $fmod_vals.get($fmod_var_name)
+                #set $fmod_string += "; " + ",".join([str($fmod_val),str($fmod_wf_name),str($fmod_bool),"-1"])
+            #end for
+            #set $fmod_string = $fmod_string[2:]
+            #set $msfragger_dict['table.fix-mods'] = $fmod_string
+
             #for $k in $msfragger_dict.keys()
                 #set $kv = $k + '=' + str($msfragger_dict[$k])
                 #set $wfk = 'msfragger.' + $k
@@ -325,6 +427,14 @@
             @PTM_SHEPHERD@
             @LABEL_FREE_QUANTIFICATION@
             @ISOBARIC_QUANTIFICATION@
+            @DIANN_QUANTIFICATION@
+            @DIA_PSEUDO_MS2@
+
+            ## These values are specifically set by the GUI when running DIA_SpecLib_Quant
+            #if $wf.workflow_name == "DIA_SpecLib_Quant"
+                #set $wfdict["ptmshepherd.annotate_assigned_mods"] = "false"
+                #set $wfdict["ptmshepherd.use_msfragger_localization"] = "true"
+            #end if
 
             ## Populate the workflow with configuration and comment dictionary entries populated by tool params.
             #for $comment in $comments
@@ -339,10 +449,10 @@
     </xml>
 
     <!-- Percolator options -->
-    <xml name="percolator">
+    <xml name="percolator" token_perc_minprob="0.5">
         <section name="percolator" expanded="true" title="Percolator">
             <param name="keep_tsv_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep intermediate files"/>
-            <param name="min_prob" type="float" value="0.5" label="Minimum probability (default 0.5)"/>
+            <param name="min_prob" type="float" value="@PERC_MINPROB@" label="Minimum probability (default 0.5)"/>
         </section>
     </xml>
 
@@ -358,15 +468,25 @@
         <section name="msbooster" expanded="true" title="MSBooster">
             <param name="predict_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict RT"/>
             <param name="predict_spectra" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict spectra"/>
-            <param name="use_correlated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use correlated features"/>
+            <param name="predict_im" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict IM"/>
+            <param name="use_koina" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Koina server" help="The public server used is https://koina.wilhelmlab.org:443/v2/models"/>
+            <param name="find_best_rt_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find best RT model (requires Koina server)"/>
+            <param name="find_best_im_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find best IM model if applicable (requires Koina server)"/>
+            <param name="find_best_spectra_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find best spectral model (requires Koina server)"/>
         </section>
     </xml>
     <token name="@MSBOOSTER@"><![CDATA[
         #set $prfx = $wf.validation.validation_tab.psm_validation.msbooster
         #set $wfdict['msbooster.run-msbooster'] = 'true'
-        #set $wfdict['msbooster.predict-rt'] = str($prfx.predict_rt)
-        #set $wfdict['msbooster.predict-spectra'] = str($prfx.predict_spectra)
-        #set $wfdict['msbooster.use-correlated-features'] = str($prfx.use_correlated_features)
+        #set $wfdict['msbooster.predict-rt'] = $prfx.predict_rt
+        #set $wfdict['msbooster.predict-spectra'] = $prfx.predict_spectra
+        #set $wfdict['msbooster.predict-im'] = $prfx.predict_im
+        #if $prfx.use_koina == 'true'
+            #set $wfdict['msbooster.koina-url'] = 'https://koina.wilhelmlab.org:443/v2/models/'
+        #end if
+        #set $wfdict['msbooster.find-best-rt-model'] = $prfx.find_best_rt_model
+        #set $wfdict['msbooster.find-best-spectra-model'] = $prfx.find_best_spectra_model
+        #set $wfdict['msbooster.find-best-im-model'] = $prfx.find_best_im_model
     ]]></token>
 
 
@@ -379,7 +499,7 @@
             </param>
             <when value="true">
               <section name="phi_report_opts" expanded="false" title="FDR Filter and Report">
-                  <param name="dont_use_prot_prophet_file" type="boolean" truevalue="true" falsevalue="false" checked="false"/>
+                  <param name="dont_use_prot_proph_file" type="boolean" truevalue="true" falsevalue="false" checked="false"/>
                   <param name="print_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false"/>
               </section>
             </when>
@@ -394,6 +514,7 @@
           #set $wfdict['phi-report.run-report'] = 'true'
           #set $prfx = $wf.validation.validation_tab.phi_report.phi_report_opts
           #set $wfdict['phi-report.print-decoys'] = $prfx.print_decoys
+          #set $wfdict['phi-report.dont-use-prot-proph-file'] = $prfx.dont_use_prot_proph_file
         #else
           #set $wfdict['phi-report.run-report'] = 'false'
         #end if
@@ -438,7 +559,7 @@
     </xml>
 
     <!-- Protein Prophet options -->
-    <xml name="protein_prophet" token_minprob="0.05">
+    <xml name="protein_prophet" token_protp_minprob="0.05">
         <conditional name="protein_prophet">
             <param name="run_protein_prophet" type="select" label="Run Protein Prophet">
                 <option value="true" selected="true">Yes</option>
@@ -448,7 +569,7 @@
               <section name="protein_prophet_opts" expanded="true" title="Protein Prophet">
                 <param argument="--iprophet" type="boolean" truevalue="--iprophet" falsevalue="" checked="false" label="input is from iProphet" />
                 <param argument="--maxppmdiff" type="integer" value="2000000" label="maximum peptide mass difference in ppm (default 2000000)" />
-                <param argument="--minprob" type="float" value="@MINPROB@" label="PeptideProphet probability threshold (default 0.05)" />
+                <param argument="--minprob" type="float" value="@PROTP_MINPROB@" label="PeptideProphet probability threshold (default 0.05)" />
                 <param argument="--nonsp" type="boolean" truevalue="--nonsp" falsevalue="" checked="false" label="do not use NSP model" />
                 <param argument="--subgroups" type="boolean" truevalue="--subgroups" falsevalue="" checked="false" label="do not use NOGROUPS" />
                 <param argument="--unmapped" type="boolean" truevalue="--unmapped" falsevalue="" checked="false" label="report results for UNMAPPED proteins" />
@@ -462,19 +583,19 @@
     <token name="@PROTEINPROPHET@"><![CDATA[
         #set $prfx = $wf.validation.validation_tab.protein_prophet
         #if $prfx.run_protein_prophet == 'true'
-        #set $prfx = $wf.validation.validation_tab.protein_prophet.protein_prophet_opts
+            #set $prfx = $wf.validation.validation_tab.protein_prophet.protein_prophet_opts
             #set $wfdict['protein-prophet.run-protein-prophet'] = 'true'
             #set $cmd_opts = [str($prfx.iprophet),str($prfx.nonsp),str($prfx.subgroups),str($prfx.unmapped)]
             #silent $cmd_opts.append('--maxppmdiff ' + str($prfx.maxppmdiff))
             #silent $cmd_opts.append('--minprob ' + str($prfx.minprob))
             #set $wfdict['protein-prophet.cmd-opts'] = ' '.join($cmd_opts).strip()
         #else
-            #set $wfdict[protein-prophet.run-protein-prophet] = 'false'
+            #set $wfdict['protein-prophet.run-protein-prophet'] = 'false'
         #end if
     ]]></token>
 
     <!-- Validation options. Includes PeptideProphet, Percolator, MSBooster, ProteinProphet, and CrystalC -->
-    <xml name="validation" token_expand="false" token_pep="false" token_perc="false" token_boost="false" token_no="true" token_masswidth="5" token_clevel="0" token_accmass="true" token_decoyprobs="true" token_nonparam="true" token_expectscore="true" token_ppm="true" token_combined_pepxml="false" token_protp_minprob="0.05">
+    <xml name="validation" token_expand="false" token_pep="false" token_perc="false" token_boost="false" token_no="true" token_masswidth="5" token_clevel="0" token_accmass="true" token_decoyprobs="true" token_nonparam="true" token_expectscore="true" token_ppm="true" token_combined_pepxml="false" token_protp_minprob="0.05" token_perc_minprob="0.5">
         <section name="validation" expanded="@EXPAND@" title="Validation">
             <conditional name="validation_tab">
                 <param name="run_validation" type="select" label="Run Validation">
@@ -494,16 +615,16 @@
                             <expand macro="peptide_prophet" masswidth="@MASSWIDTH@" clevel="@CLEVEL@" accmass="@ACCMASS@" decoyprobs="@DECOYPROBS@" nonparam="@NONPARAM@" expectscore="@EXPECTSCORE@" ppm="@PPM@" combined_pepxml="@COMBINED_PEPXML@"/>
                         </when>
                         <when value="percolator">
-                            <expand macro="percolator"/>
+                            <expand macro="percolator" perc_minprob="@PERC_MINPROB@"/>
                         </when>
                         <when value="msbooster_percolator">
                             <expand macro="msbooster"/>
-                            <expand macro="percolator"/>
+                            <expand macro="percolator" perc_minprob="@PERC_MINPROB@"/>
                         </when>
                         <when value="no">
                         </when>
                     </conditional>
-                    <expand macro="protein_prophet" minprob="@PROTP_MINPROB@"/>
+                    <expand macro="protein_prophet" protp_minprob="@PROTP_MINPROB@"/>
                     <expand macro="phi_report"/>
                 </when>
                 <when value="false">
@@ -514,25 +635,34 @@
 
     <!-- Set validation workflow options -->
     <token name="@VALIDATION@"><![CDATA[
-        #set $prfx = $wf.validation.validation_tab.psm_validation
-        #if $prfx.run_psm_validation == 'peptide_prophet'
-            #set $wfdict['run-psm-validation'] = 'true'
-            #set $wfdict['msbooster.run-msbooster'] = 'false'
-            #set $wfdict['percolator.run-percolator'] = 'false'
-            @PEPTIDEPROPHET@
-        #elif $prfx.run_psm_validation == 'percolator'
-            #set $wfdict['run-psm-validation'] = 'true'
+        #if $wf.validation.validation_tab.run_validation == "true"
+            #set $prfx = $wf.validation.validation_tab.psm_validation
+            #if $prfx.run_psm_validation == 'peptide_prophet'
+                #set $wfdict['run-psm-validation'] = 'true'
+                #set $wfdict['msbooster.run-msbooster'] = 'false'
+                #set $wfdict['percolator.run-percolator'] = 'false'
+                @PEPTIDEPROPHET@
+            #elif $prfx.run_psm_validation == 'percolator'
+                #set $wfdict['run-psm-validation'] = 'true'
+                #set $wfdict['msbooster.run-msbooster'] = 'false'
+                #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
+                @PERCOLATOR@
+            #elif $prfx.run_psm_validation == 'msbooster_percolator'
+                #set $wfdict['run-psm-validation'] = 'true'
+                #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
+                @MSBOOSTER@
+                @PERCOLATOR@
+            #end if
+            @PROTEINPROPHET@
+            @PHIREPORT@
+        #else
+            #set $wfdict['run-psm-validation'] = 'false'
             #set $wfdict['msbooster.run-msbooster'] = 'false'
             #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
-            @PERCOLATOR@
-        #elif $prfx.run_psm_validation == 'msbooster_percolator'
-            #set $wfdict['run-psm-validation'] = 'true'
-            #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
-            @MSBOOSTER@
-            @PERCOLATOR@
+            #set $wfdict['percolator.run-percolator'] = 'false'
+            #set $wfdict['protein-prophet.run-protein-prophet'] = 'false'
+            #set $wfdict['phi-report.run-report'] = 'false'
         #end if
-        @PROTEINPROPHET@
-        @PHIREPORT@
     ]]></token>
 
     <!-- PTM-Sheperd options -->
@@ -597,7 +727,6 @@
                             <option value="z" selected="@Z@">z</option>
                         </param>
                         <param name="spectra_maxfragcharge" type="integer" value="" min="0" optional="true" label="Max fragment charge" help="ptmshepherd.spectra_maxfragcharge"/>
-                        <param name="localization_background" type="integer" value="" min="0" optional="true" label="Localization background" help="ptmshepherd.localization_background"/>
                         <param name="localization_allowed_res" type="select" label="Restrict localization to" help="ptmshepherd.localization_allowed_res">
                             <option value="" selected="true">none</option>
                             <option value="all">all</option>
@@ -628,14 +757,14 @@
                 #set $wfdict['ptmshepherd.histo_smoothbins'] = $cxt.histo_smoothbins
             #end if
             #if $cxt.precursor_tol != ''
-                #set $wfdict['ptmshepherd.precursor_mass_units'] = $ctx.precursor_mass_units
+                #set $wfdict['ptmshepherd.precursor_mass_units'] = $cxt.precursor_mass_units
                 #set $wfdict['ptmshepherd.precursor_tol'] = $cxt.precursor_tol
             #end if
             #if $cxt.peakpicking_promRatio != ''
                 #set $wfdict['ptmshepherd.peakpicking_promRatio'] = $cxt.peakpicking_promRatio
             #end if
             #if $cxt.peakpicking_width != ''
-                #set $wfdict['ptmshepherd.peakpicking_mass_units'] = $ctx.peakpicking_mass_units
+                #set $wfdict['ptmshepherd.peakpicking_mass_units'] = $cxt.peakpicking_mass_units
                 #set $wfdict['ptmshepherd.peakpicking_width'] = $cxt.peakpicking_width
             #end if
             #if $cxt.peakpicking_minPsm != ''
@@ -696,9 +825,6 @@
             #if $cxt.spectra_maxfragcharge != ''
                 #set $wfdict['ptmshepherd.spectra_maxfragcharge'] = $cxt.spectra_maxfragcharge
             #end if
-            #if $cxt.localization_background != ''
-                #set $wfdict['ptmshepherd.localization_background'] = $cxt.localization_background
-            #end if
             #set $wfdict['ptmshepherd.localization_allowed_res'] = $cxt.localization_allowed_res
         #else
             #set $wfdict['ptmshepherd.run-shepherd'] = 'false'
@@ -715,10 +841,94 @@
                 <param name="label_free_quantification_run" type="select" label="Perform Label-Free Quantification">
                     <option value="default" selected="true">Use workflow default</option>
                     <option value="no">No Label-Free Quantification</option>
+                    <option value="ionquant">Run IonQuant</option>
                     <option value="freequant">Run FreeQuant</option>
                 </param>
                 <when value="default"/>
                 <when value="no"/>
+                <when value="ionquant">
+                    <section name="ionquant" expanded="false" title="IonQuant Label-Free Quantification">
+                        <param name="mbr_select" type="select" optional="true" label="Match between runs (MBR)" help="ionquant.mbr">
+                            <option value="0">No</option>
+                            <option value="1">Yes</option>
+                        </param>
+                        <param name="normalization" type="select" optional="true" label="Normalize" help="ionquant.normalization">
+                            <option value="0">No</option>
+                            <option value="1">Yes</option>
+                        </param>
+                        <section name="feature_detection" expanded="false" title="Feature detection">
+                            <param name="mztol" type="integer" value="" optional="true" label="m/z tolerance in ppm" help="ionquant.mztol (default 10)"/>
+                            <param name="rttol" type="float" value="" optional="true" label="RT tolerance (minutes)" help="ionquant.rttol (default 0.4)"/>
+                            <param name="imtol" type="float" value="" optional="true" label="IM tolerance (1/k0)" help="ionquant.imtol (default 0.05)"/>
+                        </section>
+                        <section name="mbr" expanded="false" title="Match between runs (MBR)">
+                            <param name="mbrrttol" type="float" value="" optional="true" label="MBR RT tolerance (minutes)" help="ionquant.mbrrttol"/>
+                            <param name="mbrimtol" type="float" value="" optional="true" label="MBR IM tolerance (1/k0)" help="ionquant.mbrimtol"/>
+                            <param name="mbrmincorr" type="float" value="" optional="true" label="MBR min correlation" help="ionquant.mbrmincorr"/>
+                            <param name="mbrtoprun" type="integer" value="" optional="true" label="MBR top runs" help="ionquant.mbrtoprun"/>
+                            <param name="ionfdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR ion FDR" help="ionquant.ionfdr"/>
+                            <param name="peptidefdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR peptide FDR" help="ionquant.peptidefdr"/>
+                            <param name="proteinfdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR protein FDR" help="ionquant.proteinfdr"/>
+                        </section>
+                        <section name="topn" expanded="false" title="Top-N options">
+                            <param name="tp" type="integer" value="" min="0" optional="true" label="Top N ions" help="ionquant.tp"/>
+                            <param name="minfreq" type="float" value="" min="0.0" max="1.0" optional="true" label="Min freq" help="ionquant.minfreq"/>
+                        </section>
+                        <conditional name="labeling_conditional">
+                            <param name="labeling_option" type="select" label="Labeling option">
+                              <option value="lfq" selected="true">LFQ</option>
+                              <option value="labeling">Labeling</option>
+                            </param>
+                            <when value="lfq">
+                              <section name="lfq" expanded="false" title="LFQ">
+                                <param name="maxlfq" type="select" optional="true" label="MaxLFQ" help="ionquant.maxlfq">
+                                    <option value="0">No</option>
+                                    <option value="1">Yes</option>
+                                </param>
+                                <param name="minions" type="integer" value="" optional="true" label="Min ions" help="ionquant.minions"/>
+                              </section>
+                            </when>
+                            <when value="labeling">
+                              <section name="labeling" expanded="false" title="Labeling-based quant">
+                                  <param name="light" type="select" label="Light" help="ionquant.light">
+                                      <option value="" selected="true">none</option>
+                                      <option value="C463.2366">C463.2366</option>
+                                      <option value="C464.28596">C464.28596</option>
+                                      <option value="C561.3387">C561.3387</option>
+                                      <option value="K0;R0">K0;R0</option>
+                                  </param>
+                                  <param name="medium" type="select" label="Medium" help="ionquant.medium">
+                                      <option value="" selected="true">none</option>
+                                      <option value="K4.025107;R6.020129">K4.025107;R6.020129</option>
+                                  </param>
+                                  <param name="heavy" type="select" label="Heavy" help="ionquant.heavy">
+                                      <option value="" selected="true">none</option>
+                                      <option value="C467.2529">C467.2529</option>
+                                      <option value="C470.29977">C470.29977</option>
+                                      <option value="C567.3462">C567.3462</option>
+                                      <option value="K8.014199;R10.008269">K8.014199;R10.008269</option>
+                                  </param>
+                                  <param name="requantify" type="select" label="Re-quantify" help="ionquant.requantify">
+                                      <option value="0">No</option>
+                                      <option value="1" selected="true">Yes</option>
+                                  </param>
+                              </section>
+                            </when>
+                        </conditional>
+                        <section name="advanced" expanded="false" title="Advanced options">
+                            <param name="excludemods" type="text" optional="true" label="excludemods" help="ionquant.excludemods">
+                                <validator type="regex">^\s*@RE_EXCLUDEMODS@\s*$</validator>
+                            </param>
+                            <param name="minscans" type="integer" value="" min="0" optional="true" label="Min scans" help="ionquant.minscans"/>
+                            <param name="minisotopes" type="integer" value="" min="1" max="3" optional="true" label="Min isotopes" help="ionquant.minisotopes"/>
+                            <param name="locprob" type="float" value="" min="0.0" max="1.0" optional="true" label="Min site probability" help="ionquant.locprob"/>
+                            <param name="writeindex" type="select" optional="true" label="Write index" help="ionquant.writeindex">
+                                <option value="0">No</option>
+                                <option value="1">Yes</option>
+                            </param>
+                        </section>
+                    </section>
+                </when>
                 <when value="freequant">
                     <section name="freequant" expanded="false" title="IonQuant Label-Free Quantification">
                         <param name="rt_tol" type="float" value="" min="0" optional="true" label="RT Window (minutes)"/>
@@ -734,8 +944,96 @@
         #set $prfx = $wf.quant_ms1.label_free_quantification
         #if $prfx.label_free_quantification_run == 'no'
             #set $wfdict['quantitation.run-label-free-quant'] = 'false'
+            #set $wfdict['ionquant.run-ionquant'] = 'false'
+            #set $wfdict['freequant.run-freequant'] = 'false'
+        #elif $prfx.label_free_quantification_run == 'ionquant'
+            #set $wfdict['quantitation.run-label-free-quant'] = 'true'
+            #set $wfdict['ionquant.run-ionquant'] = 'true'
+            #set $wfdict['freequant.run-freequant'] = 'false'
+            #set $cxt = $prfx.ionquant
+            #if $cxt.mbr_select != 'None'
+                #set $wfdict['ionquant.mbr'] = $cxt.mbr_select
+            #end if
+            #if $cxt.normalization != 'None'
+                #set $wfdict['ionquant.normalization'] = $cxt.normalization
+            #end if
+            #set $cxt = $prfx.ionquant.feature_detection
+            #if $cxt.mztol != ''
+                #set $wfdict['ionquant.mztol'] = $cxt.mztol
+            #end if
+            #if $cxt.rttol != ''
+                #set $wfdict['ionquant.rttol'] = $cxt.rttol
+            #end if
+            #if $cxt.imtol != ''
+                #set $wfdict['ionquant.imtol'] = $cxt.imtol
+            #end if
+            #set $cxt = $prfx.ionquant.mbr
+            #if $cxt.mbrrttol != ''
+                #set $wfdict['ionquant.mbrrttol'] = $cxt.mbrrttol
+            #end if
+            #if $cxt.mbrimtol != ''
+                #set $wfdict['ionquant.mbrimtol'] = $cxt.mbrimtol
+            #end if
+            #if $cxt.mbrmincorr != ''
+                #set $wfdict['ionquant.mbrmincorr'] = $cxt.mbrmincorr
+            #end if
+            #if $cxt.mbrtoprun != ''
+                #set $wfdict['ionquant.mbrtoprun'] = $cxt.mbrtoprun
+            #end if
+            #if $cxt.ionfdr != ''
+                #set $wfdict['ionquant.ionfdr'] = $cxt.ionfdr
+            #end if
+            #if $cxt.peptidefdr != ''
+                #set $wfdict['ionquant.peptidefdr'] = $cxt.peptidefdr
+            #end if
+            #if $cxt.proteinfdr != ''
+                #set $wfdict['ionquant.proteinfdr'] = $cxt.proteinfdr
+            #end if
+            #set $cxt = $prfx.ionquant.topn
+            #if $cxt.tp != ''
+                #set $wfdict['ionquant.tp'] = $cxt.tp
+            #end if
+            #if $cxt.minfreq != ''
+                #set $wfdict['ionquant.minfreq'] = $cxt.minfreq
+            #end if
+            #set $cxt = $prfx.ionquant.labeling_conditional
+            #if $cxt.labeling_option == 'labeling'
+                #set $cxt = $prfx.ionquant.labeling_conditional.labeling
+                #set $wfdict['ionquant.use-labeling'] = 'true'
+                #set $wfdict['ionquant.use-lfq'] = 'false'
+                #set $wfdict['ionquant.light'] = $cxt.light
+                #set $wfdict['ionquant.medium'] = $cxt.medium
+                #set $wfdict['ionquant.heavy'] = $cxt.heavy
+                #set $wfdict['ionquant.requantify'] = $cxt.requantify
+            #else
+                #set $cxt = $prfx.ionquant.labeling_conditional.lfq
+                #set $wfdict['ionquant.use-labeling'] = 'false'
+                #set $wfdict['ionquant.use-lfq'] = 'true'
+                #if $cxt.maxlfq != 'None'
+                    #set $wfdict['ionquant.maxlfq'] = $cxt.maxlfq
+                #end if
+                #if $cxt.minions != ''
+                    #set $wfdict['ionquant.minions'] = $cxt.minions
+                #end if
+            #end if
+            #set $cxt = $prfx.ionquant.advanced
+            #if $cxt.excludemods != ''
+                #set $wfdict['ionquant.excludemods'] = $cxt.excludemods
+            #end if
+            #if $cxt.minscans != ''
+                #set $wfdict['ionquant.minscans'] = $cxt.minscans
+            #end if
+            #if $cxt.minisotopes != ''
+                #set $wfdict['ionquant.minisotopes'] = $cxt.minisotopes
+            #end if
+            #if $cxt.locprob != ''
+                #set $wfdict['ionquant.locprob'] = $cxt.locprob
+            #end if
+            #if $cxt.writeindex != 'None'
+                #set $wfdict['ionquant.writeindex'] = $cxt.writeindex
+            #end if
         #elif $prfx.label_free_quantification_run == 'freequant'
-            #set $wfdict['quantitation.run-label-free-quant'] = 'false'
+            #set $wfdict['quantitation.run-label-free-quant'] = 'true'
             #set $wfdict['ionquant.run-ionquant'] = 'false'
             #set $wfdict['freequant.run-freequant'] = 'true'
             #set $cxt = $prfx.freequant
@@ -796,9 +1094,11 @@
                         <conditional name="glycan_conditional">
                             <param name="use_glycan_composition" type="select" label="Perform Isobaric Quantification">
                                 <option value="default">Use workflow defaults</option>
+                                <option value="no">no</option>
                                 <option value="yes">yes</option>
                             </param>
                             <when value="default"/>
+                            <when value="no"/>
                             <when value="yes">
                               <param name="mod_tag" type="select" optional="true" label="PTM Mod tag">
                                   <option value="none">none</option>
@@ -885,7 +1185,6 @@
             #set $wfdict['tmtintegrator.run-tmtintegrator'] = 'false'
         #elif $prfx.isobaric_quantification_step == 'yes'
             #set $wfdict['tmtintegrator.run-tmtintegrator'] = 'true'
-            #set $wfdict['tmtintegrator.dont-run-fq-lq'] = 'false'
             #set $cxt = $prfx.options
             #set $wfdict['tmtintegrator.quant_level'] = $cxt.quant_level
             #set $wfdict['tmtintegrator.channel_num'] = $cxt.channel_num
@@ -895,14 +1194,17 @@
                 #set $wfdict['tmtintegrator.add_Ref'] = 1
                 #set $wfdict['tmtintegrator.ref_tag'] = $cxt.ref_tag
             #end if
-            #if $cxt.groupby != ''
+            #if $cxt.groupby != 'None'
                 #set $wfdict['tmtintegrator.groupby'] = $cxt.groupby
             #end if
             #set $wfdict['tmtintegrator.log2transformed'] = $cxt.log2transformed
             #if $cxt.prot_norm != 'None'
                 #set $wfdict['tmtintegrator.prot_norm'] = $cxt.prot_norm
             #end if
-            #if $cxt.glycan_conditional.use_glycan_composition == 'yes'
+            #if $cxt.glycan_conditional.use_glycan_composition == 'no'
+                #set $wfdict['tmtintegrator.use_glycan_composition'] = 'false'
+            #elif $cxt.glycan_conditional.use_glycan_composition == 'yes'
+                #set $wfdict['tmtintegrator.use_glycan_composition'] = 'true'
                 #if $cxt.glycan_conditional.mod_tag != 'None'
                     #set $wfdict['tmtintegrator.mod_tag'] = $cxt.glycan_conditional.mod_tag
                 #end if
@@ -970,18 +1272,110 @@
         #end if
     ]]></token>
 
+    <xml name="dia_pseuedo_ms2" token_expand="false" token_yes="false" token_no="true">
+        <section name="dia_pseudo" expanded="@EXPAND@" title="DIA Pseudo MS2">
+            <conditional name="diatracer">
+                <param name="diatracer_step" type="select" label="Run diaTracer">
+                    <option value="default">Use workflow defaults</option>
+                    <option value="yes" selected="@YES@">yes</option>
+                    <option value="no" selected="@NO@">no</option>
+                </param>
+                <when value="default"/>
+                <when value="no"/>
+                <when value="yes">
+                    <section name="options" expanded="true" title="diaPASEF Spectrum Deconvolution">
+                        <param name="corr_threshold" type="float" value="0.3" label="Corr Threshold"/>
+                        <param name="delta_apex_im" type="float" value="0.01" label="Delta Apex IM"/>
+                        <param name="delta_apex_rt" type="integer" value="3" label="Delta Apex RT"/>
+                        <param name="rf_max" type="integer" value="500" label="RF max" />
+                        <param name="mass_defect_offset" type="float" value="0.1" label="Mass Defect Offset"/>
+                        <param name="mass_defect_filter" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Mass Defect Filter"/>
+                    </section>
+                </when>
+            </conditional>
+        </section>
+    </xml>
+    <token name="@DIA_PSEUDO_MS2@"><![CDATA[
+#set $prfx = $wf.dia_pseudo.diatracer
+#if $prfx.diatracer_step == 'no'
+  #set $wfdict['diatracer.run-diatracer'] = 'false'
+#elif $prfx.diatracer_step == 'yes'
+  #set $wfdict['diatracer.run-diatracer'] = 'true'
+  #set $cxt = $prfx.options
+  #set $wfdict['diatracer.corr-threshold'] = $cxt.corr_threshold
+  #set $wfdict['diatracer.delta-apex-im'] = $cxt.delta_apex_im
+  #set $wfdict['diatracer.delta-apex-rt'] = $cxt.delta_apex_rt
+  #set $wfdict['diatracer.rf-max'] = $cxt.rf_max
+  #set $wfdict['diatracer.mass-defect-offset'] = $cxt.mass_defect_offset
+  #set $wfdict['diatracer.mass-defect-filter'] = $cxt.mass_defect_filter
+#end if
+]]></token>
+
+    <xml name="diann_quantification" token_expand="false" token_yes="true" token_no="false">
+        <section name="quant_dia" expanded="@EXPAND@" title="Quant (DIA)">
+            <conditional name="diann_quantification">
+                <param name="diann_quantification_step" type="select" label="Perform DIA Quantification with DIA-NN">
+                    <option value="default">Use workflow defaults</option>
+                    <option value="yes" selected="@YES@">yes</option>
+                    <option value="no" selected="@NO@">no</option>
+                </param>
+                <when value="default"/>
+                <when value="no"/>
+                <when value="yes">
+                    <section name="options" expanded="true" title="Isobaric Quantification">
+                        <param name="qvalue" type="float" value="0.01" min="0.0" max="1.0" optional="true" label="Precursor FDR" help="default 0.01"/>
+                        <param name="generate_msstats" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Generate MSStats input"/>
+                        <param name="unrelated_runs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Unrelated runs"/>
+                        <param name="use_predicted_spectra" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Replace library spectra with predicted"/>
+                        <param name="library" type="data" format="csv,tsv,xls,txt,binary" optional="true" label="Spectral Library"/>
+                        <param name="quantification_strategy" type="select" optional="true" label="Quantification strategy" help="default: Robust LC (high precision)">
+                            <option value="0">Any LC (high accuracy)</option>
+                            <option value="1">Any LC (high precision)</option>
+                            <option value="2">Robust LC (high accuracy)</option>
+                            <option value="3">Robust LC (high precision)</option>
+                        </param>
+                    </section>
+                </when>
+            </conditional>
+        </section>
+    </xml>
+    <token name="@DIANN_QUANTIFICATION@"><![CDATA[
+#set $prfx = $wf.quant_dia.diann_quantification
+#if $prfx.diann_quantification_step == 'no'
+  #set $wfdict['diann.run-dia-nn'] = 'false'
+#elif $prfx.diann_quantification_step == 'yes'
+  #set $wfdict['diann.run-dia-nn'] = 'true'
+  #set $cxt = $prfx.options
+  #if $cxt.qvalue != ''
+    #set $wfdict['diann.q-value'] = $cxt.qvalue
+  #end if
+  #set $wfdict['diann.generate-msstats'] = $cxt.generate_msstats
+  #set $wfdict['diann.unrelated-runs'] = $cxt.unrelated_runs
+  #set $wfdict['diann.use-predicted-spectra'] = $cxt.use_predicted_spectra
+  #if $cxt.quantification_strategy != ''
+    #set $wfdict['diann.quantification-strategy'] = $cxt.quantification_strategy
+  #end if
+  #if $cxt.library
+    ln -s '$cxt.library' './diann_lib.speclib'
+    #set $wfdict['diann.library'] = 'diann_lib.speclib'
+  #end if
+#end if
+]]></token>
+
+
+
     <!-- License agreement texts. -->
     <token name="@MSFRAGGER_LICENSE_AGREEMENT@">
-MSFragger is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: http://msfragger-upgrader.nesvilab.org/upgrader/MSFragger-LICENSE.pdf. This license provides with non-exclusive, non-transferable right to use MSFragger solely for academic research, non-commercial or educational purposes. I agree to be subject to the terms and conditions of this license. I understand that to use MSFragger for other purposes requires a commercial license from the University of Michigan Office of Tech Transfer.
+MSFragger is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: http://msfragger-upgrader.nesvilab.org/upgrader/LICENSE-ACADEMIC.pdf. This license provides with non-exclusive, non-transferable right to use MSFragger solely for academic research, non-commercial or educational purposes. I agree to be subject to the terms and conditions of this license. I understand that to use MSFragger for other purposes requires a commercial license from the University of Michigan Office of Tech Transfer.
     </token>
     <token name="@IONQUANT_LICENSE_AGREEMENT@">
-IonQuant is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf
+IonQuant is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: https://msfragger-upgrader.nesvilab.org/ionquant/LICENSE-ACADEMIC.pdf
     </token>
     <token name="@THERMO_RAW_READER_LICENSE_AGREEMENT@">
 I agree to the terms of Thermo (c) Raw File Reader License Agreement: http://msfragger-upgrader.nesvilab.org/upgrader/RawFileRdr_License_Agreement_RevA.pdf
     </token>
     <token name="@BRUKER_LICENSE_AGREEMENT@">
-I agree to the terms of Bruker SDK library distribution conditions: http://msfragger-upgrader.nesvilab.org/upgrader/redist.txt
+I agree to the terms of Bruker SDK library distribution conditions: http://msfragger-upgrader.nesvilab.org/upgrader/EULA%20TDF-SDK.pdf
     </token>
     <token name="@LICENSE_AGREEMENTS@">
 @MSFRAGGER_LICENSE_AGREEMENT@
diff -r 59fec1e2a6c3 -r b4f6df8fa89b msfragger_macros.xml
--- a/msfragger_macros.xml	Sun Mar 30 23:00:45 2025 +0000
+++ b/msfragger_macros.xml	Wed Oct 01 22:20:54 2025 +0000
@@ -38,7 +38,7 @@
     <xml name="msfragger_default">
         <expand macro="search_tolerances"/>
         <expand macro="digestion"/>
-        <expand macro="variable_modification"/>
+        <expand macro="variable_modification" mod_3="true"/>
         <expand macro="static_modification"/>
         <expand macro="glyco_labile"/>
         <expand macro="mass_offsets"/>
@@ -50,7 +50,7 @@
     <xml name="msfragger_open">
         <expand macro="search_tolerances"/>
         <expand macro="digestion"/>
-        <expand macro="variable_modification"/>
+        <expand macro="variable_modification" mod_3="true"/>
         <expand macro="static_modification"/>
         <expand macro="glyco_labile"/>
         <expand macro="mass_offsets"/>
@@ -62,8 +62,8 @@
     <xml name="msfragger_nonspecific_HLA">
         <expand macro="search_tolerances" precursor_mass_lower="-20" precursor_mass_upper="20"/>
         <expand macro="digestion" stricttrypsin="false" nonspecific="true" digest_max_length="25" termini_0="true" termini_2="false" digest_mass_range_min="200.0"/>
-        <expand macro="variable_modification"/>
-        <expand macro="static_modification"/>
+        <expand macro="variable_modification" mod_2="true" mod_group_hla="true"/>
+        <expand macro="static_modification" check_cysteine="false"/>
         <expand macro="glyco_labile"/>
         <expand macro="mass_offsets"/>
         <expand macro="spectrum_processing" transform_none="false" transform_sqrt="true"/>
@@ -74,7 +74,7 @@
     <xml name="msfragger_LFQ_MBR">
         <expand macro="search_tolerances"/>
         <expand macro="digestion"/>
-        <expand macro="variable_modification"/>
+        <expand macro="variable_modification" mod_3="true"/>
         <expand macro="static_modification"/>
         <expand macro="glyco_labile"/>
         <expand macro="mass_offsets"/>
@@ -86,11 +86,23 @@
     <xml name="msfragger_TMT">
         <expand macro="search_tolerances"/>
         <expand macro="digestion" digest_mass_range_min="200.0"/>
-        <expand macro="variable_modification"/>
+        <expand macro="variable_modification" mod_3="true" mod_group_tmt="true"/>
+        <expand macro="static_modification" lysine_value="229.16293"/>
+        <expand macro="glyco_labile"/>
+        <expand macro="mass_offsets"/>
+        <expand macro="spectrum_processing" clear_mz_range_min="125.5" clear_mz_range_max="131.5"/>
+        <expand macro="open_search_options"/>
+        <expand macro="modeling_output"/>
+        <expand macro="advanced_options"/>
+    </xml>
+    <xml name="msfragger_dia_speclib_quant">
+        <expand macro="search_tolerances"/>
+        <expand macro="digestion" allowed_missed_cleavage_1="1" allowed_missed_cleavage_2="1"/>
+        <expand macro="variable_modification" mod_1="true"/>
         <expand macro="static_modification"/>
         <expand macro="glyco_labile"/>
         <expand macro="mass_offsets"/>
-        <expand macro="spectrum_processing" clear_mz_range_min="125.5" clear_mz_range_max="131.5"/>
+        <expand macro="spectrum_processing" check_spectral_files="false"/>
         <expand macro="open_search_options"/>
         <expand macro="modeling_output"/>
         <expand macro="advanced_options"/>
@@ -223,12 +235,11 @@
             <param name="search_enzyme_name" type="text" value="@SEARCH_ENZYME_NAME@"
                 label="Digestion Enzyme" help="Name of enzyme to be written to the pepXML file."/>
             <param name="search_enzyme_cut" type="text" value="@CUT@"
-                label="Residues after which the enzyme cuts" help="search_enzyme_cutafter Residues after which the enzyme cuts Default: KR"/>
+                label="Residues after which the enzyme cuts" help="search_enzyme_cutafter Residues after which the enzyme cuts"/>
             <param name="search_enzyme_nocut" type="text" value="@NOCUT@"
-                label="Residues that the enzyme will not cut before" help="search_enzyme_butnotafter - (misnomer: should really be called butnotbefore) Default: P"/>
+                label="Residues that the enzyme will not cut before" help="search_enzyme_butnotafter - (misnomer: should really be called butnotbefore)"/>
     </xml>
-                              <!-- wagnerr here in final param review -->
-    <xml name="digest" token_stricttrypsin="true" token_nonspecific="false">
+    <xml name="digest" token_stricttrypsin="true" token_nonspecific="false" token_allowed_missed_cleavage="2">
             <conditional name="digest">
                 <param name="search_enzyme" type="select" label="Protein Digestion Enzyme">
                     <option value="trypsin">trypsin</option>
@@ -284,7 +295,7 @@
                     <expand macro="cleavage" search_enzyme_name="lysc-p" cut="K" nocut=""/>
                 </when>
                 <when value="nonspecific">
-                    <expand macro="cleavage" search_enzyme_name="nonspecific" cut="-" nocut=""/>
+                    <expand macro="cleavage" search_enzyme_name="nonspecific" cut="@" nocut=""/>
                  </when>
                 <when value="custom">
                     <expand macro="cleavage" search_enzyme_name="custom" cut="" nocut=""/>
@@ -305,17 +316,17 @@
                     <expand macro="cleavage" search_enzyme_name="trypsin_r" cut="R" nocut="P"/>
                 </when>
             </conditional>
-            <param name="allowed_missed_cleavage" type="integer" value="2" min="0" max="5" optional="true"
+            <param name="allowed_missed_cleavage" type="integer" value="@ALLOWED_MISSED_CLEAVAGE@" min="0" max="5" optional="true"
                 label="Allowed number of missed cleavages"/>
-            <param name="search_enzyme_sense" type="select" label="Protein Digestion Enzyme">
+            <param name="search_enzyme_sense" type="select" label="Search Enzyme Sense">
                 <option value="C">C</option>
                 <option value="N">N</option>
             </param>
     </xml>
 
-    <xml name="digestion" token_stricttrypsin="true" token_nonspecific="false" token_digest_max_length="50" token_termini_0="false" token_termini_1="false" token_termini_2="true" token_digest_mass_range_min="500.0" token_digest_mass_range_max="5000.0">
+    <xml name="digestion" token_stricttrypsin="true" token_nonspecific="false" token_digest_max_length="50" token_termini_0="false" token_termini_1="false" token_termini_2="true" token_digest_mass_range_min="500.0" token_digest_mass_range_max="5000.0" token_allowed_missed_cleavage_1="2" token_allowed_missed_cleavage_2="2">
         <section name="digestion" expanded="false" title="In-silico Digestion Parameters">
-            <expand macro="digest" stricttrypsin="@STRICTTRYPSIN@" nonspecific="@NONSPECIFIC@"/>
+            <expand macro="digest" stricttrypsin="@STRICTTRYPSIN@" nonspecific="@NONSPECIFIC@" allowed_missed_cleavage="@ALLOWED_MISSED_CLEAVAGE_1@"/>
             <conditional name="enzyme2">
                 <param name="digest2" type="select" label="Second Enzyme Digest">
                     <option value="no">No</option>
@@ -323,7 +334,7 @@
                 </param>
                 <when value="no"/>
                 <when value="yes">
-                    <expand macro="digest" stricttrypsin="false" nonspecific="false"/>
+                    <expand macro="digest" stricttrypsin="false" nonspecific="false" allowed_missed_cleavage="@ALLOWED_MISSED_CLEAVAGE_2@"/>
                 </when>
             </conditional>
             <param name="num_enzyme_termini" type="select" label="Number of enzyme termini">
@@ -346,7 +357,11 @@
         ##enzyme_1
         #set $msfragger_dict['search_enzyme_name_1'] = $prefix.digestion.digest.search_enzyme_name
         #set $msfragger_dict['misc.fragger.enzyme-dropdown-1'] = $prefix.digestion.digest.search_enzyme_name
-        #set $msfragger_dict['search_enzyme_cut_1'] = $prefix.digestion.digest.search_enzyme_cut
+        #if $prefix.digestion.search_enzyme_cut == '__at__'
+            #set $msfragger_dict['search_enzyme_cut_1'] = '@'
+        #else
+            #set $msfragger_dict['search_enzyme_cut_1'] = $prefix.digestion.digest.search_enzyme_cut
+        #end if
         #set $msfragger_dict['search_enzyme_nocut_1'] = $prefix.digestion.digest.search_enzyme_nocut
         #if $prefix.digestion.allowed_missed_cleavage != ''
             #set $msfragger_dict['allowed_missed_cleavage_1'] = $prefix.digestion.allowed_missed_cleavage
@@ -358,7 +373,11 @@
         #if $prefix.digestion.enzyme2.digest2 == 'yes'
             #set $msfragger_dict['search_enzyme_name_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name
             #set $msfragger_dict['misc.fragger.enzyme-dropdown-2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name
-            #set $msfragger_dict['search_enzyme_cut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_cut
+            #if $prefix.digestion.enzyme2.digest.search_enzyme_cut == '__at__'
+                #set $msfragger_dict['search_enzyme_cut_2'] = '@'
+            #else
+                #set $msfragger_dict['search_enzyme_cut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_cut
+            #end if
             #set $msfragger_dict['search_enzyme_nocut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_nocut
             #if $prefix.digestion.enzyme2.allowed_missed_cleavage != ''
                 #set $msfragger_dict['allowed_missed_cleavage_2'] = $prefix.digestion.enzyme2.allowed_missed_cleavage
@@ -386,27 +405,26 @@
         #end if
     ]]></token>
 
-    <xml name="variable_modifications">
-        <option value="15.99491461956 M 3">Oxidation of M (15.99491461956) modaa</option>
-        <option value="42.0105646837 &#91;^ 1">Acetylation of peptide N-term (42.0105646837) modn_peptide</option>
-        <option value="79.96633052074999 STY 3">Phosphorylation of STY (79.96633052074999) modaa</option>
-        <option value="229.16293213472 n^ 1">TMT 10-plex of peptide N-term (229.16293213472) modn_peptide</option>
-        <option value="229.169252 n^ 1">TMT 11-plex of peptide N-term (229.169252) modn_peptide</option>
-        <option value="229.16293213472 S 1">TMT 10-plex of S (229.16293213472) modaa</option>
-        <option value="229.169252 S 1">TMT 11-plex of S (229.169252) modaa</option>
-        <option value="-18.0105646837 nE 1">Pyrolidone from E (-18.0105646837) modnaa_peptide</option>
-    </xml>
-
     <token name="@RE_FLOAT@">[+-]?\d+(\.\d*)?</token>
     <token name="@RE_AA@">([A-Z]+|(c[A-Z*])+|(n[\^A-Z*])+|\[\^|\])</token>
     <token name="@RE_MOD@">@RE_FLOAT@,@RE_AA@,\d</token>
     <token name="@RE_MODS@">@RE_MOD@(;\s*@RE_MOD@)*</token>
-    <xml name="variable_modification" token_max_variable_mods_per_peptide="3">
+    <xml name="variable_modification" token_max_variable_mods_per_peptide="3" token_mod_1="false" token_mod_2="false" token_mod_3="false" token_mod_4="true" token_mod_group_hla="false" token_mod_group_tmt="false">
         <section name="variable_modification" expanded="false" title="Variable Modifications">
             <param name="max_variable_mods_per_peptide" type="integer" value="@MAX_VARIABLE_MODS_PER_PEPTIDE@" min="0" max="5" optional="true"
                 label="Maximum total number of variable modifications per peptide"/>
             <param name="variable_mods_select" type="select" optional="true" multiple="true" label="Select Variable Modifications">
-                <expand macro="variable_modifications"/>
+                <option value="15.99491461956 M 1" selected="@MOD_1@">15.99491461956 M 1</option>
+                <option value="15.99491461956 M 2" selected="@MOD_2@">15.99491461956 M 2</option>
+                <option value="15.99491461956 M 3" selected="@MOD_3@">15.99491461956 M 3</option>
+                <option value="42.0105646837 ntermsite^ 1" selected="@MOD_4@">42.0105646837 [^ 1</option>
+                <option value="-17.0265 nQ 1" selected="@MOD_GROUP_HLA@">-17.0265 nQ 1</option>
+                <option value="-18.0106 nE 1" selected="@MOD_GROUP_HLA@">-18.0106 nE 1</option>
+                <option value="119.0041 C 1" selected="@MOD_GROUP_HLA@">119.0041 C 1</option>
+                <option value="79.96633052074999 STY 3">79.96633052074999 STY 3</option>
+                <option value="229.16293213472 n^ 1" selected="@MOD_GROUP_TMT@">229.16293213472 n^ 1</option>
+                <option value="229.16293213472 S 1" selected="@MOD_GROUP_TMT@">229.16293213472 S 1</option>
+                <option value="-18.0105646837 nE 1">-18.0105646837 nE 1</option>
             </param>
             <param name="variable_mods" type="text" area="True" size="120x7" value="" optional="true"
                 label="Enter Variable Modifications">
@@ -436,10 +454,6 @@
                 <option value="true">Yes</option>
                 <option value="false">No</option>
             </param>
-            <param name="allow_multiple_variable_mods_on_residue" type="select" optional="true" label="Allow each amino acid to be modified by multiple variable modifications">
-                <option value="true">Yes</option>
-                <option value="false">No</option>
-            </param>
 
             <param name="max_variable_mods_combinations" type="integer" value="5000" min="0" max="65534" optional="true"
                 label="Maximum allowed number of modified variably modified peptides from each peptide sequence"
@@ -464,184 +478,241 @@
         #if $prefix.variable_modification.clip_nTerm_M != 'None'
             #set $msfragger_dict['clip_nTerm_M'] = $prefix.variable_modification.clip_nTerm_M
         #end if
-        #if $prefix.variable_modification.allow_multiple_variable_mods_on_residue != 'None'
-            #set $msfragger_dict['allow_multiple_variable_mods_on_residue'] = $prefix.variable_modification.allow_multiple_variable_mods_on_residue
-        #end if
         #if $prefix.variable_modification.max_variable_mods_combinations != "None"
             #set $msfragger_dict['max_variable_mods_combinations'] = $prefix.variable_modification.max_variable_mods_combinations
         #end if
         #set $vmods = []
         #if $prefix.variable_modification.variable_mods_select != 'None'
-            #set $vmods = [x.replace(' ',',') for x in str($prefix.variable_modification.variable_mods_select).split(',')]
+            #set $vmods = [x.replace(' ',',').replace('ntermsite','[') for x in str($prefix.variable_modification.variable_mods_select).split(',')]
         #end if
         #if $prefix.variable_modification.variable_mods != ''
             #set $vmods += [x.strip() for x in str($prefix.variable_modification.variable_mods).split(';')]
         #end if
     ]]></token>
 
-    <xml name="static_modification">
+    <xml name="static_modification" token_check_cysteine="true" token_lysine_value="0.0">
         <section name="static_modification" expanded="false" title="Static Modifications">
-            <param name="add_Cterm_peptide" type="float" value="" optional="true"
-                label="Statically add mass in Da to C-terminal of peptide Default: 0.0" />
-            <param name="add_Nterm_peptide" type="float" value="" optional="true"
-                label="Statically add mass in Da to N-terminal of peptide Default: 0.0" />
-            <param name="add_Cterm_protein" type="float" value="" optional="true"
-                label="Statically add mass in Da to C-terminal of protein Default: 0.0" />
-            <param name="add_Nterm_protein" type="float" value="" optional="true"
-                label="Statically add mass in Da to N-terminal of protein Default: 0.0" />
-            <param name="add_A_alanine" type="float" value="" optional="true"
-                label="Statically add mass in Da to A (alanine) Default: 0.0" />
-            <param name="add_R_arginine" type="float" value="" optional="true"
-                label="Statically add mass in Da to R (arginine) Default: 0.0" />
-            <param name="add_N_asparagine" type="float" value="" optional="true"
-                label="Statically add mass in Da to N (asparagine) Default: 0.0" />
-            <param name="add_D_aspartic_acid" type="float" value="" optional="true"
-                label="Statically add mass in Da to D (aspartic_acid) Default: 0.0" />
-            <param name="add_C_cysteine" type="float" value="" optional="true"
-                label="Statically add mass in Da to C (cysteine) Default: 0.0" />
-            <param name="add_E_glutamic_acid" type="float" value="" optional="true"
-                label="Statically add mass in Da to E (glutamic_acid) Default: 0.0" />
-            <param name="add_Q_glutamine" type="float" value="" optional="true"
-                label="Statically add mass in Da to Q (glutamine) Default: 0.0" />
-            <param name="add_G_glycine" type="float" value="" optional="true"
-                label="Statically add mass in Da to G (glycine) Default: 0.0" />
-            <param name="add_H_histidine" type="float" value="" optional="true"
-                label="Statically add mass in Da to H (histidine) Default: 0.0" />
-            <param name="add_I_isoleucine" type="float" value="" optional="true"
-                label="Statically add mass in Da to I (isoleucine) Default: 0.0" />
-            <param name="add_L_leucine" type="float" value="" optional="true"
-                label="Statically add mass in Da to L (leucine) Default: 0.0" />
-            <param name="add_K_lysine" type="float" value="" optional="true"
-                label="Statically add mass in Da to K (lysine) Default: 0.0" />
-            <param name="add_M_methionine" type="float" value="" optional="true"
-                label="Statically add mass in Da to M (methionine) Default: 0.0" />
-            <param name="add_F_phenylalanine" type="float" value="" optional="true"
-                label="Statically add mass in Da to F (phenylalanine) Default: 0.0" />
-            <param name="add_P_proline" type="float" value="" optional="true"
-                label="Statically add mass in Da to P (proline) Default: 0.0" />
-            <param name="add_S_serine" type="float" value="" optional="true"
-                label="Statically add mass in Da to S (serine) Default: 0.0" />
-            <param name="add_T_threonine" type="float" value="" optional="true"
-                label="Statically add mass in Da to T (threonine) Default: 0.0" />
-            <param name="add_W_tryptophan" type="float" value="" optional="true"
-                label="Statically add mass in Da to W (tryptophan) Default: 0.0" />
-            <param name="add_Y_tyrosine" type="float" value="" optional="true"
-                label="Statically add mass in Da to Y (tyrosine) Default: 0.0" />
-            <param name="add_V_valine" type="float" value="" optional="true"
-                label="Statically add mass in Da to V (valine) Default: 0.0" />
-            <param name="add_B_user_amino_acid" type="float" value="" optional="true"
-                label="Statically add mass in Da to B (iuser_amino_acid) Default: 0.0" />
-            <param name="add_J_user_amino_acid" type="float" value="" optional="true"
-                label="Statically add mass in Da to J (iuser_amino_acid) Default: 0.0" />
-            <param name="add_O_user_amino_acid" type="float" value="" optional="true"
-                label="Statically add mass in Da to O (user_amino_acid) Default: 0.0" />
-            <param name="add_U_user_amino_acid" type="float" value="" optional="true"
-                label="Statically add mass in Da to U (iuser_amino_acid) Default: 0.0" />
-            <param name="add_X_user_amino_acid" type="float" value="" optional="true"
-                label="Statically add mass in Da to X (iuser_amino_acid) Default: 0.0" />
-            <param name="add_Z_user_amino_acid" type="float" value="" optional="true"
-                label="Statically add mass in Da to Z (iuser_amino_acid) Default: 0.0" />
+            <param name="add_Cterm_peptide_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to C-terminal of peptide"/>
+            <param name="add_Cterm_peptide" type="float" value="0.0"
+                label="Statically add mass in Da to C-terminal of peptide" />
+
+            <param name="add_Nterm_peptide_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to N-terminal of peptide"/>
+            <param name="add_Nterm_peptide" type="float" value="0.0"
+                label="Statically add mass in Da to N-terminal of peptide" />
+
+            <param name="add_Cterm_protein_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to C-terminal of protein"/>
+            <param name="add_Cterm_protein" type="float" value="0.0"
+                label="Statically add mass in Da to C-terminal of protein" />
+
+            <param name="add_Nterm_protein_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to N-terminal of protein"/>
+            <param name="add_Nterm_protein" type="float" value="0.0"
+                label="Statically add mass in Da to N-terminal of protein" />
+
+            <param name="add_A_alanine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to A (alanine)"/>
+            <param name="add_A_alanine" type="float" value="0.0"
+                label="Statically add mass in Da to A (alanine)" />
+
+            <param name="add_R_arginine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to R (arginine)"/>
+            <param name="add_R_arginine" type="float" value="0.0"
+                label="Statically add mass in Da to R (arginine)" />
+
+            <param name="add_N_asparagine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to N (asparagine)"/>
+            <param name="add_N_asparagine" type="float" value="0.0"
+                label="Statically add mass in Da to N (asparagine)" />
+
+            <param name="add_D_aspartic_acid_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to D (aspartic_acid)"/>
+            <param name="add_D_aspartic_acid" type="float" value="0.0"
+                label="Statically add mass in Da to D (aspartic_acid)" />
+
+            <param name="add_C_cysteine_bool" type="boolean" checked="@CHECK_CYSTEINE@"
+                label="Statically add mass in Da to C (cysteine)"/>
+            <param name="add_C_cysteine" type="float" value="57.02146"
+                label="Statically add mass in Da to C (cysteine)" />
+
+            <param name="add_E_glutamic_acid_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to E (glutamic_acid)"/>
+            <param name="add_E_glutamic_acid" type="float" value="0.0"
+                label="Statically add mass in Da to E (glutamic_acid)" />
+
+            <param name="add_Q_glutamine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to Q (glutamine)"/>
+            <param name="add_Q_glutamine" type="float" value="0.0"
+                label="Statically add mass in Da to Q (glutamine)" />
+
+            <param name="add_G_glycine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to G (glycine)"/>
+            <param name="add_G_glycine" type="float" value="0.0"
+                label="Statically add mass in Da to G (glycine)" />
+
+            <param name="add_H_histidine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to H (histidine)"/>
+            <param name="add_H_histidine" type="float" value="0.0"
+                label="Statically add mass in Da to H (histidine)" />
+
+            <param name="add_I_isoleucine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to I (isoleucine)"/>
+            <param name="add_I_isoleucine" type="float" value="0.0"
+                label="Statically add mass in Da to I (isoleucine)" />
+
+            <param name="add_L_leucine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to L (leucine)"/>
+            <param name="add_L_leucine" type="float" value="0.0"
+                label="Statically add mass in Da to L (leucine)" />
+
+            <param name="add_K_lysine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to K (lysine)"/>
+            <param name="add_K_lysine" type="float" value="@LYSINE_VALUE@"
+                label="Statically add mass in Da to K (lysine)" />
+
+            <param name="add_M_methionine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to M (methionine)"/>
+            <param name="add_M_methionine" type="float" value="0.0"
+                label="Statically add mass in Da to M (methionine)" />
+
+            <param name="add_F_phenylalanine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to F (phenylalanine)"/>
+            <param name="add_F_phenylalanine" type="float" value="0.0"
+                label="Statically add mass in Da to F (phenylalanine)" />
+
+            <param name="add_P_proline_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to P (proline)"/>
+            <param name="add_P_proline" type="float" value="0.0"
+                label="Statically add mass in Da to P (proline)" />
+
+            <param name="add_S_serine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to S (serine)"/>
+            <param name="add_S_serine" type="float" value="0.0"
+                label="Statically add mass in Da to S (serine)" />
+
+            <param name="add_T_threonine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to T (threonine)"/>
+            <param name="add_T_threonine" type="float" value="0.0"
+                label="Statically add mass in Da to T (threonine)" />
+
+            <param name="add_W_tryptophan_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to W (tryptophan)"/>
+            <param name="add_W_tryptophan" type="float" value="0.0"
+                label="Statically add mass in Da to W (tryptophan)" />
+
+            <param name="add_Y_tyrosine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to Y (tyrosine)"/>
+            <param name="add_Y_tyrosine" type="float" value="0.0"
+                label="Statically add mass in Da to Y (tyrosine)" />
+
+            <param name="add_V_valine_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to V (valine)"/>
+            <param name="add_V_valine" type="float" value="0.0"
+                label="Statically add mass in Da to V (valine)" />
+
+            <param name="add_B_user_amino_acid_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to B (iuser_amino_acid)"/>
+            <param name="add_B_user_amino_acid" type="float" value="0.0"
+                label="Statically add mass in Da to B (iuser_amino_acid)" />
+
+            <param name="add_J_user_amino_acid_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to J (iuser_amino_acid)"/>
+            <param name="add_J_user_amino_acid" type="float" value="0.0"
+                label="Statically add mass in Da to J (iuser_amino_acid)" />
+
+            <param name="add_O_user_amino_acid_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to O (user_amino_acid)"/>
+            <param name="add_O_user_amino_acid" type="float" value="0.0"
+                label="Statically add mass in Da to O (user_amino_acid)" />
+
+            <param name="add_U_user_amino_acid_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to U (iuser_amino_acid)"/>
+            <param name="add_U_user_amino_acid" type="float" value="0.0"
+                label="Statically add mass in Da to U (iuser_amino_acid)" />
+
+            <param name="add_X_user_amino_acid_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to X (iuser_amino_acid)"/>
+            <param name="add_X_user_amino_acid" type="float" value="0.0"
+                label="Statically add mass in Da to X (iuser_amino_acid)" />
+
+            <param name="add_Z_user_amino_acid_bool" type="boolean" checked="true"
+                label="Statically add mass in Da to Z (iuser_amino_acid)"/>
+            <param name="add_Z_user_amino_acid" type="float" value="0.0"
+                label="Statically add mass in Da to Z (iuser_amino_acid)" />
         </section>
     </xml>
     <token name="@STATIC_MODIFICATION@"><![CDATA[
-        #set $fmods = {}
-        #if $prefix.static_modification.add_Cterm_peptide  != ''
-            #set $fmods['Cterm_peptide'] = $prefix.static_modification.add_Cterm_peptide
-        #end if
-        #if $prefix.static_modification.add_Nterm_peptide  != ''
-            #set $fmods['Nterm_peptide'] = $prefix.static_modification.add_Nterm_peptide
-        #end if
-        #if $prefix.static_modification.add_Cterm_protein  != ''
-            #set $fmods['Cterm_protein'] = $prefix.static_modification.add_Cterm_protein
-        #end if
-        #if $prefix.static_modification.add_Nterm_protein  != ''
-            #set $fmods['Nterm_protein'] = $prefix.static_modification.add_Nterm_protein
-        #end if
-        #if $prefix.static_modification.add_G_glycine  != ''
-            #set $fmods['G_glycine'] = $prefix.static_modification.add_G_glycine
-        #end if
-        #if $prefix.static_modification.add_A_alanine  != ''
-            #set $fmods['A_alanine'] = $prefix.static_modification.add_A_alanine
-        #end if
-        #if $prefix.static_modification.add_S_serine  != ''
-            #set $fmods['S_serine'] = $prefix.static_modification.add_S_serine
-        #end if
-        #if $prefix.static_modification.add_P_proline  != ''
-            #set $fmods['P_proline'] = $prefix.static_modification.add_P_proline
-        #end if
-        #if $prefix.static_modification.add_V_valine  != ''
-            #set $fmods['V_valine'] = $prefix.static_modification.add_V_valine
-        #end if
-        #if $prefix.static_modification.add_T_threonine  != ''
-            #set $fmods['T_threonine'] = $prefix.static_modification.add_T_threonine
-        #end if
-        #if $prefix.static_modification.add_C_cysteine  != ''
-            #set $fmods['C_cysteine'] = $prefix.static_modification.add_C_cysteine
-        #end if
-        #if $prefix.static_modification.add_L_leucine  != ''
-            #set $fmods['L_leucine'] = $prefix.static_modification.add_L_leucine
-        #end if
-        #if $prefix.static_modification.add_I_isoleucine  != ''
-            #set $fmods['I_isoleucine'] = $prefix.static_modification.add_I_isoleucine
-        #end if
-        #if $prefix.static_modification.add_N_asparagine  != ''
-            #set $fmods['N_asparagine'] = $prefix.static_modification.add_N_asparagine
-        #end if
-        #if $prefix.static_modification.add_D_aspartic_acid  != ''
-            #set $fmods['D_aspartic_acid'] = $prefix.static_modification.add_D_aspartic_acid
-        #end if
-        #if $prefix.static_modification.add_Q_glutamine  != ''
-            #set $fmods['Q_glutamine'] = $prefix.static_modification.add_Q_glutamine
-        #end if
-        #if $prefix.static_modification.add_K_lysine  != ''
-            #set $fmods['K_lysine'] = $prefix.static_modification.add_K_lysine
-        #end if
-        #if $prefix.static_modification.add_E_glutamic_acid  != ''
-            #set $fmods['E_glutamic_acid'] = $prefix.static_modification.add_E_glutamic_acid
-        #end if
-        #if $prefix.static_modification.add_M_methionine  != ''
-            #set $fmods['M_methionine'] = $prefix.static_modification.add_M_methionine
-        #end if
-        #if $prefix.static_modification.add_H_histidine  != ''
-            #set $fmods['H_histidine'] = $prefix.static_modification.add_H_histidine
-        #end if
-        #if $prefix.static_modification.add_F_phenylalanine  != ''
-            #set $fmods['F_phenylalanine'] = $prefix.static_modification.add_F_phenylalanine
-        #end if
-        #if $prefix.static_modification.add_R_arginine  != ''
-            #set $fmods['R_arginine'] = $prefix.static_modification.add_R_arginine
-        #end if
-        #if $prefix.static_modification.add_Y_tyrosine  != ''
-            #set $fmods['Y_tyrosine'] = $prefix.static_modification.add_Y_tyrosine
-        #end if
-        #if $prefix.static_modification.add_W_tryptophan  != ''
-            #set $fmods['W_tryptophan'] = $prefix.static_modification.add_W_tryptophan
-        #end if
-        #*
-        #if $prefix.static_modification.add_B_user_amino_acid  != ''
-            #set $fmods['B_user_amino_acid'] = $prefix.static_modification.add_B_user_amino_acid
-        #end if
-        #if $prefix.static_modification.add_J_user_amino_acid  != ''
-            #set $fmods['J_user_amino_acid'] = $prefix.static_modification.add_J_user_amino_acid
-        #end if
-        #if $prefix.static_modification.add_O_user_amino_acid  != ''
-            #set $fmods['O_user_amino_acid'] = $prefix.static_modification.add_O_user_amino_acid
-        #end if
-        #if $prefix.static_modification.add_U_user_amino_acid  != ''
-            #set $fmods['U_user_amino_acid'] = $prefix.static_modification.add_U_user_amino_acid
-        #end if
-        #if $prefix.static_modification.add_X_user_amino_acid  != ''
-            #set $fmods['X_user_amino_acid'] = $prefix.static_modification.add_X_user_amino_acid
-        #end if
-        #if $prefix.static_modification.add_Z_user_amino_acid  != ''
-            #set $fmods['Z_user_amino_acid'] = $prefix.static_modification.add_Z_user_amino_acid
-        #end if
-        *#
+        #set $fmod_vals = {}
+        #set $fmod_vals['add_Cterm_peptide'] = $prefix.static_modification.add_Cterm_peptide
+        #set $fmod_vals['add_Nterm_peptide'] = $prefix.static_modification.add_Nterm_peptide
+        #set $fmod_vals['add_Cterm_protein'] = $prefix.static_modification.add_Cterm_protein
+        #set $fmod_vals['add_Nterm_protein'] = $prefix.static_modification.add_Nterm_protein
+        #set $fmod_vals['add_G_glycine'] = $prefix.static_modification.add_G_glycine
+        #set $fmod_vals['add_A_alanine'] = $prefix.static_modification.add_A_alanine
+        #set $fmod_vals['add_S_serine'] = $prefix.static_modification.add_S_serine
+        #set $fmod_vals['add_P_proline'] = $prefix.static_modification.add_P_proline
+        #set $fmod_vals['add_V_valine'] = $prefix.static_modification.add_V_valine
+        #set $fmod_vals['add_T_threonine'] = $prefix.static_modification.add_T_threonine
+        #set $fmod_vals['add_C_cysteine'] = $prefix.static_modification.add_C_cysteine
+        #set $fmod_vals['add_L_leucine'] = $prefix.static_modification.add_L_leucine
+        #set $fmod_vals['add_I_isoleucine'] = $prefix.static_modification.add_I_isoleucine
+        #set $fmod_vals['add_N_asparagine'] = $prefix.static_modification.add_N_asparagine
+        #set $fmod_vals['add_D_aspartic_acid'] = $prefix.static_modification.add_D_aspartic_acid
+        #set $fmod_vals['add_Q_glutamine'] = $prefix.static_modification.add_Q_glutamine
+        #set $fmod_vals['add_K_lysine'] = $prefix.static_modification.add_K_lysine
+        #set $fmod_vals['add_E_glutamic_acid'] = $prefix.static_modification.add_E_glutamic_acid
+        #set $fmod_vals['add_M_methionine'] = $prefix.static_modification.add_M_methionine
+        #set $fmod_vals['add_H_histidine'] = $prefix.static_modification.add_H_histidine
+        #set $fmod_vals['add_F_phenylalanine'] = $prefix.static_modification.add_F_phenylalanine
+        #set $fmod_vals['add_R_arginine'] = $prefix.static_modification.add_R_arginine
+        #set $fmod_vals['add_Y_tyrosine'] = $prefix.static_modification.add_Y_tyrosine
+        #set $fmod_vals['add_W_tryptophan'] = $prefix.static_modification.add_W_tryptophan
+        #set $fmod_vals['add_B_user_amino_acid'] = $prefix.static_modification.add_B_user_amino_acid
+        #set $fmod_vals['add_J_user_amino_acid'] = $prefix.static_modification.add_J_user_amino_acid
+        #set $fmod_vals['add_O_user_amino_acid'] = $prefix.static_modification.add_O_user_amino_acid
+        #set $fmod_vals['add_U_user_amino_acid'] = $prefix.static_modification.add_U_user_amino_acid
+        #set $fmod_vals['add_X_user_amino_acid'] = $prefix.static_modification.add_X_user_amino_acid
+        #set $fmod_vals['add_Z_user_amino_acid'] = $prefix.static_modification.add_Z_user_amino_acid
+
+        #set $fmod_bools = {}
+        #set $fmod_bools['add_Cterm_peptide_bool'] = $prefix.static_modification.add_Cterm_peptide_bool
+        #set $fmod_bools['add_Nterm_peptide_bool'] = $prefix.static_modification.add_Nterm_peptide_bool
+        #set $fmod_bools['add_Cterm_protein_bool'] = $prefix.static_modification.add_Cterm_protein_bool
+        #set $fmod_bools['add_Nterm_protein_bool'] = $prefix.static_modification.add_Nterm_protein_bool
+        #set $fmod_bools['add_G_glycine_bool'] = $prefix.static_modification.add_G_glycine_bool
+        #set $fmod_bools['add_A_alanine_bool'] = $prefix.static_modification.add_A_alanine_bool
+        #set $fmod_bools['add_S_serine_bool'] = $prefix.static_modification.add_S_serine_bool
+        #set $fmod_bools['add_P_proline_bool'] = $prefix.static_modification.add_P_proline_bool
+        #set $fmod_bools['add_V_valine_bool'] = $prefix.static_modification.add_V_valine_bool
+        #set $fmod_bools['add_T_threonine_bool'] = $prefix.static_modification.add_T_threonine_bool
+        #set $fmod_bools['add_C_cysteine_bool'] = $prefix.static_modification.add_C_cysteine_bool
+        #set $fmod_bools['add_L_leucine_bool'] = $prefix.static_modification.add_L_leucine_bool
+        #set $fmod_bools['add_I_isoleucine_bool'] = $prefix.static_modification.add_I_isoleucine_bool
+        #set $fmod_bools['add_N_asparagine_bool'] = $prefix.static_modification.add_N_asparagine_bool
+        #set $fmod_bools['add_D_aspartic_acid_bool'] = $prefix.static_modification.add_D_aspartic_acid_bool
+        #set $fmod_bools['add_Q_glutamine_bool'] = $prefix.static_modification.add_Q_glutamine_bool
+        #set $fmod_bools['add_K_lysine_bool'] = $prefix.static_modification.add_K_lysine_bool
+        #set $fmod_bools['add_E_glutamic_acid_bool'] = $prefix.static_modification.add_E_glutamic_acid_bool
+        #set $fmod_bools['add_M_methionine_bool'] = $prefix.static_modification.add_M_methionine_bool
+        #set $fmod_bools['add_H_histidine_bool'] = $prefix.static_modification.add_H_histidine_bool
+        #set $fmod_bools['add_F_phenylalanine_bool'] = $prefix.static_modification.add_F_phenylalanine_bool
+        #set $fmod_bools['add_R_arginine_bool'] = $prefix.static_modification.add_R_arginine_bool
+        #set $fmod_bools['add_Y_tyrosine_bool'] = $prefix.static_modification.add_Y_tyrosine_bool
+        #set $fmod_bools['add_W_tryptophan_bool'] = $prefix.static_modification.add_W_tryptophan_bool
+        #set $fmod_bools['add_B_user_amino_acid_bool'] = $prefix.static_modification.add_B_user_amino_acid_bool
+        #set $fmod_bools['add_J_user_amino_acid_bool'] = $prefix.static_modification.add_J_user_amino_acid_bool
+        #set $fmod_bools['add_O_user_amino_acid_bool'] = $prefix.static_modification.add_O_user_amino_acid_bool
+        #set $fmod_bools['add_U_user_amino_acid_bool'] = $prefix.static_modification.add_U_user_amino_acid_bool
+        #set $fmod_bools['add_X_user_amino_acid_bool'] = $prefix.static_modification.add_X_user_amino_acid_bool
+        #set $fmod_bools['add_Z_user_amino_acid_bool'] = $prefix.static_modification.add_Z_user_amino_acid_bool
+
     ]]></token>
 
-    <xml name="spectrum_processing" token_mode_selected="false" token_mode_isolated="false" token_mode_corrected="false" token_override_charge="false" token_rm_peak0="false" token_rm_peak1="true" token_rm_peak2="false" token_clear_mz_range_min="0.0" token_clear_mz_range_max="0.0" token_transform_none="true" token_transform_sqrt="false">
+    <xml name="spectrum_processing" token_mode_selected="true" token_mode_isolated="false" token_mode_corrected="false" token_override_charge="false" token_rm_peak0="false" token_rm_peak1="true" token_rm_peak2="false" token_clear_mz_range_min="0.0" token_clear_mz_range_max="0.0" token_transform_none="true" token_transform_sqrt="false" token_check_spectral_files="true">
         <section name="spectrum_processing" expanded="false" title="Spectrum Processing">
-            <param name="precursor_mass_mode" type="select" optional="true" label="Precursor mass mode">
+            <param name="precursor_mass_mode" type="select" label="Precursor mass mode">
                 <option value="isolated" selected="@MODE_ISOLATED@">isolated</option>
                 <option value="selected" selected="@MODE_SELECTED@">selected</option>
                 <option value="corrected" selected="@MODE_CORRECTED@">corrected</option>
@@ -683,7 +754,7 @@
                 <option value="0" selected="@TRANSFORM_NONE@">None, not removed</option>
                 <option value="1" selected="@TRANSFORM_SQRT@">Square root</option>
             </param>
-            <param name="check_spectral_files" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Check spectral files"/>
+            <param name="check_spectral_files" type="boolean" truevalue="true" falsevalue="false" checked="@CHECK_SPECTRAL_FILES@" label="Check spectral files"/>
             <param name="require_precursor" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require precursor"/>
             <param name="reuse_dia_fragment_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Reuse DIA fragment peaks"/>
             <param name="activation_types" type="select" optional="true" label="Activation Type Filter">
@@ -770,14 +841,6 @@
             <param name="zero_bin_mult_expect" type="float" value="" min="0.0" optional="true"
                 label="Multiplies expect value of PSMs in the zero-bin during results ordering"
                 help="(set to less than 1 for boosting) Default: 1.0" />
-            <param name="add_topN_complementary" type="integer" value="" min="0" optional="true"
-                label="Insert complementary ions corresponding to the top N most intense fragments in each experimental spectra." >
-                <help>
-                    Useful for recovery of modified peptides near C-terminal in open search.
-                    Should be set to 0 (disabled) otherwise.
-                    Default: 0
-                </help>
-            </param>
             <param name="delta_mass_exclude_ranges_min" type="float" value="-1.5" label="Delta mass exclude range minimum" />
             <param name="delta_mass_exclude_ranges_max" type="float" value="3.5" label="Delta mass exclude range maximum" />
             <param name="localize_delta_mass" type="boolean" truevalue="true" falsevalue="false" checked="@LOCALIZE@"
@@ -798,9 +861,6 @@
         #if $prefix.open_search.zero_bin_mult_expect != ''
             #set $msfragger_dict['zero_bin_mult_expect'] = $prefix.open_search.zero_bin_mult_expect
         #end if
-        #if $prefix.open_search.add_topN_complementary != ''
-            #set $msfragger_dict['add_topN_complementary'] = $prefix.open_search.add_topN_complementary
-        #end if
         #set $msfragger_dict['localize_delta_mass'] = $prefix.open_search.localize_delta_mass
         #set $msfragger_dict['delta_mass_exclude_ranges'] = '(' + ','.join([str($prefix.open_search.delta_mass_exclude_ranges_min),str($prefix.open_search.delta_mass_exclude_ranges_max)]) + ')'
 ]]></token>
@@ -938,7 +998,7 @@
     <!-- Formatting options for output files. -->
     <xml name="advanced_options">
         <section name="advanced_options" expanded="false" title="Advanced Options">
-            <param name="output_format" type="select" multiple="true" label="output format">
+            <param name="output_format" type="select" label="output format">
                 <option value="pepXML">PEPXML</option>
                 <option value="tsv">TSV</option>
                 <option value="tsv_pepXML">TSV_PEPXML</option>
@@ -955,7 +1015,6 @@
                 label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" />
 
             <param name="write_calibrated_mzml" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write calibrated mzML"/>
-            <param name="write_uncalibrated_mgf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write uncalibrated MGF"/>
             <param name="group_variable" type="select" optional="true" label="Group variable">
                 <option value="0">None</option>
                 <option value="1">Number of enzymatic termini</option>
@@ -966,16 +1025,14 @@
 
     <!-- Does not enter into msfragger_dict, instead produces configuration text. -->
     <token name="@MSFRAGGER_ADVANCED_OPTIONS@"><![CDATA[
-        #set $msfragger_dict['output_format'] = $prefix.advanced_options.output_format.__str__.replace(',mgf','').replace(',','_')
-        #if $prefix.advanced_options.output_report_topN != ''
-            #set $msfragger_dict['output_report_topN'] = $prefix.advanced_options.output_report_topN
-        #end if
+        #set $msfragger_dict['output_format'] = $prefix.advanced_options.output_format
+        #set $msfragger_dict['output_report_topN'] = $prefix.advanced_options.output_report_topN
         #set $msfragger_dict['report_alternative_proteins'] = $prefix.advanced_options.report_alternative_proteins
+        #set $msfragger_dict['output_max_expect'] = $prefix.advanced_options.output_max_expect
         #if $prefix.advanced_options.output_max_expect != ''
             #set $msfragger_dict['output_max_expect'] = $prefix.advanced_options.output_max_expect
         #end if
         #set $msfragger_dict['write_calibrated_mzml'] = $prefix.advanced_options.write_calibrated_mzml
-        #set $msfragger_dict['write_uncalibrated_mgf'] = $prefix.advanced_options.write_uncalibrated_mgf
         #if $prefix.advanced_options.group_variable != 'None'
             #set $msfragger_dict['group_variable'] = $prefix.advanced_options.group_variable
         #end if
diff -r 59fec1e2a6c3 -r b4f6df8fa89b test-data/basic-search/outputs/workflow.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/basic-search/outputs/workflow.txt	Wed Oct 01 22:20:54 2025 +0000
@@ -0,0 +1,363 @@
+# Workflow: Basic-Search
+
+
+crystalc.run-crystalc=false
+database.db-path=final_db.fas
+database.decoy-tag=rev_
+diann.channel-normalization-strategy=0
+diann.cmd-opts=
+diann.generate-msstats=true
+diann.heavy=
+diann.library=
+diann.light=
+diann.medium=
+diann.min-site-prob=0.75
+diann.mod-tag=
+diann.q-value=0.01
+diann.quantification-strategy=3
+diann.quantification-strategy-2=2
+diann.run-dia-nn=false
+diann.run-dia-plex=false
+diann.run-specific-protein-q-value=false
+diann.unrelated-runs=false
+diann.use-predicted-spectra=false
+diatracer.corr-threshold=0.3
+diatracer.delta-apex-im=0.01
+diatracer.delta-apex-rt=3
+diatracer.mass-defect-filter=true
+diatracer.mass-defect-offset=0.1
+diatracer.rf-max=500
+diatracer.run-diatracer=false
+diatracer.write-intermediate-files=false
+diaumpire.AdjustFragIntensity=true
+diaumpire.BoostComplementaryIon=false
+diaumpire.CorrThreshold=0
+diaumpire.DeltaApex=0.2
+diaumpire.ExportPrecursorPeak=false
+diaumpire.Q1=true
+diaumpire.Q2=true
+diaumpire.Q3=true
+diaumpire.RFmax=500
+diaumpire.RPmax=25
+diaumpire.RTOverlap=0.3
+diaumpire.SE.EstimateBG=false
+diaumpire.SE.IsoPattern=0.3
+diaumpire.SE.MS1PPM=10
+diaumpire.SE.MS2PPM=20
+diaumpire.SE.MS2SN=1.1
+diaumpire.SE.MassDefectFilter=true
+diaumpire.SE.MassDefectOffset=0.1
+diaumpire.SE.NoMissedScan=1
+diaumpire.SE.SN=1.1
+diaumpire.run-diaumpire=false
+fpop.coadaptr.fpop.fpop_masses=
+fpop.coadaptr.fpop.run-fpop-coadaptr=false
+fpop.fragpipe.fpop.fpop-tmt=false
+fpop.fragpipe.fpop.label_control=
+fpop.fragpipe.fpop.label_fpop=
+fpop.fragpipe.fpop.region_size=1
+fpop.fragpipe.fpop.run-fpop=false
+fpop.fragpipe.fpop.subtract-control=false
+freequant.mz-tol=10
+freequant.rt-tol=0.4
+freequant.run-freequant=false
+ionquant.excludemods=
+ionquant.formula=
+ionquant.heavy=
+ionquant.imtol=0.05
+ionquant.ionfdr=0.01
+ionquant.light=
+ionquant.locprob=0.75
+ionquant.maxlfq=1
+ionquant.mbr=1
+ionquant.mbrimtol=0.05
+ionquant.mbrmincorr=0
+ionquant.mbrrttol=1
+ionquant.mbrtoprun=10
+ionquant.medium=
+ionquant.minfreq=0
+ionquant.minions=1
+ionquant.minisotopes=2
+ionquant.minscans=3
+ionquant.mztol=10
+ionquant.normalization=1
+ionquant.peptidefdr=1
+ionquant.proteinfdr=1
+ionquant.requantify=1
+ionquant.rttol=0.4
+ionquant.run-ionquant=true
+ionquant.tp=0
+ionquant.uniqueness=0
+ionquant.use-labeling=false
+ionquant.use-lfq=true
+ionquant.writeindex=0
+msbooster.find-best-im-model=false
+msbooster.find-best-rt-model=false
+msbooster.find-best-spectra-model=false
+msbooster.fragmentation-type=0
+msbooster.im-model=DIA-NN
+msbooster.koina-url=
+msbooster.predict-im=true
+msbooster.predict-rt=true
+msbooster.predict-spectra=true
+msbooster.rt-model=DIA-NN
+msbooster.run-msbooster=false
+msbooster.spectra-model=DIA-NN
+msbooster.spectral-library-path=
+msfragger.Y_type_masses=
+msfragger.activation_types=all
+msfragger.allowed_missed_cleavage_1=2
+msfragger.allowed_missed_cleavage_2=2
+msfragger.analyzer_types=all
+msfragger.calibrate_mass=2
+msfragger.check_spectral_files=true
+msfragger.clip_nTerm_M=true
+msfragger.deisotope=1
+msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
+msfragger.deneutralloss=1
+msfragger.diagnostic_fragments=
+msfragger.diagnostic_intensity_filter=0
+msfragger.digest_max_length=50
+msfragger.digest_min_length=7
+msfragger.fragment_ion_series=b,y
+msfragger.fragment_mass_tolerance=20
+msfragger.fragment_mass_units=1
+msfragger.group_variable=0
+msfragger.intensity_transform=0
+msfragger.ion_series_definitions=
+msfragger.isotope_error=0/1/2/3
+msfragger.labile_search_mode=off
+msfragger.localize_delta_mass=false
+msfragger.mass_diff_to_variable_mod=0
+msfragger.mass_offsets=0
+msfragger.mass_offsets_detailed=
+msfragger.max_fragment_charge=2
+msfragger.max_variable_mods_combinations=5000
+msfragger.max_variable_mods_per_peptide=3
+msfragger.min_fragments_modelling=2
+msfragger.min_matched_fragments=4
+msfragger.min_sequence_matches=2
+msfragger.minimum_peaks=15
+msfragger.minimum_ratio=0.01
+msfragger.misc.fragger.clear-mz-hi=0.0
+msfragger.misc.fragger.clear-mz-lo=0.0
+msfragger.misc.fragger.digest-mass-hi=5000.0
+msfragger.misc.fragger.digest-mass-lo=500.0
+msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
+msfragger.misc.fragger.enzyme-dropdown-2=null
+msfragger.misc.fragger.precursor-charge-hi=4
+msfragger.misc.fragger.precursor-charge-lo=1
+msfragger.misc.fragger.remove-precursor-range-hi=1.5
+msfragger.misc.fragger.remove-precursor-range-lo=-1.5
+msfragger.misc.slice-db=1
+msfragger.num_enzyme_termini=2
+msfragger.output_format=pepXML_pin
+msfragger.output_max_expect=50.0
+msfragger.output_report_topN=1
+msfragger.output_report_topN_dda_plus=5
+msfragger.output_report_topN_dia1=5
+msfragger.override_charge=false
+msfragger.precursor_mass_lower=-20
+msfragger.precursor_mass_mode=selected
+msfragger.precursor_mass_units=1
+msfragger.precursor_mass_upper=20
+msfragger.precursor_true_tolerance=20
+msfragger.precursor_true_units=1
+msfragger.remainder_fragment_masses=
+msfragger.remove_precursor_peak=1
+msfragger.report_alternative_proteins=true
+msfragger.require_precursor=true
+msfragger.restrict_deltamass_to=all
+msfragger.reuse_dia_fragment_peaks=false
+msfragger.run-msfragger=true
+msfragger.search_enzyme_cut_1=KR
+msfragger.search_enzyme_cut_2=
+msfragger.search_enzyme_name_1=stricttrypsin
+msfragger.search_enzyme_name_2=null
+msfragger.search_enzyme_nocut_1=
+msfragger.search_enzyme_nocut_2=
+msfragger.search_enzyme_sense_1=C
+msfragger.search_enzyme_sense_2=C
+msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
+msfragger.table.var-mods=15.99491461956,M,true,3; 42.0105646837,[^,true,1
+msfragger.track_zero_topN=0
+msfragger.use_all_mods_in_first_search=false
+msfragger.use_detailed_offsets=false
+msfragger.use_topN_peaks=150
+msfragger.write_calibrated_mzml=false
+msfragger.zero_bin_accept_expect=0
+msfragger.zero_bin_mult_expect=1
+opair.activation1=HCD
+opair.activation2=ETD
+opair.allowed_sites=
+opair.filterOxonium=true
+opair.glyco_db=
+opair.max_glycans=4
+opair.max_isotope_error=2
+opair.min_isotope_error=0
+opair.ms1_tol=20
+opair.ms2_tol=20
+opair.oxonium_filtering_file=
+opair.oxonium_minimum_intensity=0.05
+opair.reverse_scan_order=false
+opair.run-opair=false
+opair.single_scan_type=false
+peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
+peptide-prophet.combine-pepxml=false
+peptide-prophet.run-peptide-prophet=false
+percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
+percolator.keep-tsv-files=false
+percolator.min-prob=0.5
+percolator.run-percolator=true
+phi-report.dont-use-prot-proph-file=false
+phi-report.filter=--sequential --picked --prot 0.01
+phi-report.pep-level-summary=false
+phi-report.print-decoys=false
+phi-report.prot-level-summary=true
+phi-report.remove-contaminants=false
+phi-report.run-report=true
+protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.05
+protein-prophet.run-protein-prophet=true
+ptmprophet.cmdline=NOSTACK KEEPOLD STATIC FRAGPPMTOL\=10 EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
+ptmprophet.override-defaults=false
+ptmprophet.run-ptmprophet=false
+ptmshepherd.adv_params=false
+ptmshepherd.annotation-common=false
+ptmshepherd.annotation-custom=false
+ptmshepherd.annotation-glyco=false
+ptmshepherd.annotation-unimod=true
+ptmshepherd.annotation_file=
+ptmshepherd.annotation_tol=0.01
+ptmshepherd.cap_y_ions=
+ptmshepherd.decoy_type=1
+ptmshepherd.diag_ions=
+ptmshepherd.diagmine_diagMinFoldChange=3.0
+ptmshepherd.diagmine_diagMinSpecDiff=00.2
+ptmshepherd.diagmine_fragMinFoldChange=3.0
+ptmshepherd.diagmine_fragMinPropensity=00.1
+ptmshepherd.diagmine_fragMinSpecDiff=00.1
+ptmshepherd.diagmine_minIonsPerSpec=2
+ptmshepherd.diagmine_minPeps=25
+ptmshepherd.diagmine_pepMinFoldChange=3.0
+ptmshepherd.diagmine_pepMinSpecDiff=00.2
+ptmshepherd.glyco_fdr=1.00
+ptmshepherd.glyco_isotope_max=3
+ptmshepherd.glyco_isotope_min=-1
+ptmshepherd.glyco_ppm_tol=50
+ptmshepherd.glycodatabase=
+ptmshepherd.histo_smoothbins=2
+ptmshepherd.iontype_a=false
+ptmshepherd.iontype_b=true
+ptmshepherd.iontype_c=true
+ptmshepherd.iontype_x=false
+ptmshepherd.iontype_y=true
+ptmshepherd.iontype_z=true
+ptmshepherd.iterloc_maxEpoch=100
+ptmshepherd.iterloc_mode=false
+ptmshepherd.localization_allowed_res=
+ptmshepherd.n_glyco=true
+ptmshepherd.normalization-psms=true
+ptmshepherd.normalization-scans=false
+ptmshepherd.output_extended=false
+ptmshepherd.peakpicking_mass_units=0
+ptmshepherd.peakpicking_minPsm=10
+ptmshepherd.peakpicking_promRatio=0.3
+ptmshepherd.peakpicking_width=0.002
+ptmshepherd.precursor_mass_units=0
+ptmshepherd.precursor_tol=0.01
+ptmshepherd.print_decoys=false
+ptmshepherd.print_full_glyco_params=false
+ptmshepherd.prob_mass=0.5
+ptmshepherd.remainder_masses=
+ptmshepherd.remove_glycan_delta_mass=true
+ptmshepherd.run-shepherd=false
+ptmshepherd.run_diagextract_mode=false
+ptmshepherd.run_diagmine_mode=false
+ptmshepherd.run_glyco_mode=false
+ptmshepherd.spectra_condPeaks=150
+ptmshepherd.spectra_condRatio=0.0001
+ptmshepherd.spectra_maxPrecursorCharge=4
+ptmshepherd.spectra_maxfragcharge=2
+ptmshepherd.spectra_ppmtol=20
+ptmshepherd.varmod_masses=
+quantitation.run-label-free-quant=false
+run-psm-validation=true
+run-validation-tab=true
+saintexpress.cmd-opts=
+saintexpress.max-replicates=10
+saintexpress.run-saint-express=false
+saintexpress.virtual-controls=100
+skyline.run-skyline=false
+skyline.skyline=false
+skyline.skyline-custom=false
+skyline.skyline-custom-path=
+skyline.skyline-daily=true
+skyline.skyline-fragment-tolerance=10
+skyline.skyline-mods-mode=Default
+skyline.skyline-precursor-tolerance=10
+skyline.use-ssl=false
+speclibgen.convert-pepxml=true
+speclibgen.convert-psm=false
+speclibgen.easypqp.extras.max_delta_ppm=15
+speclibgen.easypqp.extras.max_delta_unimod=0.02
+speclibgen.easypqp.extras.max_glycan_qval=1
+speclibgen.easypqp.extras.rt_lowess_fraction=0
+speclibgen.easypqp.fragment.a=false
+speclibgen.easypqp.fragment.b=true
+speclibgen.easypqp.fragment.c=false
+speclibgen.easypqp.fragment.x=false
+speclibgen.easypqp.fragment.y=true
+speclibgen.easypqp.fragment.z=false
+speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
+speclibgen.easypqp.labile_mode=Regular (not glyco)
+speclibgen.easypqp.neutral_loss=false
+speclibgen.easypqp.rt-cal=ciRT
+speclibgen.easypqp.select-file.text=
+speclibgen.easypqp.select-im-file.text=
+speclibgen.keep-intermediate-files=false
+speclibgen.run-speclibgen=false
+tab-run.delete_calibrated_mzml=false
+tab-run.delete_temp_files=false
+tab-run.export_matched_fragments=false
+tab-run.sub_mzml_prob_threshold=0.5
+tab-run.write_sub_mzml=false
+tmtintegrator.add_Ref=-1
+tmtintegrator.aggregation_method=0
+tmtintegrator.allow_overlabel=true
+tmtintegrator.allow_unlabeled=true
+tmtintegrator.best_psm=true
+tmtintegrator.channel_num=TMT-6
+tmtintegrator.extraction_tool=IonQuant
+tmtintegrator.glyco_qval=-1
+tmtintegrator.groupby=-1
+tmtintegrator.log2transformed=true
+tmtintegrator.max_pep_prob_thres=0
+tmtintegrator.min_ntt=0
+tmtintegrator.min_pep_prob=0.9
+tmtintegrator.min_percent=0.05
+tmtintegrator.min_purity=0.5
+tmtintegrator.min_resolution=0
+tmtintegrator.min_site_prob=-1
+tmtintegrator.min_snr=0
+tmtintegrator.mod_tag=none
+tmtintegrator.ms1_int=true
+tmtintegrator.outlier_removal=true
+tmtintegrator.philosopher-msstats=false
+tmtintegrator.print_RefInt=false
+tmtintegrator.prot_exclude=none
+tmtintegrator.prot_norm=0
+tmtintegrator.psm_norm=false
+tmtintegrator.quant_level=2
+tmtintegrator.ref_d_tag=Pool
+tmtintegrator.ref_tag=Bridge
+tmtintegrator.run-tmtintegrator=false
+tmtintegrator.tolerance=20
+tmtintegrator.top3_pep=true
+tmtintegrator.unique_gene=0
+tmtintegrator.unique_pep=false
+tmtintegrator.use_glycan_composition=false
+workflow.input.data-type.im-ms=false
+workflow.input.data-type.regular-ms=true
+workflow.misc.save-sdrf=true
+workflow.misc.sdrf-type=Default
+workflow.saved-with-ver=23.0-build14
diff -r 59fec1e2a6c3 -r b4f6df8fa89b test-data/basic-search/test.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/basic-search/test.fasta	Wed Oct 01 22:20:54 2025 +0000
@@ -0,0 +1,72 @@
+>generic|U00096.3_prot_AAC76339.1_3292|30SribosomalsubunitproteinS3-Ecoli_MG1655
+MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
+AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
+TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
+DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK
+>generic|OFI31430.1|phosphateacetyltransferase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079]
+MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIVRAN
+STLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQS
+LNYEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDE
+QGRTRPDLSEIFDDSSKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNA
+TIINEGDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIG
+ALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKV
+QEYVANYVNAEWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGDEPRTVKAA
+AICAERGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKGM
+TEPVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF
+FMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGSD
+VEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGN
+TTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQQQQ
+>generic|OFI30005.1|serinehydroxymethyltransferase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079]
+MLKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYP
+GKRYYGGCEYVDVVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLQPGDTVLGMN
+LAQGGHLTHGSPVNFSGKLYNIVPYGIDESGKIDYDEMAKLAKEHKPKMIIGGFSAYSGV
+VDWAKMREIADSIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLIL
+AKGGDEELYKKLNSAVFPSAQGGPLMHVIAGKAVALKEAMEPEFKVYQQQVAKNAKAMVE
+VFLNRGYKVVSGGTENHLFLLDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTS
+GIRIGSPAVTRRGFKEAEVKELAGWMCDVLDNINDEATIERVKAKVLDICARFPVYA
+>generic|OFI28972.1|translationelongationfactorTu,partial[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079]
+MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARG
+ITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI
+LLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE
+GDAEWEAKIIELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVG
+EEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIK
+PHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV
+VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVL
+>generic|OFI28767.1|chitinase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079]
+MATSKLIQGDTITETTHAANGFDPATSDDKISYTSARVAKPVYNKYKNSTTKPKVFGYYT
+DWSQYDSRLQGNMSQPGRGYDLTKVSPTAYDKLIFGFVGITGFRKIDTEDRDVVAEAAAL
+CGKVKYEPTFLDPWGDFQSYINLGFDVSGWDVDPKTVTQSNAKGLLGALRDMQAKAKAAG
+HTLALSMSIGGWSMSNGFHETAASDSSRKIFAKGVVKLFKQFPMFSEVDIDWEYPNNEGA
+GNPFGPEDGANYALLIAELRKQLDSAGLSNVKISIAASAVTTIFDYAKVKDLMAAGLYGI
+NLMTYDFFGTPWAETLGHHTNRKALEEGGWAVETIVDHLLAEGFSADRINIGYAGYTRNA
+RQVEIESLSPLKGSYNPGSGPTTGSFESGTSEWYDVIYSYLDLENQKGRNGFNVYTDQVA
+DADYLYSPESKLFLSLDTPRTVKAKGEYAAKLGLGGVFTWTIDQDNGVLVNAVREGLGYE
+IESEVIDMEPFYFEGINVEKDEEQSDSDDAQKVNHAPKAAIELMVVGGSTVQLSGAGSSD
+EDNDELSFSWGVPSQIDVADKTAEIIEVVVPEVSEKTAFQFTLFVRDCYNEPSSQQRFVL
+TAVPALSQVQPEPEEEEEIIVPVPDEEEDTTPAEDDTPADDKTSPYAQWDASTVYGANWG
+SFEIVSWKGHNYQVKWWSMGNQPDLNCGVGGAWTDLGAY
+>generic|OFI28186.1|50SribosomalproteinL3[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079]
+MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAVQVTTGAKKANRV
+TKPEAGHFAKAGVEAGRGLWEFRLAEGEEYTVGQSISVELFADVKKVDVTGTSKGKGFAG
+TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
+DAERNLLLVKGGVPGATGCDLIVKPAVKA
+>generic|AL009126.3_prot_CAB11777.1_1|chromosomalreplicationinitiatorinformationalATPase-BSU
+MENILDLWNQALAQIEKKLSKPSFETWMKSTKAHSLQGDTLTITAPNEFARDWLESRYLHLIADTIYELTGEELSIKFVIPQNQDVEDFMPKPQVKKAVKEDTSDFPQNMLNPKYTFDTFVIGSGNRFAHAASLAVAEAPAKAYNPLFIYGGVGLGKTHLMHAIGHYVIDHNPSAKVVYLSSEKFTNEFINSIRDNKAVDFRNRYRNVDVLLIDDIQFLAGKEQTQEEFFHTFNTLHEESKQIVISSDRPPKEIPTLEDRLRSRFEWGLITDITPPDLETRIAILRKKAKAEGLDIPNEVMLYIANQIDSNIRELEGALIRVVAYSSLINKDINADLAAEALKDIIPSSKPKVITIKEIQRVVGQQFNIKLEDFKAKKRTKSVAFPRQIAMYLSREMTDSSLPKIGEEFGGRDHTTVIHAHEKISKLLADDEQLQQHVKEIKEQLK
+>generic|AL009126.3_prot_CAB11778.1_2|DNApolymeraseIII(betasubunit)-BSU
+MKFTIQKDRLVESVQDVLKAVSSRTTIPILTGIKIVASDDGVSFTGSDSDISIESFIPKEEGDKEIVTIEQPGSIVLQARFFSEIVKKLPMATVEIEVQNQYLTIIRSGKAEFNLNGLDADEYPHLPQIEEHHAIQIPTDLLKNLIRQTVFAVSTSETRPILTGVNWKVEQSELLCTATDSHRLALRKAKLDIPEDRSYNVVIPGKSLTELSKILDDNQELVDIVITETQVLFKAKNVLFFSRLLDGNYPDTTSLIPQDSKTEIIVNTKEFLQAIDRASLLAREGRNNVVKLSAKPAESIEISSNSPEIGKVVEAIVADQIEGEELNISFSPKYMLDALKVLEGAEIRVSFTGAMRPFLIRTPNDETIVQLILPVRTY
+>generic|AL009126.3_prot_CAB11779.1_3|RNAbindingproteininvolvedinribosomematuration-BSU
+MANPISIDTEMITLGQFLKLADVIQSGGMAKWFLSEHEVLVNDEPDNRRGRKLYVGDVVEIEGFGSFQVVN
+>generic|AL009126.3_prot_CAB11780.1_4|RecAfilament-DNAcomplexstabilisation,ssDNAanddsDNAbinding,ATPbinding-BSU
+MYIQNLELTSYRNYDHAELQFENKVNVIIGENAQGKTNLMEAIYVLSMAKSHRTSNDKELIRWDKDYAKIEGRVMKQNGAIPMQLVISKKGKKGKVNHIEQQKLSQYVGALNTIMFAPEDLNLVKGSPQVRRRFLDMEIGQVSPVYLHDLSLYQKILSQRNHFLKQLQTRKQTDRTMLDVLTDQLVEVAAKVVVKRLQFTAQLEKWAQPIHAGISRGLEELTLKYHTALDVSDPLDLSKIGDSYQEAFSKLREKEIERGVTLSGPHRDDVLFYVNGRDVQTYGSQGQQRTTALSLKLAEIDLIHEEIGEYPILLLDDVLSELDDYRQSHLLHTIQGRVQTFVTTTSVDGIDHETLRQAGMFRVQNGALVK
+>generic|AL009126.3_prot_CAB11781.2_5|regulatorofextracellularmatrixformation-BSU
+MYIHLGDDFVVSTRDIVGIFDFKANMSPIVEEFLKKQKHKVVPSVNGTPKSIVVTVQNIYYSPLSSSTLKKRAQFMFEIDS
+>generic|AL009126.3_prot_CAB11782.1_6|DNAgyrase(subunitB)-BSU
+MEQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDVTVHRDGKIHRQTYKRGVPVTDLEIIGETDHTGTTTHFVPDPEIFSETTEYDYDLLANRVRELAFLTKGVNITIEDKREGQERKNEYHYEGGIKSYVEYLNRSKEVVHEEPIYIEGEKDGITVEVALQYNDSYTSNIYSFTNNINTYEGGTHEAGFKTGLTRVINDYARKKGLIKENDPNLSGDDVREGLTAIISIKHPDPQFEGQTKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDKGLMAARARMAAKKARELTRRKSALEISNLPGKLADCSSKDPSISELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALGTGIGEDFNLEKARYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQPPLYKVQQGKRVEYAYNDKELEELLKTLPQTPKPGLQRYKGLGEMNATQLWETTMDPSSRTLLQVTLEDAMDADETFEMLMGDKVEPRRNFIEANARYVKNLDI
+>generic|AL009126.3_prot_CAB11783.1_7|DNAgyrase(subunitA)-BSU
+MSEQNTPQVREINISQEMRTSFLDYAMSVIVSRALPDVRDGLKPVHRRILYAMNDLGMTSDKPYKKSARIVGEVIGKYHPHGDSAVYESMVRMAQDFNYRYMLVDGHGNFGSVDGDSAAAMRYTEARMSKISMEILRDITKDTIDYQDNYDGSEREPVVMPSRFPNLLVNGAAGIAVGMATNIPPHQLGEIIDGVLAVSENPDITIPELMEVIPGPDFPTAGQILGRSGIRKAYESGRGSITIRAKAEIEQTSSGKERIIVTELPYQVNKAKLIEKIADLVRDKKIEGITDLRDESDRTGMRIVIEIRRDANANVILNNLYKQTALQTSFGINLLALVDGQPKVLTLKQCLEHYLDHQKVVIRRRTAYELRKAEARAHILEGLRVALDHLDAVISLIRNSQTAEIARTGLIEQFSLTEKQAQAILDMRLQRLTGLEREKIEEEYQSLVKLIAELKDILANEYKVLEIIREELTEIKERFNDERRTEIVTSGLETIEDEDLIERENIVVTLTHNGYVKRLPASTYRSQKRGGKGVQGMGTNEDDFVEHLISTSTHDTILFFSNKGKVYRAKGYEIPEYGRTAKGIPIINLLEVEKGEWINAIIPVTEFNAELYLFFTTKHGVSKRTSLSQFANIRNNGLIALSLREDDELMGVRLTDGTKQIIIGTKNGLLIRFPETDVREMGRTAAGVKGITLTDDDVVVGMEILEEESHVLIVTEKGYGKRTPAEEYRTQSRGGKGLKTAKITENNGQLVAVKATKGEEDLMIITASGVLIRMDINDISITGRVTQGVRLIRMAEEEHVATVALVEKNEEDENEEEQEEV
+>generic|AL009126.3_prot_CAB11784.1_8|conservedproteinofunknownfunction-BSU
+MTYHEWKDLALFYSVESTQKFLEKVYILNGINDAKKNSFKNSERFIYFLKHAESFYKQAAYSPLEIKPILLFYGMAQLIKACLITRDPHYPSHTSVLAHGVTTRKRKKQNYCFSDDEVKIQRNGLCVHFMKHLFGQSDIVDERYTMKKLLMAIPELSDIFYFQQKERFMTKVEKDKNEIFVPEEVVINYKMSDSRFAEYMSHHYQWSFTKKNEHGLLFEISPQDKEPWTSTSLLFDMEKNQYYIPSQREQFLRLPEMTIHYLILYNVGMIARYETEWWYELLTQHISDDYVLIQQFLLVSEKKFPKYASQFLLHF
+>generic|AL009126.3_prot_CAB11785.1_9|inosine-monophosphatedehydrogenase-BSU
+MWESKFSKEGLTFDDVLLVPAKSEVLPRDVDLSVELTKTLKLNIPVISAGMDTVTESAMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSERGVITNPFFLTPDHQVFDAEHLMGKYRISGVPIVNNEEDQKLVGIITNRDLRFISDYSMKISDVMTKEELVTASVGTTLDEAEKILQKHKIEKLPLVDDQNKLKGLITIKDIEKVIEFPNSSKDIHGRLIVGAAVGVTGDTMTRVKKLVEANVDVIVIDTAHGHSQGVLNTVTKIRETYPELNIIAGNVATAEATRALIEAGADVVKVGIGPGSICTTRVVAGVGVPQITAIYDCATEARKHGKTIIADGGIKFSGDITKALAAGGHAVMLGSLLAGTSESPGETEIYQGRRFKVYRGMGSVAAMEKGSKDRYFQEENKKFVPEGIEGRTPYKGPVEETVYQLVGGLRSGMGYCGSKDLRALREEAQFIRMTGAGLRESHPHDVQITKESPNYTIS
+>generic|AL009126.3_prot_CAB11786.1_10|D-alanyl-D-alaninecarboxypeptidase(penicillin-bindingprotein5)-BSU
+MNIKKCKQLLMSLVVLTLAVTCLAPMSKAKAASDPIDINASAAIMIEASSGKILYSKNADKRLPIASMTKMMTEYLLLEAIDQGKVKWDQTYTPDDYVYEISQDNSLSNVPLRKDGKYTVKELYQATAIYSANAAAIAIAEIVAGSETKFVEKMNAKAKELGLTDYKFVNATGLENKDLHGHQPEGTSVNEESEVSAKDMAVLADHLITDYPEILETSSIAKTKFREGTDDEMDMPNWNFMLKGLVSEYKKATVDGLKTGSTDSAGSCFTGTAERNGMRVITVVLNAKGNLHTGRFDETKKMFDYAFDNFSMKEIYAEGDQVKGHKTISVDKGKEKEVGIVTNKAFSLPVKNGEEKNYKAKVTLNKDNLTAPVKKGTKVGKLTAEYTGDEKDYGFLNSDLAGVDLVTKENVEKANWFVLTMRSIGGFFAGIWGSIVDTVTGWF
diff -r 59fec1e2a6c3 -r b4f6df8fa89b test-data/basic-search/test.manifest
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/basic-search/test.manifest	Wed Oct 01 22:20:54 2025 +0000
@@ -0,0 +1,2 @@
+test1.mzML	sample1		DDA
+test2.mzML	sample2		DDA
diff -r 59fec1e2a6c3 -r b4f6df8fa89b test-data/basic-search/test1.mzML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/basic-search/test1.mzML	Wed Oct 01 22:20:54 2025 +0000
@@ -0,0 +1,721 @@
+<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">
+  <mzML xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="191016JAT02_Mix_2_1ug" version="1.1.0">
+    <cvList count="2">
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.51" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" />
+      <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" />
+    </cvList>
+    <fileDescription>
+      <fileContent>
+        <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
+        <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value="" />
+      </fileContent>
+      <sourceFileList count="1">
+        <sourceFile id="RAW1" name="191016JAT02_Mix_2_1ug.raw" location="file:///">
+          <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value="" />
+          <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value="" />
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d76055ac4d0ddd1b1d9b09af4a790bd5fd25d109" />
+        </sourceFile>
+      </sourceFileList>
+    </fileDescription>
+    <referenceableParamGroupList count="1">
+      <referenceableParamGroup id="CommonInstrumentParams">
+        <cvParam cvRef="MS" accession="MS:1002732" name="Orbitrap Fusion Lumos" value="" />
+        <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="FSN20187" />
+      </referenceableParamGroup>
+    </referenceableParamGroupList>
+    <sampleList count="1">
+      <sample id="_x0031_" name="">
+        <cvParam cvRef="MS" accession="MS:1000002" name="sample name" value="1" />
+      </sample>
+    </sampleList>
+    <softwareList count="2">
+      <software id="Xcalibur" version="3.0.2041">
+        <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value="" />
+      </software>
+      <software id="pwiz" version="3.0.21258">
+        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value="" />
+      </software>
+    </softwareList>
+    <instrumentConfigurationList count="2">
+      <instrumentConfiguration id="IC1">
+        <referenceableParamGroupRef ref="CommonInstrumentParams" />
+        <componentList count="4">
+          <source order="1">
+            <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value="" />
+            <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value="" />
+          </source>
+          <analyzer order="2">
+            <cvParam cvRef="MS" accession="MS:1000081" name="quadrupole" value="" />
+          </analyzer>
+          <analyzer order="3">
+            <cvParam cvRef="MS" accession="MS:1000484" name="orbitrap" value="" />
+          </analyzer>
+          <detector order="4">
+            <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value="" />
+          </detector>
+        </componentList>
+        <softwareRef ref="Xcalibur" />
+      </instrumentConfiguration>
+      <instrumentConfiguration id="IC2">
+        <referenceableParamGroupRef ref="CommonInstrumentParams" />
+        <componentList count="4">
+          <source order="1">
+            <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value="" />
+            <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value="" />
+          </source>
+          <analyzer order="2">
+            <cvParam cvRef="MS" accession="MS:1000081" name="quadrupole" value="" />
+          </analyzer>
+          <analyzer order="3">
+            <cvParam cvRef="MS" accession="MS:1000083" name="radial ejection linear ion trap" value="" />
+          </analyzer>
+          <detector order="4">
+            <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value="" />
+          </detector>
+        </componentList>
+        <softwareRef ref="Xcalibur" />
+      </instrumentConfiguration>
+    </instrumentConfigurationList>
+    <dataProcessingList count="1">
+      <dataProcessing id="pwiz_Reader_Thermo_conversion">
+        <processingMethod order="0" softwareRef="pwiz">
+          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value="" />
+        </processingMethod>
+        <processingMethod order="1" softwareRef="pwiz">
+          <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value="" />
+          <userParam name="Thermo/Xcalibur peak picking" />
+        </processingMethod>
+      </dataProcessing>
+    </dataProcessingList>
+    <run id="_x0031_91016JAT02_Mix_2_1ug" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2019-10-16T22:35:54Z" defaultSourceFileRef="RAW1">
+      <spectrumList count="91592" defaultDataProcessingRef="pwiz_Reader_Thermo_conversion">
+        <spectrum index="822" id="controllerType=0 controllerNumber=1 scan=823" defaultArrayLength="624">
+          <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value="" />
+          <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
+          <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value="" />
+          <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />
+          <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="397.101043701172" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
+          <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="24557.994140625" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts" />
+          <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="1.327848919525e05" />
+          <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="101.147010803223" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
+          <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="803.531066894531" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
+          <scanList count="1">
+            <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />
+            <scan instrumentConfigurationRef="IC2">
+              <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="21.262366404017" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute" />
+              <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS + c NSI r d Full ms2 396.7281@hcd30.00 [100.0000-804.0000]" />
+              <cvParam cvRef="MS" accession="MS:1000927" name="ion injection time" value="100.0" unitCvRef="UO" unitAccession="UO:0000028" unitName="millisecond" />
+              <userParam name="[Thermo Trailer Extra]Monoisotopic M/Z:" value="396.72808837890625" type="xsd:float" />
+              <scanWindowList count="1">
+                <scanWindow>
+                  <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="100.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
+                  <cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="804.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
+                </scanWindow>
+              </scanWindowList>
+            </scan>
+          </scanList>
+          <precursorList count="1">
+            <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=820">
+              <isolationWindow>
+                <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="396.728088378906" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
+                <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="0.34999999404" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
+                <cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0.34999999404" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
+                <userParam name="ms level" value="1" />
+              </isolationWindow>
+              <selectedIonList count="1">
+                <selectedIon>
+                  <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="396.728088378906" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />
+                  <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2" />
+                  <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="1.305380339844e06" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts" />
+                </selectedIon>
+              </selectedIonList>
+              <activation>
+                <cvParam cvRef="MS" accession="MS:1000422" name="beam-type collision-induced dissociation" value="" />
+                <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="30.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt" />
+              </activation>
+            </precursor>
+          </precursorList>
+          <binaryDataArrayList count="2">
+            <binaryDataArray encodedLength="2996">
+              <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value="" />
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diff -r 59fec1e2a6c3 -r b4f6df8fa89b test-data/basic-search/test2.mzML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/basic-search/test2.mzML	Wed Oct 01 22:20:54 2025 +0000
@@ -0,0 +1,721 @@
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diff -r 59fec1e2a6c3 -r b4f6df8fa89b test-data/default/outputs/workflow.txt
--- a/test-data/default/outputs/workflow.txt	Sun Mar 30 23:00:45 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,308 +0,0 @@
-database.decoy-tag=rev_
-diann.fragpipe.cmd-opts=
-diann.heavy=
-diann.library=
-diann.light=
-diann.medium=
-diann.q-value=0.01
-diann.quantification-strategy=3
-diann.run-dia-nn=false
-diann.run-dia-plex=false
-diann.run-specific-protein-q-value=false
-diann.unrelated-runs=false
-diann.use-predicted-spectra=true
-diaumpire.AdjustFragIntensity=true
-diaumpire.BoostComplementaryIon=false
-diaumpire.CorrThreshold=0
-diaumpire.DeltaApex=0.2
-diaumpire.ExportPrecursorPeak=false
-diaumpire.Q1=true
-diaumpire.Q2=true
-diaumpire.Q3=true
-diaumpire.RFmax=500
-diaumpire.RPmax=25
-diaumpire.RTOverlap=0.3
-diaumpire.SE.EstimateBG=false
-diaumpire.SE.IsoPattern=0.3
-diaumpire.SE.MS1PPM=10
-diaumpire.SE.MS2PPM=20
-diaumpire.SE.MS2SN=1.1
-diaumpire.SE.MassDefectFilter=true
-diaumpire.SE.MassDefectOffset=0.1
-diaumpire.SE.NoMissedScan=1
-diaumpire.SE.SN=1.1
-diaumpire.run-diaumpire=false
-freequant.mz-tol=10
-freequant.rt-tol=0.4
-freequant.run-freequant=false
-ionquant.excludemods=
-ionquant.heavy=
-ionquant.imtol=0.05
-ionquant.ionfdr=0.01
-ionquant.light=
-ionquant.locprob=0.75
-ionquant.maxlfq=1
-ionquant.mbr=1
-ionquant.mbrimtol=0.05
-ionquant.mbrmincorr=0
-ionquant.mbrrttol=1
-ionquant.mbrtoprun=10
-ionquant.medium=
-ionquant.minfreq=0
-ionquant.minions=2
-ionquant.minisotopes=2
-ionquant.minscans=3
-ionquant.mztol=10
-ionquant.normalization=1
-ionquant.peptidefdr=1
-ionquant.proteinfdr=1
-ionquant.requantify=1
-ionquant.rttol=0.4
-ionquant.run-ionquant=true
-ionquant.tp=0
-ionquant.uniqueness=0
-ionquant.use-labeling=false
-ionquant.use-lfq=true
-ionquant.writeindex=0
-msbooster.predict-rt=true
-msbooster.predict-spectra=true
-msbooster.run-msbooster=false
-msbooster.use-correlated-features=false
-msfragger.Y_type_masses=
-msfragger.activation_types=all
-msfragger.add_topN_complementary=0
-msfragger.allowed_missed_cleavage_1=2
-msfragger.allowed_missed_cleavage_2=2
-msfragger.calibrate_mass=2
-msfragger.check_spectral_files=true
-msfragger.clip_nTerm_M=true
-msfragger.deisotope=1
-msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
-msfragger.deneutralloss=1
-msfragger.diagnostic_fragments=
-msfragger.diagnostic_intensity_filter=0
-msfragger.digest_max_length=50
-msfragger.digest_min_length=7
-msfragger.fragment_ion_series=b,y
-msfragger.fragment_mass_tolerance=20
-msfragger.fragment_mass_units=1
-msfragger.group_variable=0
-msfragger.intensity_transform=0
-msfragger.ion_series_definitions=
-msfragger.isotope_error=0/1/2/3
-msfragger.labile_search_mode=off
-msfragger.localize_delta_mass=false
-msfragger.mass_diff_to_variable_mod=0
-msfragger.mass_offsets=0
-msfragger.max_fragment_charge=2
-msfragger.max_variable_mods_combinations=5000
-msfragger.max_variable_mods_per_peptide=3
-msfragger.min_fragments_modelling=2
-msfragger.min_matched_fragments=4
-msfragger.min_sequence_matches=2
-msfragger.minimum_peaks=15
-msfragger.minimum_ratio=0.01
-msfragger.misc.fragger.clear-mz-hi=0.0
-msfragger.misc.fragger.clear-mz-lo=0.0
-msfragger.misc.fragger.digest-mass-hi=5000
-msfragger.misc.fragger.digest-mass-lo=500
-msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
-msfragger.misc.fragger.enzyme-dropdown-2=null
-msfragger.misc.fragger.precursor-charge-hi=4
-msfragger.misc.fragger.precursor-charge-lo=1
-msfragger.misc.fragger.remove-precursor-range-hi=1.5
-msfragger.misc.fragger.remove-precursor-range-lo=-1.5
-msfragger.misc.slice-db=1
-msfragger.num_enzyme_termini=2
-msfragger.output_format=pepXML_pin
-msfragger.output_max_expect=50.0
-msfragger.output_report_topN=1
-msfragger.output_report_topN_dia1=5
-msfragger.output_report_topN_dia2=3
-msfragger.override_charge=false
-msfragger.precursor_mass_lower=-20
-msfragger.precursor_mass_mode=selected
-msfragger.precursor_mass_units=1
-msfragger.precursor_mass_upper=20
-msfragger.precursor_true_tolerance=20
-msfragger.precursor_true_units=1
-msfragger.remainder_fragment_masses=
-msfragger.remove_precursor_peak=1
-msfragger.report_alternative_proteins=true
-msfragger.require_precursor=true
-msfragger.restrict_deltamass_to=all
-msfragger.reuse_dia_fragment_peaks=false
-msfragger.run-msfragger=true
-msfragger.search_enzyme_cut_1=KR
-msfragger.search_enzyme_cut_2=
-msfragger.search_enzyme_name_1=stricttrypsin
-msfragger.search_enzyme_name_2=null
-msfragger.search_enzyme_nocut_1=
-msfragger.search_enzyme_nocut_2=
-msfragger.search_enzyme_sense_1=C
-msfragger.search_enzyme_sense_2=C
-msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
-msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
-msfragger.track_zero_topN=0
-msfragger.use_all_mods_in_first_search=false
-msfragger.use_topN_peaks=150
-msfragger.write_calibrated_mzml=false
-msfragger.write_uncalibrated_mgf=false
-msfragger.zero_bin_accept_expect=0
-msfragger.zero_bin_mult_expect=1
-opair.activation1=HCD
-opair.activation2=ETD
-opair.filterOxonium=true
-opair.glyco_db=
-opair.max_glycans=4
-opair.max_isotope_error=2
-opair.min_isotope_error=0
-opair.ms1_tol=20
-opair.ms2_tol=20
-opair.oxonium_filtering_file=
-opair.oxonium_minimum_intensity=0.05
-opair.reverse_scan_order=false
-opair.run-opair=false
-opair.single_scan_type=false
-peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
-peptide-prophet.combine-pepxml=false
-peptide-prophet.run-peptide-prophet=false
-percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
-percolator.keep-tsv-files=false
-percolator.min-prob=0.5
-percolator.run-percolator=true
-phi-report.dont-use-prot-proph-file=false
-phi-report.filter=--sequential --picked --prot 0.01
-phi-report.pep-level-summary=false
-phi-report.philosoher-msstats=false
-phi-report.print-decoys=false
-phi-report.prot-level-summary=true
-phi-report.remove-contaminants=false
-phi-report.run-report=true
-protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.05
-protein-prophet.run-protein-prophet=true
-ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
-ptmprophet.run-ptmprophet=false
-ptmshepherd.adv_params=false
-ptmshepherd.annotation-common=false
-ptmshepherd.annotation-custom=false
-ptmshepherd.annotation-glyco=false
-ptmshepherd.annotation-unimod=true
-ptmshepherd.annotation_file=
-ptmshepherd.annotation_tol=0.01
-ptmshepherd.cap_y_ions=
-ptmshepherd.decoy_type=1
-ptmshepherd.diag_ions=
-ptmshepherd.diagextract_mode=false
-ptmshepherd.diagmine_diagMinFoldChange=3.0
-ptmshepherd.diagmine_diagMinSpecDiff=00.2
-ptmshepherd.diagmine_fragMinFoldChange=3.0
-ptmshepherd.diagmine_fragMinPropensity=00.1
-ptmshepherd.diagmine_fragMinSpecDiff=00.1
-ptmshepherd.diagmine_minIonsPerSpec=2
-ptmshepherd.diagmine_minPeps=25
-ptmshepherd.diagmine_mode=false
-ptmshepherd.diagmine_pepMinFoldChange=3.0
-ptmshepherd.diagmine_pepMinSpecDiff=00.2
-ptmshepherd.glyco_adducts=
-ptmshepherd.glyco_fdr=1.00
-ptmshepherd.glyco_isotope_max=3
-ptmshepherd.glyco_isotope_min=-1
-ptmshepherd.glyco_mode=false
-ptmshepherd.glyco_ppm_tol=50
-ptmshepherd.glycodatabase=
-ptmshepherd.histo_smoothbins=2
-ptmshepherd.iontype_a=false
-ptmshepherd.iontype_b=true
-ptmshepherd.iontype_c=true
-ptmshepherd.iontype_x=false
-ptmshepherd.iontype_y=true
-ptmshepherd.iontype_z=true
-ptmshepherd.localization_allowed_res=
-ptmshepherd.localization_background=4
-ptmshepherd.max_adducts=0
-ptmshepherd.n_glyco=true
-ptmshepherd.normalization-psms=true
-ptmshepherd.normalization-scans=false
-ptmshepherd.output_extended=false
-ptmshepherd.peakpicking_mass_units=0
-ptmshepherd.peakpicking_minPsm=10
-ptmshepherd.peakpicking_promRatio=0.3
-ptmshepherd.peakpicking_width=0.002
-ptmshepherd.precursor_mass_units=0
-ptmshepherd.precursor_tol=0.01
-ptmshepherd.print_decoys=false
-ptmshepherd.prob_dhexOx=2,0.5,0.1
-ptmshepherd.prob_dhexY=2,0.5
-ptmshepherd.prob_neuacOx=2,0.05,0.2
-ptmshepherd.prob_neugcOx=2,0.05,0.2
-ptmshepherd.prob_phosphoOx=2,0.05,0.2
-ptmshepherd.prob_regY=5,0.5
-ptmshepherd.prob_sulfoOx=2,0.05,0.2
-ptmshepherd.remainder_masses=
-ptmshepherd.remove_glycan_delta_mass=true
-ptmshepherd.run-shepherd=false
-ptmshepherd.spectra_maxfragcharge=2
-ptmshepherd.spectra_ppmtol=20
-ptmshepherd.varmod_masses=
-quantitation.run-label-free-quant=false
-run-psm-validation=true
-run-validation-tab=true
-saintexpress.fragpipe.cmd-opts=
-saintexpress.max-replicates=10
-saintexpress.run-saint-express=false
-saintexpress.virtual-controls=100
-speclibgen.easypqp.extras.max_delta_ppm=15
-speclibgen.easypqp.extras.max_delta_unimod=0.02
-speclibgen.easypqp.extras.rt_lowess_fraction=0
-speclibgen.easypqp.fragment.a=false
-speclibgen.easypqp.fragment.b=true
-speclibgen.easypqp.fragment.c=false
-speclibgen.easypqp.fragment.x=false
-speclibgen.easypqp.fragment.y=true
-speclibgen.easypqp.fragment.z=false
-speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
-speclibgen.easypqp.neutral_loss=false
-speclibgen.easypqp.rt-cal=ciRT
-speclibgen.easypqp.select-file.text=
-speclibgen.easypqp.select-im-file.text=
-speclibgen.keep-intermediate-files=false
-speclibgen.run-speclibgen=false
-tab-run.delete_calibrated_mzml=false
-tab-run.delete_temp_files=false
-tab-run.sub_mzml_prob_threshold=0.5
-tab-run.write_sub_mzml=false
-tmtintegrator.add_Ref=-1
-tmtintegrator.aggregation_method=0
-tmtintegrator.allow_overlabel=true
-tmtintegrator.allow_unlabeled=true
-tmtintegrator.best_psm=true
-tmtintegrator.channel_num=TMT-6
-tmtintegrator.dont-run-fq-lq=false
-tmtintegrator.glyco_qval=-1
-tmtintegrator.groupby=0
-tmtintegrator.log2transformed=true
-tmtintegrator.max_pep_prob_thres=0
-tmtintegrator.min_ntt=0
-tmtintegrator.min_pep_prob=0.9
-tmtintegrator.min_percent=0.05
-tmtintegrator.min_purity=0.5
-tmtintegrator.min_site_prob=-1
-tmtintegrator.mod_tag=none
-tmtintegrator.ms1_int=true
-tmtintegrator.outlier_removal=true
-tmtintegrator.print_RefInt=false
-tmtintegrator.prot_exclude=none
-tmtintegrator.prot_norm=0
-tmtintegrator.psm_norm=false
-tmtintegrator.quant_level=2
-tmtintegrator.ref_tag=Bridge
-tmtintegrator.run-tmtintegrator=false
-tmtintegrator.tolerance=20
-tmtintegrator.top3_pep=true
-tmtintegrator.unique_gene=0
-tmtintegrator.unique_pep=false
-tmtintegrator.use_glycan_composition=false
-workflow.input.data-type.im-ms=false
-workflow.input.data-type.regular-ms=true
-workflow.saved-with-ver=20.0-build5
diff -r 59fec1e2a6c3 -r b4f6df8fa89b test-data/default/outputs/workflow_msbooster_percolator.txt
--- a/test-data/default/outputs/workflow_msbooster_percolator.txt	Sun Mar 30 23:00:45 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,308 +0,0 @@
-database.decoy-tag=rev_
-diann.fragpipe.cmd-opts=
-diann.heavy=
-diann.library=
-diann.light=
-diann.medium=
-diann.q-value=0.01
-diann.quantification-strategy=3
-diann.run-dia-nn=false
-diann.run-dia-plex=false
-diann.run-specific-protein-q-value=false
-diann.unrelated-runs=false
-diann.use-predicted-spectra=true
-diaumpire.AdjustFragIntensity=true
-diaumpire.BoostComplementaryIon=false
-diaumpire.CorrThreshold=0
-diaumpire.DeltaApex=0.2
-diaumpire.ExportPrecursorPeak=false
-diaumpire.Q1=true
-diaumpire.Q2=true
-diaumpire.Q3=true
-diaumpire.RFmax=500
-diaumpire.RPmax=25
-diaumpire.RTOverlap=0.3
-diaumpire.SE.EstimateBG=false
-diaumpire.SE.IsoPattern=0.3
-diaumpire.SE.MS1PPM=10
-diaumpire.SE.MS2PPM=20
-diaumpire.SE.MS2SN=1.1
-diaumpire.SE.MassDefectFilter=true
-diaumpire.SE.MassDefectOffset=0.1
-diaumpire.SE.NoMissedScan=1
-diaumpire.SE.SN=1.1
-diaumpire.run-diaumpire=false
-freequant.mz-tol=10
-freequant.rt-tol=0.4
-freequant.run-freequant=false
-ionquant.excludemods=
-ionquant.heavy=
-ionquant.imtol=0.05
-ionquant.ionfdr=0.01
-ionquant.light=
-ionquant.locprob=0.75
-ionquant.maxlfq=1
-ionquant.mbr=1
-ionquant.mbrimtol=0.05
-ionquant.mbrmincorr=0
-ionquant.mbrrttol=1
-ionquant.mbrtoprun=10
-ionquant.medium=
-ionquant.minfreq=0
-ionquant.minions=2
-ionquant.minisotopes=2
-ionquant.minscans=3
-ionquant.mztol=10
-ionquant.normalization=1
-ionquant.peptidefdr=1
-ionquant.proteinfdr=1
-ionquant.requantify=1
-ionquant.rttol=0.4
-ionquant.run-ionquant=true
-ionquant.tp=0
-ionquant.uniqueness=0
-ionquant.use-labeling=false
-ionquant.use-lfq=true
-ionquant.writeindex=0
-msbooster.predict-rt=true
-msbooster.predict-spectra=true
-msbooster.run-msbooster=true
-msbooster.use-correlated-features=false
-msfragger.Y_type_masses=
-msfragger.activation_types=all
-msfragger.add_topN_complementary=0
-msfragger.allowed_missed_cleavage_1=2
-msfragger.allowed_missed_cleavage_2=2
-msfragger.calibrate_mass=2
-msfragger.check_spectral_files=true
-msfragger.clip_nTerm_M=true
-msfragger.deisotope=1
-msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
-msfragger.deneutralloss=1
-msfragger.diagnostic_fragments=
-msfragger.diagnostic_intensity_filter=0
-msfragger.digest_max_length=50
-msfragger.digest_min_length=7
-msfragger.fragment_ion_series=b,y
-msfragger.fragment_mass_tolerance=20
-msfragger.fragment_mass_units=1
-msfragger.group_variable=0
-msfragger.intensity_transform=0
-msfragger.ion_series_definitions=
-msfragger.isotope_error=0/1/2/3
-msfragger.labile_search_mode=off
-msfragger.localize_delta_mass=false
-msfragger.mass_diff_to_variable_mod=0
-msfragger.mass_offsets=0
-msfragger.max_fragment_charge=2
-msfragger.max_variable_mods_combinations=5000
-msfragger.max_variable_mods_per_peptide=3
-msfragger.min_fragments_modelling=2
-msfragger.min_matched_fragments=4
-msfragger.min_sequence_matches=2
-msfragger.minimum_peaks=15
-msfragger.minimum_ratio=0.01
-msfragger.misc.fragger.clear-mz-hi=0.0
-msfragger.misc.fragger.clear-mz-lo=0.0
-msfragger.misc.fragger.digest-mass-hi=5000
-msfragger.misc.fragger.digest-mass-lo=500
-msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
-msfragger.misc.fragger.enzyme-dropdown-2=null
-msfragger.misc.fragger.precursor-charge-hi=4
-msfragger.misc.fragger.precursor-charge-lo=1
-msfragger.misc.fragger.remove-precursor-range-hi=1.5
-msfragger.misc.fragger.remove-precursor-range-lo=-1.5
-msfragger.misc.slice-db=1
-msfragger.num_enzyme_termini=2
-msfragger.output_format=pepXML_pin
-msfragger.output_max_expect=50.0
-msfragger.output_report_topN=1
-msfragger.output_report_topN_dia1=5
-msfragger.output_report_topN_dia2=3
-msfragger.override_charge=false
-msfragger.precursor_mass_lower=-20
-msfragger.precursor_mass_mode=selected
-msfragger.precursor_mass_units=1
-msfragger.precursor_mass_upper=20
-msfragger.precursor_true_tolerance=20
-msfragger.precursor_true_units=1
-msfragger.remainder_fragment_masses=
-msfragger.remove_precursor_peak=1
-msfragger.report_alternative_proteins=true
-msfragger.require_precursor=true
-msfragger.restrict_deltamass_to=all
-msfragger.reuse_dia_fragment_peaks=false
-msfragger.run-msfragger=true
-msfragger.search_enzyme_cut_1=KR
-msfragger.search_enzyme_cut_2=
-msfragger.search_enzyme_name_1=stricttrypsin
-msfragger.search_enzyme_name_2=null
-msfragger.search_enzyme_nocut_1=
-msfragger.search_enzyme_nocut_2=
-msfragger.search_enzyme_sense_1=C
-msfragger.search_enzyme_sense_2=C
-msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
-msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
-msfragger.track_zero_topN=0
-msfragger.use_all_mods_in_first_search=false
-msfragger.use_topN_peaks=150
-msfragger.write_calibrated_mzml=false
-msfragger.write_uncalibrated_mgf=false
-msfragger.zero_bin_accept_expect=0
-msfragger.zero_bin_mult_expect=1
-opair.activation1=HCD
-opair.activation2=ETD
-opair.filterOxonium=true
-opair.glyco_db=
-opair.max_glycans=4
-opair.max_isotope_error=2
-opair.min_isotope_error=0
-opair.ms1_tol=20
-opair.ms2_tol=20
-opair.oxonium_filtering_file=
-opair.oxonium_minimum_intensity=0.05
-opair.reverse_scan_order=false
-opair.run-opair=false
-opair.single_scan_type=false
-peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
-peptide-prophet.combine-pepxml=false
-peptide-prophet.run-peptide-prophet=false
-percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
-percolator.keep-tsv-files=false
-percolator.min-prob=0.5
-percolator.run-percolator=true
-phi-report.dont-use-prot-proph-file=false
-phi-report.filter=--sequential --picked --prot 0.01
-phi-report.pep-level-summary=false
-phi-report.philosoher-msstats=false
-phi-report.print-decoys=false
-phi-report.prot-level-summary=true
-phi-report.remove-contaminants=false
-phi-report.run-report=true
-protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.05
-protein-prophet.run-protein-prophet=true
-ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
-ptmprophet.run-ptmprophet=false
-ptmshepherd.adv_params=false
-ptmshepherd.annotation-common=false
-ptmshepherd.annotation-custom=false
-ptmshepherd.annotation-glyco=false
-ptmshepherd.annotation-unimod=true
-ptmshepherd.annotation_file=
-ptmshepherd.annotation_tol=0.01
-ptmshepherd.cap_y_ions=
-ptmshepherd.decoy_type=1
-ptmshepherd.diag_ions=
-ptmshepherd.diagextract_mode=false
-ptmshepherd.diagmine_diagMinFoldChange=3.0
-ptmshepherd.diagmine_diagMinSpecDiff=00.2
-ptmshepherd.diagmine_fragMinFoldChange=3.0
-ptmshepherd.diagmine_fragMinPropensity=00.1
-ptmshepherd.diagmine_fragMinSpecDiff=00.1
-ptmshepherd.diagmine_minIonsPerSpec=2
-ptmshepherd.diagmine_minPeps=25
-ptmshepherd.diagmine_mode=false
-ptmshepherd.diagmine_pepMinFoldChange=3.0
-ptmshepherd.diagmine_pepMinSpecDiff=00.2
-ptmshepherd.glyco_adducts=
-ptmshepherd.glyco_fdr=1.00
-ptmshepherd.glyco_isotope_max=3
-ptmshepherd.glyco_isotope_min=-1
-ptmshepherd.glyco_mode=false
-ptmshepherd.glyco_ppm_tol=50
-ptmshepherd.glycodatabase=
-ptmshepherd.histo_smoothbins=2
-ptmshepherd.iontype_a=false
-ptmshepherd.iontype_b=true
-ptmshepherd.iontype_c=true
-ptmshepherd.iontype_x=false
-ptmshepherd.iontype_y=true
-ptmshepherd.iontype_z=true
-ptmshepherd.localization_allowed_res=
-ptmshepherd.localization_background=4
-ptmshepherd.max_adducts=0
-ptmshepherd.n_glyco=true
-ptmshepherd.normalization-psms=true
-ptmshepherd.normalization-scans=false
-ptmshepherd.output_extended=false
-ptmshepherd.peakpicking_mass_units=0
-ptmshepherd.peakpicking_minPsm=10
-ptmshepherd.peakpicking_promRatio=0.3
-ptmshepherd.peakpicking_width=0.002
-ptmshepherd.precursor_mass_units=0
-ptmshepherd.precursor_tol=0.01
-ptmshepherd.print_decoys=false
-ptmshepherd.prob_dhexOx=2,0.5,0.1
-ptmshepherd.prob_dhexY=2,0.5
-ptmshepherd.prob_neuacOx=2,0.05,0.2
-ptmshepherd.prob_neugcOx=2,0.05,0.2
-ptmshepherd.prob_phosphoOx=2,0.05,0.2
-ptmshepherd.prob_regY=5,0.5
-ptmshepherd.prob_sulfoOx=2,0.05,0.2
-ptmshepherd.remainder_masses=
-ptmshepherd.remove_glycan_delta_mass=true
-ptmshepherd.run-shepherd=false
-ptmshepherd.spectra_maxfragcharge=2
-ptmshepherd.spectra_ppmtol=20
-ptmshepherd.varmod_masses=
-quantitation.run-label-free-quant=false
-run-psm-validation=true
-run-validation-tab=true
-saintexpress.fragpipe.cmd-opts=
-saintexpress.max-replicates=10
-saintexpress.run-saint-express=false
-saintexpress.virtual-controls=100
-speclibgen.easypqp.extras.max_delta_ppm=15
-speclibgen.easypqp.extras.max_delta_unimod=0.02
-speclibgen.easypqp.extras.rt_lowess_fraction=0
-speclibgen.easypqp.fragment.a=false
-speclibgen.easypqp.fragment.b=true
-speclibgen.easypqp.fragment.c=false
-speclibgen.easypqp.fragment.x=false
-speclibgen.easypqp.fragment.y=true
-speclibgen.easypqp.fragment.z=false
-speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
-speclibgen.easypqp.neutral_loss=false
-speclibgen.easypqp.rt-cal=ciRT
-speclibgen.easypqp.select-file.text=
-speclibgen.easypqp.select-im-file.text=
-speclibgen.keep-intermediate-files=false
-speclibgen.run-speclibgen=false
-tab-run.delete_calibrated_mzml=false
-tab-run.delete_temp_files=false
-tab-run.sub_mzml_prob_threshold=0.5
-tab-run.write_sub_mzml=false
-tmtintegrator.add_Ref=-1
-tmtintegrator.aggregation_method=0
-tmtintegrator.allow_overlabel=true
-tmtintegrator.allow_unlabeled=true
-tmtintegrator.best_psm=true
-tmtintegrator.channel_num=TMT-6
-tmtintegrator.dont-run-fq-lq=false
-tmtintegrator.glyco_qval=-1
-tmtintegrator.groupby=0
-tmtintegrator.log2transformed=true
-tmtintegrator.max_pep_prob_thres=0
-tmtintegrator.min_ntt=0
-tmtintegrator.min_pep_prob=0.9
-tmtintegrator.min_percent=0.05
-tmtintegrator.min_purity=0.5
-tmtintegrator.min_site_prob=-1
-tmtintegrator.mod_tag=none
-tmtintegrator.ms1_int=true
-tmtintegrator.outlier_removal=true
-tmtintegrator.print_RefInt=false
-tmtintegrator.prot_exclude=none
-tmtintegrator.prot_norm=0
-tmtintegrator.psm_norm=false
-tmtintegrator.quant_level=2
-tmtintegrator.ref_tag=Bridge
-tmtintegrator.run-tmtintegrator=false
-tmtintegrator.tolerance=20
-tmtintegrator.top3_pep=true
-tmtintegrator.unique_gene=0
-tmtintegrator.unique_pep=false
-tmtintegrator.use_glycan_composition=false
-workflow.input.data-type.im-ms=false
-workflow.input.data-type.regular-ms=true
-workflow.saved-with-ver=20.0-build5
diff -r 59fec1e2a6c3 -r b4f6df8fa89b test-data/default/test.fasta
--- a/test-data/default/test.fasta	Sun Mar 30 23:00:45 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
->generic|U00096.3_prot_AAC76339.1_3292|30SribosomalsubunitproteinS3-Ecoli_MG1655
-MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
-AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
-TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
-DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK
->generic|OFI31430.1|phosphateacetyltransferase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079]
-MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIVRAN
-STLPAAEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQS
-LNYEIAKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDE
-QGRTRPDLSEIFDDSSKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNA
-TIINEGDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIG
-ALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKV
-QEYVANYVNAEWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGDEPRTVKAA
-AICAERGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKGM
-TEPVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVF
-FMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGSD
-VEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGN
-TTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQQQQ
->generic|OFI30005.1|serinehydroxymethyltransferase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079]
-MLKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYP
-GKRYYGGCEYVDVVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLQPGDTVLGMN
-LAQGGHLTHGSPVNFSGKLYNIVPYGIDESGKIDYDEMAKLAKEHKPKMIIGGFSAYSGV
-VDWAKMREIADSIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLIL
-AKGGDEELYKKLNSAVFPSAQGGPLMHVIAGKAVALKEAMEPEFKVYQQQVAKNAKAMVE
-VFLNRGYKVVSGGTENHLFLLDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTS
-GIRIGSPAVTRRGFKEAEVKELAGWMCDVLDNINDEATIERVKAKVLDICARFPVYA
->generic|OFI28972.1|translationelongationfactorTu,partial[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079]
-MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARG
-ITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI
-LLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE
-GDAEWEAKIIELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVG
-EEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIK
-PHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV
-VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVL
->generic|OFI28767.1|chitinase[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079]
-MATSKLIQGDTITETTHAANGFDPATSDDKISYTSARVAKPVYNKYKNSTTKPKVFGYYT
-DWSQYDSRLQGNMSQPGRGYDLTKVSPTAYDKLIFGFVGITGFRKIDTEDRDVVAEAAAL
-CGKVKYEPTFLDPWGDFQSYINLGFDVSGWDVDPKTVTQSNAKGLLGALRDMQAKAKAAG
-HTLALSMSIGGWSMSNGFHETAASDSSRKIFAKGVVKLFKQFPMFSEVDIDWEYPNNEGA
-GNPFGPEDGANYALLIAELRKQLDSAGLSNVKISIAASAVTTIFDYAKVKDLMAAGLYGI
-NLMTYDFFGTPWAETLGHHTNRKALEEGGWAVETIVDHLLAEGFSADRINIGYAGYTRNA
-RQVEIESLSPLKGSYNPGSGPTTGSFESGTSEWYDVIYSYLDLENQKGRNGFNVYTDQVA
-DADYLYSPESKLFLSLDTPRTVKAKGEYAAKLGLGGVFTWTIDQDNGVLVNAVREGLGYE
-IESEVIDMEPFYFEGINVEKDEEQSDSDDAQKVNHAPKAAIELMVVGGSTVQLSGAGSSD
-EDNDELSFSWGVPSQIDVADKTAEIIEVVVPEVSEKTAFQFTLFVRDCYNEPSSQQRFVL
-TAVPALSQVQPEPEEEEEIIVPVPDEEEDTTPAEDDTPADDKTSPYAQWDASTVYGANWG
-SFEIVSWKGHNYQVKWWSMGNQPDLNCGVGGAWTDLGAY
->generic|OFI28186.1|50SribosomalproteinL3[Salmonellaentericasubsp.entericaserovarTyphimuriumstr.TT9079]
-MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAVQVTTGAKKANRV
-TKPEAGHFAKAGVEAGRGLWEFRLAEGEEYTVGQSISVELFADVKKVDVTGTSKGKGFAG
-TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
-DAERNLLLVKGGVPGATGCDLIVKPAVKA
->generic|AL009126.3_prot_CAB11777.1_1|chromosomalreplicationinitiatorinformationalATPase-BSU
-MENILDLWNQALAQIEKKLSKPSFETWMKSTKAHSLQGDTLTITAPNEFARDWLESRYLHLIADTIYELTGEELSIKFVIPQNQDVEDFMPKPQVKKAVKEDTSDFPQNMLNPKYTFDTFVIGSGNRFAHAASLAVAEAPAKAYNPLFIYGGVGLGKTHLMHAIGHYVIDHNPSAKVVYLSSEKFTNEFINSIRDNKAVDFRNRYRNVDVLLIDDIQFLAGKEQTQEEFFHTFNTLHEESKQIVISSDRPPKEIPTLEDRLRSRFEWGLITDITPPDLETRIAILRKKAKAEGLDIPNEVMLYIANQIDSNIRELEGALIRVVAYSSLINKDINADLAAEALKDIIPSSKPKVITIKEIQRVVGQQFNIKLEDFKAKKRTKSVAFPRQIAMYLSREMTDSSLPKIGEEFGGRDHTTVIHAHEKISKLLADDEQLQQHVKEIKEQLK
->generic|AL009126.3_prot_CAB11778.1_2|DNApolymeraseIII(betasubunit)-BSU
-MKFTIQKDRLVESVQDVLKAVSSRTTIPILTGIKIVASDDGVSFTGSDSDISIESFIPKEEGDKEIVTIEQPGSIVLQARFFSEIVKKLPMATVEIEVQNQYLTIIRSGKAEFNLNGLDADEYPHLPQIEEHHAIQIPTDLLKNLIRQTVFAVSTSETRPILTGVNWKVEQSELLCTATDSHRLALRKAKLDIPEDRSYNVVIPGKSLTELSKILDDNQELVDIVITETQVLFKAKNVLFFSRLLDGNYPDTTSLIPQDSKTEIIVNTKEFLQAIDRASLLAREGRNNVVKLSAKPAESIEISSNSPEIGKVVEAIVADQIEGEELNISFSPKYMLDALKVLEGAEIRVSFTGAMRPFLIRTPNDETIVQLILPVRTY
->generic|AL009126.3_prot_CAB11779.1_3|RNAbindingproteininvolvedinribosomematuration-BSU
-MANPISIDTEMITLGQFLKLADVIQSGGMAKWFLSEHEVLVNDEPDNRRGRKLYVGDVVEIEGFGSFQVVN
->generic|AL009126.3_prot_CAB11780.1_4|RecAfilament-DNAcomplexstabilisation,ssDNAanddsDNAbinding,ATPbinding-BSU
-MYIQNLELTSYRNYDHAELQFENKVNVIIGENAQGKTNLMEAIYVLSMAKSHRTSNDKELIRWDKDYAKIEGRVMKQNGAIPMQLVISKKGKKGKVNHIEQQKLSQYVGALNTIMFAPEDLNLVKGSPQVRRRFLDMEIGQVSPVYLHDLSLYQKILSQRNHFLKQLQTRKQTDRTMLDVLTDQLVEVAAKVVVKRLQFTAQLEKWAQPIHAGISRGLEELTLKYHTALDVSDPLDLSKIGDSYQEAFSKLREKEIERGVTLSGPHRDDVLFYVNGRDVQTYGSQGQQRTTALSLKLAEIDLIHEEIGEYPILLLDDVLSELDDYRQSHLLHTIQGRVQTFVTTTSVDGIDHETLRQAGMFRVQNGALVK
->generic|AL009126.3_prot_CAB11781.2_5|regulatorofextracellularmatrixformation-BSU
-MYIHLGDDFVVSTRDIVGIFDFKANMSPIVEEFLKKQKHKVVPSVNGTPKSIVVTVQNIYYSPLSSSTLKKRAQFMFEIDS
->generic|AL009126.3_prot_CAB11782.1_6|DNAgyrase(subunitB)-BSU
-MEQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDVTVHRDGKIHRQTYKRGVPVTDLEIIGETDHTGTTTHFVPDPEIFSETTEYDYDLLANRVRELAFLTKGVNITIEDKREGQERKNEYHYEGGIKSYVEYLNRSKEVVHEEPIYIEGEKDGITVEVALQYNDSYTSNIYSFTNNINTYEGGTHEAGFKTGLTRVINDYARKKGLIKENDPNLSGDDVREGLTAIISIKHPDPQFEGQTKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDKGLMAARARMAAKKARELTRRKSALEISNLPGKLADCSSKDPSISELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALGTGIGEDFNLEKARYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQPPLYKVQQGKRVEYAYNDKELEELLKTLPQTPKPGLQRYKGLGEMNATQLWETTMDPSSRTLLQVTLEDAMDADETFEMLMGDKVEPRRNFIEANARYVKNLDI
->generic|AL009126.3_prot_CAB11783.1_7|DNAgyrase(subunitA)-BSU
-MSEQNTPQVREINISQEMRTSFLDYAMSVIVSRALPDVRDGLKPVHRRILYAMNDLGMTSDKPYKKSARIVGEVIGKYHPHGDSAVYESMVRMAQDFNYRYMLVDGHGNFGSVDGDSAAAMRYTEARMSKISMEILRDITKDTIDYQDNYDGSEREPVVMPSRFPNLLVNGAAGIAVGMATNIPPHQLGEIIDGVLAVSENPDITIPELMEVIPGPDFPTAGQILGRSGIRKAYESGRGSITIRAKAEIEQTSSGKERIIVTELPYQVNKAKLIEKIADLVRDKKIEGITDLRDESDRTGMRIVIEIRRDANANVILNNLYKQTALQTSFGINLLALVDGQPKVLTLKQCLEHYLDHQKVVIRRRTAYELRKAEARAHILEGLRVALDHLDAVISLIRNSQTAEIARTGLIEQFSLTEKQAQAILDMRLQRLTGLEREKIEEEYQSLVKLIAELKDILANEYKVLEIIREELTEIKERFNDERRTEIVTSGLETIEDEDLIERENIVVTLTHNGYVKRLPASTYRSQKRGGKGVQGMGTNEDDFVEHLISTSTHDTILFFSNKGKVYRAKGYEIPEYGRTAKGIPIINLLEVEKGEWINAIIPVTEFNAELYLFFTTKHGVSKRTSLSQFANIRNNGLIALSLREDDELMGVRLTDGTKQIIIGTKNGLLIRFPETDVREMGRTAAGVKGITLTDDDVVVGMEILEEESHVLIVTEKGYGKRTPAEEYRTQSRGGKGLKTAKITENNGQLVAVKATKGEEDLMIITASGVLIRMDINDISITGRVTQGVRLIRMAEEEHVATVALVEKNEEDENEEEQEEV
->generic|AL009126.3_prot_CAB11784.1_8|conservedproteinofunknownfunction-BSU
-MTYHEWKDLALFYSVESTQKFLEKVYILNGINDAKKNSFKNSERFIYFLKHAESFYKQAAYSPLEIKPILLFYGMAQLIKACLITRDPHYPSHTSVLAHGVTTRKRKKQNYCFSDDEVKIQRNGLCVHFMKHLFGQSDIVDERYTMKKLLMAIPELSDIFYFQQKERFMTKVEKDKNEIFVPEEVVINYKMSDSRFAEYMSHHYQWSFTKKNEHGLLFEISPQDKEPWTSTSLLFDMEKNQYYIPSQREQFLRLPEMTIHYLILYNVGMIARYETEWWYELLTQHISDDYVLIQQFLLVSEKKFPKYASQFLLHF
->generic|AL009126.3_prot_CAB11785.1_9|inosine-monophosphatedehydrogenase-BSU
-MWESKFSKEGLTFDDVLLVPAKSEVLPRDVDLSVELTKTLKLNIPVISAGMDTVTESAMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSERGVITNPFFLTPDHQVFDAEHLMGKYRISGVPIVNNEEDQKLVGIITNRDLRFISDYSMKISDVMTKEELVTASVGTTLDEAEKILQKHKIEKLPLVDDQNKLKGLITIKDIEKVIEFPNSSKDIHGRLIVGAAVGVTGDTMTRVKKLVEANVDVIVIDTAHGHSQGVLNTVTKIRETYPELNIIAGNVATAEATRALIEAGADVVKVGIGPGSICTTRVVAGVGVPQITAIYDCATEARKHGKTIIADGGIKFSGDITKALAAGGHAVMLGSLLAGTSESPGETEIYQGRRFKVYRGMGSVAAMEKGSKDRYFQEENKKFVPEGIEGRTPYKGPVEETVYQLVGGLRSGMGYCGSKDLRALREEAQFIRMTGAGLRESHPHDVQITKESPNYTIS
->generic|AL009126.3_prot_CAB11786.1_10|D-alanyl-D-alaninecarboxypeptidase(penicillin-bindingprotein5)-BSU
-MNIKKCKQLLMSLVVLTLAVTCLAPMSKAKAASDPIDINASAAIMIEASSGKILYSKNADKRLPIASMTKMMTEYLLLEAIDQGKVKWDQTYTPDDYVYEISQDNSLSNVPLRKDGKYTVKELYQATAIYSANAAAIAIAEIVAGSETKFVEKMNAKAKELGLTDYKFVNATGLENKDLHGHQPEGTSVNEESEVSAKDMAVLADHLITDYPEILETSSIAKTKFREGTDDEMDMPNWNFMLKGLVSEYKKATVDGLKTGSTDSAGSCFTGTAERNGMRVITVVLNAKGNLHTGRFDETKKMFDYAFDNFSMKEIYAEGDQVKGHKTISVDKGKEKEVGIVTNKAFSLPVKNGEEKNYKAKVTLNKDNLTAPVKKGTKVGKLTAEYTGDEKDYGFLNSDLAGVDLVTKENVEKANWFVLTMRSIGGFFAGIWGSIVDTVTGWF
diff -r 59fec1e2a6c3 -r b4f6df8fa89b test-data/default/test.manifest
--- a/test-data/default/test.manifest	Sun Mar 30 23:00:45 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-test1.mzML	sample1		DDA
-test2.mzML	sample2		DDA
diff -r 59fec1e2a6c3 -r b4f6df8fa89b test-data/default/test1.mzML
--- a/test-data/default/test1.mzML	Sun Mar 30 23:00:45 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,721 +0,0 @@
-<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">
-  <mzML xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="191016JAT02_Mix_2_1ug" version="1.1.0">
-    <cvList count="2">
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-      <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" />
-    </cvList>
-    <fileDescription>
-      <fileContent>
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-        <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value="" />
-      </fileContent>
-      <sourceFileList count="1">
-        <sourceFile id="RAW1" name="191016JAT02_Mix_2_1ug.raw" location="file:///">
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-          <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value="" />
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-    </fileDescription>
-    <referenceableParamGroupList count="1">
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-        <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="FSN20187" />
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-    <sampleList count="1">
-      <sample id="_x0031_" name="">
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-      </sample>
-    </sampleList>
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-      </software>
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-    </softwareList>
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-        <componentList count="4">
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-          <analyzer order="2">
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-          <analyzer order="3">
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-            </binaryDataArray>
-          </binaryDataArrayList>
-        </spectrum>
-        </spectrumList>
-    </run>
-  </mzML>
-  <indexList count="1">
-    <index name="spectrum">
-      <offset idRef="controllerType=0 controllerNumber=1 scan=823">5044</offset>
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-    </index>
-  </indexList>
-  <indexListOffset>1357446760</indexListOffset>
-  <fileChecksum>3af4bc667298b083df087d70a02e9ca867a01650</fileChecksum>
-</indexedmzML>
diff -r 59fec1e2a6c3 -r b4f6df8fa89b test-data/nonspecific-hla/outputs/workflow.txt
--- a/test-data/nonspecific-hla/outputs/workflow.txt	Sun Mar 30 23:00:45 2025 +0000
+++ b/test-data/nonspecific-hla/outputs/workflow.txt	Wed Oct 01 22:20:54 2025 +0000
@@ -1,16 +1,34 @@
+# Workflow: Nonspecific-HLA
+
+
+crystalc.run-crystalc=false
+database.db-path=final_db.fas
 database.decoy-tag=rev_
-diann.fragpipe.cmd-opts=
+diann.channel-normalization-strategy=0
+diann.cmd-opts=
+diann.generate-msstats=true
 diann.heavy=
 diann.library=
 diann.light=
 diann.medium=
+diann.min-site-prob=0.75
+diann.mod-tag=
 diann.q-value=0.01
 diann.quantification-strategy=3
+diann.quantification-strategy-2=2
 diann.run-dia-nn=false
 diann.run-dia-plex=false
 diann.run-specific-protein-q-value=false
 diann.unrelated-runs=false
 diann.use-predicted-spectra=false
+diatracer.corr-threshold=0.3
+diatracer.delta-apex-im=0.01
+diatracer.delta-apex-rt=3
+diatracer.mass-defect-filter=true
+diatracer.mass-defect-offset=0.1
+diatracer.rf-max=500
+diatracer.run-diatracer=false
+diatracer.write-intermediate-files=false
 diaumpire.AdjustFragIntensity=true
 diaumpire.BoostComplementaryIon=false
 diaumpire.CorrThreshold=0
@@ -32,10 +50,19 @@
 diaumpire.SE.NoMissedScan=1
 diaumpire.SE.SN=1.1
 diaumpire.run-diaumpire=false
+fpop.coadaptr.fpop.fpop_masses=
+fpop.coadaptr.fpop.run-fpop-coadaptr=false
+fpop.fragpipe.fpop.fpop-tmt=false
+fpop.fragpipe.fpop.label_control=
+fpop.fragpipe.fpop.label_fpop=
+fpop.fragpipe.fpop.region_size=1
+fpop.fragpipe.fpop.run-fpop=false
+fpop.fragpipe.fpop.subtract-control=false
 freequant.mz-tol=10
 freequant.rt-tol=0.4
 freequant.run-freequant=false
 ionquant.excludemods=
+ionquant.formula=
 ionquant.heavy=
 ionquant.imtol=0.05
 ionquant.ionfdr=0.01
@@ -49,7 +76,7 @@
 ionquant.mbrtoprun=10
 ionquant.medium=
 ionquant.minfreq=0
-ionquant.minions=2
+ionquant.minions=1
 ionquant.minisotopes=2
 ionquant.minscans=3
 ionquant.mztol=10
@@ -64,15 +91,24 @@
 ionquant.use-labeling=false
 ionquant.use-lfq=true
 ionquant.writeindex=0
+msbooster.find-best-im-model=false
+msbooster.find-best-rt-model=false
+msbooster.find-best-spectra-model=false
+msbooster.fragmentation-type=0
+msbooster.im-model=DIA-NN
+msbooster.koina-url=
+msbooster.predict-im=true
 msbooster.predict-rt=true
 msbooster.predict-spectra=true
+msbooster.rt-model=DIA-NN
 msbooster.run-msbooster=true
-msbooster.use-correlated-features=false
+msbooster.spectra-model=DIA-NN
+msbooster.spectral-library-path=
 msfragger.Y_type_masses=
 msfragger.activation_types=all
-msfragger.add_topN_complementary=0
 msfragger.allowed_missed_cleavage_1=2
 msfragger.allowed_missed_cleavage_2=2
+msfragger.analyzer_types=all
 msfragger.calibrate_mass=2
 msfragger.check_spectral_files=true
 msfragger.clip_nTerm_M=true
@@ -94,6 +130,7 @@
 msfragger.localize_delta_mass=false
 msfragger.mass_diff_to_variable_mod=0
 msfragger.mass_offsets=0
+msfragger.mass_offsets_detailed=
 msfragger.max_fragment_charge=2
 msfragger.max_variable_mods_combinations=5000
 msfragger.max_variable_mods_per_peptide=3
@@ -117,8 +154,8 @@
 msfragger.output_format=pepXML_pin
 msfragger.output_max_expect=50.0
 msfragger.output_report_topN=1
+msfragger.output_report_topN_dda_plus=5
 msfragger.output_report_topN_dia1=5
-msfragger.output_report_topN_dia2=3
 msfragger.override_charge=false
 msfragger.precursor_mass_lower=-20
 msfragger.precursor_mass_mode=selected
@@ -133,8 +170,8 @@
 msfragger.restrict_deltamass_to=all
 msfragger.reuse_dia_fragment_peaks=false
 msfragger.run-msfragger=true
-msfragger.search_enzyme_cut_1=-
-msfragger.search_enzyme_cut_2=-
+msfragger.search_enzyme_cut_1=@
+msfragger.search_enzyme_cut_2=@
 msfragger.search_enzyme_name_1=nonspecific
 msfragger.search_enzyme_name_2=null
 msfragger.search_enzyme_nocut_1=
@@ -142,16 +179,17 @@
 msfragger.search_enzyme_sense_1=C
 msfragger.search_enzyme_sense_2=C
 msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),false,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
-msfragger.table.var-mods=15.9949,M,true,2; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQ,true,1; -18.0106,nE,true,1; 119.0041,C,true,1; 0.98402,N,false,1; 8.014199,K,false,1; 10.008269,R,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
+msfragger.table.var-mods=15.99491461956,M,true,2; 42.0105646837,[^,true,1; -17.0265,nQ,true,1; -18.0106,nE,true,1; 119.0041,C,true,1
 msfragger.track_zero_topN=0
 msfragger.use_all_mods_in_first_search=false
+msfragger.use_detailed_offsets=false
 msfragger.use_topN_peaks=300
 msfragger.write_calibrated_mzml=false
-msfragger.write_uncalibrated_mgf=false
 msfragger.zero_bin_accept_expect=0
 msfragger.zero_bin_mult_expect=1
 opair.activation1=HCD
 opair.activation2=ETD
+opair.allowed_sites=
 opair.filterOxonium=true
 opair.glyco_db=
 opair.max_glycans=4
@@ -174,7 +212,6 @@
 phi-report.dont-use-prot-proph-file=false
 phi-report.filter=--sequential --prot 1
 phi-report.pep-level-summary=true
-phi-report.philosoher-msstats=false
 phi-report.print-decoys=false
 phi-report.prot-level-summary=true
 phi-report.remove-contaminants=false
@@ -182,6 +219,7 @@
 protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.05
 protein-prophet.run-protein-prophet=true
 ptmprophet.cmdline=
+ptmprophet.override-defaults=false
 ptmprophet.run-ptmprophet=false
 ptmshepherd.adv_params=false
 ptmshepherd.annotation-common=false
@@ -193,7 +231,6 @@
 ptmshepherd.cap_y_ions=
 ptmshepherd.decoy_type=1
 ptmshepherd.diag_ions=
-ptmshepherd.diagextract_mode=false
 ptmshepherd.diagmine_diagMinFoldChange=3.0
 ptmshepherd.diagmine_diagMinSpecDiff=00.2
 ptmshepherd.diagmine_fragMinFoldChange=3.0
@@ -201,14 +238,11 @@
 ptmshepherd.diagmine_fragMinSpecDiff=00.1
 ptmshepherd.diagmine_minIonsPerSpec=2
 ptmshepherd.diagmine_minPeps=25
-ptmshepherd.diagmine_mode=false
 ptmshepherd.diagmine_pepMinFoldChange=3.0
 ptmshepherd.diagmine_pepMinSpecDiff=00.2
-ptmshepherd.glyco_adducts=
 ptmshepherd.glyco_fdr=1.00
 ptmshepherd.glyco_isotope_max=3
 ptmshepherd.glyco_isotope_min=-1
-ptmshepherd.glyco_mode=false
 ptmshepherd.glyco_ppm_tol=50
 ptmshepherd.glycodatabase=
 ptmshepherd.histo_smoothbins=2
@@ -218,9 +252,9 @@
 ptmshepherd.iontype_x=false
 ptmshepherd.iontype_y=true
 ptmshepherd.iontype_z=false
+ptmshepherd.iterloc_maxEpoch=100
+ptmshepherd.iterloc_mode=false
 ptmshepherd.localization_allowed_res=
-ptmshepherd.localization_background=4
-ptmshepherd.max_adducts=0
 ptmshepherd.n_glyco=true
 ptmshepherd.normalization-psms=true
 ptmshepherd.normalization-scans=false
@@ -232,28 +266,41 @@
 ptmshepherd.precursor_mass_units=0
 ptmshepherd.precursor_tol=0.01
 ptmshepherd.print_decoys=false
-ptmshepherd.prob_dhexOx=2,0.5,0.1
-ptmshepherd.prob_dhexY=2,0.5
-ptmshepherd.prob_neuacOx=2,0.05,0.2
-ptmshepherd.prob_neugcOx=2,0.05,0.2
-ptmshepherd.prob_phosphoOx=2,0.05,0.2
-ptmshepherd.prob_regY=5,0.5
-ptmshepherd.prob_sulfoOx=2,0.05,0.2
+ptmshepherd.print_full_glyco_params=false
+ptmshepherd.prob_mass=0.5
 ptmshepherd.remainder_masses=
 ptmshepherd.remove_glycan_delta_mass=true
 ptmshepherd.run-shepherd=false
+ptmshepherd.run_diagextract_mode=false
+ptmshepherd.run_diagmine_mode=false
+ptmshepherd.run_glyco_mode=false
+ptmshepherd.spectra_condPeaks=150
+ptmshepherd.spectra_condRatio=0.0001
+ptmshepherd.spectra_maxPrecursorCharge=4
 ptmshepherd.spectra_maxfragcharge=2
 ptmshepherd.spectra_ppmtol=20
 ptmshepherd.varmod_masses=
 quantitation.run-label-free-quant=false
 run-psm-validation=true
 run-validation-tab=true
-saintexpress.fragpipe.cmd-opts=
+saintexpress.cmd-opts=
 saintexpress.max-replicates=10
 saintexpress.run-saint-express=false
 saintexpress.virtual-controls=100
+skyline.run-skyline=false
+skyline.skyline=false
+skyline.skyline-custom=false
+skyline.skyline-custom-path=
+skyline.skyline-daily=true
+skyline.skyline-fragment-tolerance=10
+skyline.skyline-mods-mode=Default
+skyline.skyline-precursor-tolerance=10
+skyline.use-ssl=false
+speclibgen.convert-pepxml=true
+speclibgen.convert-psm=false
 speclibgen.easypqp.extras.max_delta_ppm=15
 speclibgen.easypqp.extras.max_delta_unimod=0.02
+speclibgen.easypqp.extras.max_glycan_qval=1
 speclibgen.easypqp.extras.rt_lowess_fraction=0
 speclibgen.easypqp.fragment.a=false
 speclibgen.easypqp.fragment.b=true
@@ -262,6 +309,7 @@
 speclibgen.easypqp.fragment.y=true
 speclibgen.easypqp.fragment.z=false
 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
+speclibgen.easypqp.labile_mode=Regular (not glyco)
 speclibgen.easypqp.neutral_loss=false
 speclibgen.easypqp.rt-cal=noiRT
 speclibgen.easypqp.select-file.text=
@@ -270,6 +318,7 @@
 speclibgen.run-speclibgen=false
 tab-run.delete_calibrated_mzml=false
 tab-run.delete_temp_files=false
+tab-run.export_matched_fragments=false
 tab-run.sub_mzml_prob_threshold=0.5
 tab-run.write_sub_mzml=false
 tmtintegrator.add_Ref=-1
@@ -278,24 +327,28 @@
 tmtintegrator.allow_unlabeled=true
 tmtintegrator.best_psm=true
 tmtintegrator.channel_num=TMT-6
-tmtintegrator.dont-run-fq-lq=false
+tmtintegrator.extraction_tool=IonQuant
 tmtintegrator.glyco_qval=-1
-tmtintegrator.groupby=0
+tmtintegrator.groupby=-1
 tmtintegrator.log2transformed=true
 tmtintegrator.max_pep_prob_thres=0
 tmtintegrator.min_ntt=0
 tmtintegrator.min_pep_prob=0.9
 tmtintegrator.min_percent=0.05
 tmtintegrator.min_purity=0.5
+tmtintegrator.min_resolution=0
 tmtintegrator.min_site_prob=-1
+tmtintegrator.min_snr=0
 tmtintegrator.mod_tag=none
 tmtintegrator.ms1_int=true
 tmtintegrator.outlier_removal=true
+tmtintegrator.philosopher-msstats=false
 tmtintegrator.print_RefInt=false
 tmtintegrator.prot_exclude=none
 tmtintegrator.prot_norm=0
 tmtintegrator.psm_norm=false
 tmtintegrator.quant_level=2
+tmtintegrator.ref_d_tag=Pool
 tmtintegrator.ref_tag=Bridge
 tmtintegrator.run-tmtintegrator=false
 tmtintegrator.tolerance=20
@@ -306,4 +359,6 @@
 workflow.description=<p style\="margin-top\: 0in">Nonspecific search, with recommended settings for HLA peptides. Peptide length 7-25. MSFragger search assumes cysteines were not alkylated (i.e. samples were not treated with iodoacetamide). Cysteinylation (C+119) is specified as variable modification. MSFragger rescoring with MSBooster. PSM validation with Percolator. Protein FDR filter is not applied, so each output file (PSM, ion, peptide) is filtered to 1% FDR at that level. If needed, extend to add label-free quantifcation (using IonQuant) or spectral library building with EasyPQP.</p>
 workflow.input.data-type.im-ms=false
 workflow.input.data-type.regular-ms=true
-workflow.saved-with-ver=20.0-build5
+workflow.misc.save-sdrf=true
+workflow.misc.sdrf-type=Default
+workflow.saved-with-ver=23.0-build14
diff -r 59fec1e2a6c3 -r b4f6df8fa89b test-data/tmt11/outputs/workflow.txt
--- a/test-data/tmt11/outputs/workflow.txt	Sun Mar 30 23:00:45 2025 +0000
+++ b/test-data/tmt11/outputs/workflow.txt	Wed Oct 01 22:20:54 2025 +0000
@@ -1,16 +1,34 @@
+# Workflow: TMT11
+
+
+crystalc.run-crystalc=false
+database.db-path=final_db.fas
 database.decoy-tag=rev_
-diann.fragpipe.cmd-opts=
+diann.channel-normalization-strategy=0
+diann.cmd-opts=
+diann.generate-msstats=true
 diann.heavy=
 diann.library=
 diann.light=
 diann.medium=
+diann.min-site-prob=0.75
+diann.mod-tag=
 diann.q-value=0.01
 diann.quantification-strategy=3
+diann.quantification-strategy-2=2
 diann.run-dia-nn=false
 diann.run-dia-plex=false
 diann.run-specific-protein-q-value=false
 diann.unrelated-runs=false
-diann.use-predicted-spectra=true
+diann.use-predicted-spectra=false
+diatracer.corr-threshold=0.3
+diatracer.delta-apex-im=0.01
+diatracer.delta-apex-rt=3
+diatracer.mass-defect-filter=true
+diatracer.mass-defect-offset=0.1
+diatracer.rf-max=500
+diatracer.run-diatracer=false
+diatracer.write-intermediate-files=false
 diaumpire.AdjustFragIntensity=true
 diaumpire.BoostComplementaryIon=false
 diaumpire.CorrThreshold=0
@@ -32,10 +50,19 @@
 diaumpire.SE.NoMissedScan=1
 diaumpire.SE.SN=1.1
 diaumpire.run-diaumpire=false
+fpop.coadaptr.fpop.fpop_masses=
+fpop.coadaptr.fpop.run-fpop-coadaptr=false
+fpop.fragpipe.fpop.fpop-tmt=false
+fpop.fragpipe.fpop.label_control=
+fpop.fragpipe.fpop.label_fpop=
+fpop.fragpipe.fpop.region_size=1
+fpop.fragpipe.fpop.run-fpop=false
+fpop.fragpipe.fpop.subtract-control=false
 freequant.mz-tol=10
 freequant.rt-tol=0.4
 freequant.run-freequant=false
 ionquant.excludemods=
+ionquant.formula=
 ionquant.heavy=
 ionquant.imtol=0.05
 ionquant.ionfdr=0.01
@@ -49,7 +76,7 @@
 ionquant.mbrtoprun=10
 ionquant.medium=
 ionquant.minfreq=0
-ionquant.minions=2
+ionquant.minions=1
 ionquant.minisotopes=2
 ionquant.minscans=3
 ionquant.mztol=10
@@ -64,15 +91,24 @@
 ionquant.use-labeling=false
 ionquant.use-lfq=true
 ionquant.writeindex=0
+msbooster.find-best-im-model=false
+msbooster.find-best-rt-model=false
+msbooster.find-best-spectra-model=false
+msbooster.fragmentation-type=0
+msbooster.im-model=DIA-NN
+msbooster.koina-url=
+msbooster.predict-im=true
 msbooster.predict-rt=true
 msbooster.predict-spectra=true
+msbooster.rt-model=DIA-NN
 msbooster.run-msbooster=true
-msbooster.use-correlated-features=false
+msbooster.spectra-model=DIA-NN
+msbooster.spectral-library-path=
 msfragger.Y_type_masses=
 msfragger.activation_types=all
-msfragger.add_topN_complementary=0
 msfragger.allowed_missed_cleavage_1=2
 msfragger.allowed_missed_cleavage_2=2
+msfragger.analyzer_types=all
 msfragger.calibrate_mass=2
 msfragger.check_spectral_files=true
 msfragger.clip_nTerm_M=true
@@ -94,6 +130,7 @@
 msfragger.localize_delta_mass=false
 msfragger.mass_diff_to_variable_mod=0
 msfragger.mass_offsets=0
+msfragger.mass_offsets_detailed=
 msfragger.max_fragment_charge=2
 msfragger.max_variable_mods_combinations=5000
 msfragger.max_variable_mods_per_peptide=3
@@ -104,8 +141,8 @@
 msfragger.minimum_ratio=0.01
 msfragger.misc.fragger.clear-mz-hi=131.5
 msfragger.misc.fragger.clear-mz-lo=125.5
-msfragger.misc.fragger.digest-mass-hi=5000
-msfragger.misc.fragger.digest-mass-lo=200
+msfragger.misc.fragger.digest-mass-hi=5000.0
+msfragger.misc.fragger.digest-mass-lo=200.0
 msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
 msfragger.misc.fragger.enzyme-dropdown-2=null
 msfragger.misc.fragger.precursor-charge-hi=4
@@ -117,8 +154,8 @@
 msfragger.output_format=pepXML_pin
 msfragger.output_max_expect=50.0
 msfragger.output_report_topN=1
+msfragger.output_report_topN_dda_plus=5
 msfragger.output_report_topN_dia1=5
-msfragger.output_report_topN_dia2=3
 msfragger.override_charge=false
 msfragger.precursor_mass_lower=-20
 msfragger.precursor_mass_mode=selected
@@ -142,16 +179,17 @@
 msfragger.search_enzyme_sense_1=C
 msfragger.search_enzyme_sense_2=C
 msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 229.16293,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
-msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.16293,n^,true,1; 229.16293,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
+msfragger.table.var-mods=15.99491461956,M,true,3; 42.0105646837,[^,true,1; 229.16293213472,n^,true,1; 229.16293213472,S,true,1
 msfragger.track_zero_topN=0
 msfragger.use_all_mods_in_first_search=false
+msfragger.use_detailed_offsets=false
 msfragger.use_topN_peaks=150
 msfragger.write_calibrated_mzml=false
-msfragger.write_uncalibrated_mgf=false
 msfragger.zero_bin_accept_expect=0
 msfragger.zero_bin_mult_expect=1
 opair.activation1=HCD
 opair.activation2=ETD
+opair.allowed_sites=
 opair.filterOxonium=true
 opair.glyco_db=
 opair.max_glycans=4
@@ -174,7 +212,6 @@
 phi-report.dont-use-prot-proph-file=false
 phi-report.filter=--sequential --picked --prot 0.01
 phi-report.pep-level-summary=false
-phi-report.philosoher-msstats=false
 phi-report.print-decoys=false
 phi-report.prot-level-summary=false
 phi-report.remove-contaminants=false
@@ -182,6 +219,7 @@
 protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5
 protein-prophet.run-protein-prophet=true
 ptmprophet.cmdline=
+ptmprophet.override-defaults=false
 ptmprophet.run-ptmprophet=false
 ptmshepherd.adv_params=false
 ptmshepherd.annotation-common=true
@@ -193,7 +231,6 @@
 ptmshepherd.cap_y_ions=
 ptmshepherd.decoy_type=1
 ptmshepherd.diag_ions=
-ptmshepherd.diagextract_mode=false
 ptmshepherd.diagmine_diagMinFoldChange=3.0
 ptmshepherd.diagmine_diagMinSpecDiff=00.2
 ptmshepherd.diagmine_fragMinFoldChange=3.0
@@ -201,14 +238,11 @@
 ptmshepherd.diagmine_fragMinSpecDiff=00.1
 ptmshepherd.diagmine_minIonsPerSpec=2
 ptmshepherd.diagmine_minPeps=25
-ptmshepherd.diagmine_mode=false
 ptmshepherd.diagmine_pepMinFoldChange=3.0
 ptmshepherd.diagmine_pepMinSpecDiff=00.2
-ptmshepherd.glyco_adducts=
 ptmshepherd.glyco_fdr=1.00
 ptmshepherd.glyco_isotope_max=3
 ptmshepherd.glyco_isotope_min=-1
-ptmshepherd.glyco_mode=false
 ptmshepherd.glyco_ppm_tol=50
 ptmshepherd.glycodatabase=
 ptmshepherd.histo_smoothbins=2
@@ -218,9 +252,9 @@
 ptmshepherd.iontype_x=false
 ptmshepherd.iontype_y=true
 ptmshepherd.iontype_z=false
+ptmshepherd.iterloc_maxEpoch=100
+ptmshepherd.iterloc_mode=false
 ptmshepherd.localization_allowed_res=
-ptmshepherd.localization_background=4
-ptmshepherd.max_adducts=0
 ptmshepherd.n_glyco=true
 ptmshepherd.normalization-psms=true
 ptmshepherd.normalization-scans=false
@@ -232,28 +266,41 @@
 ptmshepherd.precursor_mass_units=0
 ptmshepherd.precursor_tol=0.01
 ptmshepherd.print_decoys=false
-ptmshepherd.prob_dhexOx=2,0.5,0.1
-ptmshepherd.prob_dhexY=2,0.5
-ptmshepherd.prob_neuacOx=2,0.05,0.2
-ptmshepherd.prob_neugcOx=2,0.05,0.2
-ptmshepherd.prob_phosphoOx=2,0.05,0.2
-ptmshepherd.prob_regY=5,0.5
-ptmshepherd.prob_sulfoOx=2,0.05,0.2
+ptmshepherd.print_full_glyco_params=false
+ptmshepherd.prob_mass=0.5
 ptmshepherd.remainder_masses=
 ptmshepherd.remove_glycan_delta_mass=true
 ptmshepherd.run-shepherd=false
+ptmshepherd.run_diagextract_mode=false
+ptmshepherd.run_diagmine_mode=false
+ptmshepherd.run_glyco_mode=false
+ptmshepherd.spectra_condPeaks=150
+ptmshepherd.spectra_condRatio=0.0001
+ptmshepherd.spectra_maxPrecursorCharge=4
 ptmshepherd.spectra_maxfragcharge=2
 ptmshepherd.spectra_ppmtol=20
 ptmshepherd.varmod_masses=
 quantitation.run-label-free-quant=false
 run-psm-validation=true
 run-validation-tab=true
-saintexpress.fragpipe.cmd-opts=
+saintexpress.cmd-opts=
 saintexpress.max-replicates=3
 saintexpress.run-saint-express=true
 saintexpress.virtual-controls=100
+skyline.run-skyline=false
+skyline.skyline=false
+skyline.skyline-custom=false
+skyline.skyline-custom-path=
+skyline.skyline-daily=true
+skyline.skyline-fragment-tolerance=10
+skyline.skyline-mods-mode=Default
+skyline.skyline-precursor-tolerance=10
+skyline.use-ssl=false
+speclibgen.convert-pepxml=true
+speclibgen.convert-psm=false
 speclibgen.easypqp.extras.max_delta_ppm=15
 speclibgen.easypqp.extras.max_delta_unimod=0.02
+speclibgen.easypqp.extras.max_glycan_qval=1
 speclibgen.easypqp.extras.rt_lowess_fraction=0
 speclibgen.easypqp.fragment.a=false
 speclibgen.easypqp.fragment.b=true
@@ -262,6 +309,7 @@
 speclibgen.easypqp.fragment.y=true
 speclibgen.easypqp.fragment.z=false
 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
+speclibgen.easypqp.labile_mode=Regular (not glyco)
 speclibgen.easypqp.neutral_loss=false
 speclibgen.easypqp.rt-cal=noiRT
 speclibgen.easypqp.select-file.text=
@@ -270,6 +318,7 @@
 speclibgen.run-speclibgen=false
 tab-run.delete_calibrated_mzml=false
 tab-run.delete_temp_files=false
+tab-run.export_matched_fragments=false
 tab-run.sub_mzml_prob_threshold=0.5
 tab-run.write_sub_mzml=false
 tmtintegrator.add_Ref=1
@@ -278,24 +327,28 @@
 tmtintegrator.allow_unlabeled=false
 tmtintegrator.best_psm=true
 tmtintegrator.channel_num=TMT-11
-tmtintegrator.dont-run-fq-lq=false
+tmtintegrator.extraction_tool=IonQuant
 tmtintegrator.glyco_qval=-1
-tmtintegrator.groupby=0
+tmtintegrator.groupby=-1
 tmtintegrator.log2transformed=true
 tmtintegrator.max_pep_prob_thres=0.9
 tmtintegrator.min_ntt=0
 tmtintegrator.min_pep_prob=0.9
 tmtintegrator.min_percent=0.05
 tmtintegrator.min_purity=0.5
+tmtintegrator.min_resolution=0
 tmtintegrator.min_site_prob=-1
+tmtintegrator.min_snr=0
 tmtintegrator.mod_tag=none
 tmtintegrator.ms1_int=true
 tmtintegrator.outlier_removal=true
+tmtintegrator.philosopher-msstats=false
 tmtintegrator.print_RefInt=false
 tmtintegrator.prot_exclude=none
 tmtintegrator.prot_norm=1
 tmtintegrator.psm_norm=false
 tmtintegrator.quant_level=2
+tmtintegrator.ref_d_tag=Pool
 tmtintegrator.ref_tag=Bridge
 tmtintegrator.run-tmtintegrator=true
 tmtintegrator.tolerance=20
@@ -306,4 +359,6 @@
 workflow.description=<p style\="margin-top\: 0">Basic TMT 11-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.</p>
 workflow.input.data-type.im-ms=false
 workflow.input.data-type.regular-ms=true
-workflow.saved-with-ver=20.0-build5
+workflow.misc.save-sdrf=true
+workflow.misc.sdrf-type=Default
+workflow.saved-with-ver=23.0-build14
diff -r 59fec1e2a6c3 -r b4f6df8fa89b workflows/Basic-Search.workflow
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/workflows/Basic-Search.workflow	Wed Oct 01 22:20:54 2025 +0000
@@ -0,0 +1,361 @@
+# Workflow: Basic-Search
+
+crystalc.run-crystalc=false
+database.decoy-tag=rev_
+diann.channel-normalization-strategy=0
+diann.cmd-opts=
+diann.generate-msstats=true
+diann.heavy=
+diann.library=
+diann.light=
+diann.medium=
+diann.min-site-prob=0.75
+diann.mod-tag=
+diann.q-value=0.01
+diann.quantification-strategy=3
+diann.quantification-strategy-2=2
+diann.run-dia-nn=false
+diann.run-dia-plex=false
+diann.run-specific-protein-q-value=false
+diann.unrelated-runs=false
+diann.use-predicted-spectra=false
+diatracer.corr-threshold=0.3
+diatracer.delta-apex-im=0.01
+diatracer.delta-apex-rt=3
+diatracer.mass-defect-filter=true
+diatracer.mass-defect-offset=0.1
+diatracer.rf-max=500
+diatracer.run-diatracer=false
+diatracer.write-intermediate-files=false
+diaumpire.AdjustFragIntensity=true
+diaumpire.BoostComplementaryIon=false
+diaumpire.CorrThreshold=0
+diaumpire.DeltaApex=0.2
+diaumpire.ExportPrecursorPeak=false
+diaumpire.Q1=true
+diaumpire.Q2=true
+diaumpire.Q3=true
+diaumpire.RFmax=500
+diaumpire.RPmax=25
+diaumpire.RTOverlap=0.3
+diaumpire.SE.EstimateBG=false
+diaumpire.SE.IsoPattern=0.3
+diaumpire.SE.MS1PPM=10
+diaumpire.SE.MS2PPM=20
+diaumpire.SE.MS2SN=1.1
+diaumpire.SE.MassDefectFilter=true
+diaumpire.SE.MassDefectOffset=0.1
+diaumpire.SE.NoMissedScan=1
+diaumpire.SE.SN=1.1
+diaumpire.run-diaumpire=false
+fpop.coadaptr.fpop.fpop_masses=
+fpop.coadaptr.fpop.run-fpop-coadaptr=false
+fpop.fragpipe.fpop.fpop-tmt=false
+fpop.fragpipe.fpop.label_control=
+fpop.fragpipe.fpop.label_fpop=
+fpop.fragpipe.fpop.region_size=1
+fpop.fragpipe.fpop.run-fpop=false
+fpop.fragpipe.fpop.subtract-control=false
+freequant.mz-tol=10
+freequant.rt-tol=0.4
+freequant.run-freequant=false
+ionquant.excludemods=
+ionquant.formula=
+ionquant.heavy=
+ionquant.imtol=0.05
+ionquant.ionfdr=0.01
+ionquant.light=
+ionquant.locprob=0.75
+ionquant.maxlfq=1
+ionquant.mbr=1
+ionquant.mbrimtol=0.05
+ionquant.mbrmincorr=0
+ionquant.mbrrttol=1
+ionquant.mbrtoprun=10
+ionquant.medium=
+ionquant.minfreq=0
+ionquant.minions=1
+ionquant.minisotopes=2
+ionquant.minscans=3
+ionquant.mztol=10
+ionquant.normalization=1
+ionquant.peptidefdr=1
+ionquant.proteinfdr=1
+ionquant.requantify=1
+ionquant.rttol=0.4
+ionquant.run-ionquant=true
+ionquant.tp=0
+ionquant.uniqueness=0
+ionquant.use-labeling=false
+ionquant.use-lfq=true
+ionquant.writeindex=0
+msbooster.find-best-im-model=false
+msbooster.find-best-rt-model=false
+msbooster.find-best-spectra-model=false
+msbooster.fragmentation-type=0
+msbooster.im-model=DIA-NN
+msbooster.koina-url=
+msbooster.predict-im=true
+msbooster.predict-rt=true
+msbooster.predict-spectra=true
+msbooster.rt-model=DIA-NN
+msbooster.run-msbooster=true
+msbooster.spectra-model=DIA-NN
+msbooster.spectral-library-path=
+msfragger.Y_type_masses=
+msfragger.activation_types=all
+msfragger.allowed_missed_cleavage_1=2
+msfragger.allowed_missed_cleavage_2=2
+msfragger.analyzer_types=all
+msfragger.calibrate_mass=2
+msfragger.check_spectral_files=true
+msfragger.clip_nTerm_M=true
+msfragger.deisotope=1
+msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
+msfragger.deneutralloss=1
+msfragger.diagnostic_fragments=
+msfragger.diagnostic_intensity_filter=0
+msfragger.digest_max_length=50
+msfragger.digest_min_length=7
+msfragger.fragment_ion_series=b,y
+msfragger.fragment_mass_tolerance=20
+msfragger.fragment_mass_units=1
+msfragger.group_variable=0
+msfragger.intensity_transform=0
+msfragger.ion_series_definitions=
+msfragger.isotope_error=0/1/2/3
+msfragger.labile_search_mode=off
+msfragger.localize_delta_mass=false
+msfragger.mass_diff_to_variable_mod=0
+msfragger.mass_offsets=0
+msfragger.mass_offsets_detailed=
+msfragger.max_fragment_charge=2
+msfragger.max_variable_mods_combinations=5000
+msfragger.max_variable_mods_per_peptide=3
+msfragger.min_fragments_modelling=2
+msfragger.min_matched_fragments=4
+msfragger.min_sequence_matches=2
+msfragger.minimum_peaks=15
+msfragger.minimum_ratio=0.01
+msfragger.misc.fragger.clear-mz-hi=0
+msfragger.misc.fragger.clear-mz-lo=0
+msfragger.misc.fragger.digest-mass-hi=5000
+msfragger.misc.fragger.digest-mass-lo=500
+msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
+msfragger.misc.fragger.enzyme-dropdown-2=null
+msfragger.misc.fragger.precursor-charge-hi=4
+msfragger.misc.fragger.precursor-charge-lo=1
+msfragger.misc.fragger.remove-precursor-range-hi=1.5
+msfragger.misc.fragger.remove-precursor-range-lo=-1.5
+msfragger.misc.slice-db=1
+msfragger.num_enzyme_termini=2
+msfragger.output_format=pepXML_pin
+msfragger.output_max_expect=50
+msfragger.output_report_topN=1
+msfragger.output_report_topN_dda_plus=5
+msfragger.output_report_topN_dia1=5
+msfragger.override_charge=false
+msfragger.precursor_mass_lower=-20
+msfragger.precursor_mass_mode=selected
+msfragger.precursor_mass_units=1
+msfragger.precursor_mass_upper=20
+msfragger.precursor_true_tolerance=20
+msfragger.precursor_true_units=1
+msfragger.remainder_fragment_masses=
+msfragger.remove_precursor_peak=1
+msfragger.report_alternative_proteins=true
+msfragger.require_precursor=true
+msfragger.restrict_deltamass_to=all
+msfragger.reuse_dia_fragment_peaks=false
+msfragger.run-msfragger=true
+msfragger.search_enzyme_cut_1=KR
+msfragger.search_enzyme_cut_2=
+msfragger.search_enzyme_name_1=stricttrypsin
+msfragger.search_enzyme_name_2=null
+msfragger.search_enzyme_nocut_1=
+msfragger.search_enzyme_nocut_2=
+msfragger.search_enzyme_sense_1=C
+msfragger.search_enzyme_sense_2=C
+msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
+msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
+msfragger.track_zero_topN=0
+msfragger.use_all_mods_in_first_search=false
+msfragger.use_detailed_offsets=false
+msfragger.use_topN_peaks=150
+msfragger.write_calibrated_mzml=false
+msfragger.zero_bin_accept_expect=0
+msfragger.zero_bin_mult_expect=1
+opair.activation1=HCD
+opair.activation2=ETD
+opair.allowed_sites=
+opair.filterOxonium=true
+opair.glyco_db=
+opair.max_glycans=4
+opair.max_isotope_error=2
+opair.min_isotope_error=0
+opair.ms1_tol=20
+opair.ms2_tol=20
+opair.oxonium_filtering_file=
+opair.oxonium_minimum_intensity=0.05
+opair.reverse_scan_order=false
+opair.run-opair=false
+opair.single_scan_type=false
+peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
+peptide-prophet.combine-pepxml=false
+peptide-prophet.run-peptide-prophet=false
+percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
+percolator.keep-tsv-files=false
+percolator.min-prob=0.5
+percolator.run-percolator=true
+phi-report.dont-use-prot-proph-file=false
+phi-report.filter=--sequential --picked --prot 0.01
+phi-report.pep-level-summary=false
+phi-report.print-decoys=false
+phi-report.prot-level-summary=true
+phi-report.remove-contaminants=false
+phi-report.run-report=true
+protein-prophet.cmd-opts=--maxppmdiff 2000000
+protein-prophet.run-protein-prophet=true
+ptmprophet.cmdline=NOSTACK KEEPOLD STATIC FRAGPPMTOL\=10 EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
+ptmprophet.override-defaults=false
+ptmprophet.run-ptmprophet=false
+ptmshepherd.adv_params=false
+ptmshepherd.annotation-common=false
+ptmshepherd.annotation-custom=false
+ptmshepherd.annotation-glyco=false
+ptmshepherd.annotation-unimod=true
+ptmshepherd.annotation_file=
+ptmshepherd.annotation_tol=0.01
+ptmshepherd.cap_y_ions=
+ptmshepherd.decoy_type=1
+ptmshepherd.diag_ions=
+ptmshepherd.diagmine_diagMinFoldChange=3.0
+ptmshepherd.diagmine_diagMinSpecDiff=00.2
+ptmshepherd.diagmine_fragMinFoldChange=3.0
+ptmshepherd.diagmine_fragMinPropensity=00.1
+ptmshepherd.diagmine_fragMinSpecDiff=00.1
+ptmshepherd.diagmine_minIonsPerSpec=2
+ptmshepherd.diagmine_minPeps=25
+ptmshepherd.diagmine_pepMinFoldChange=3.0
+ptmshepherd.diagmine_pepMinSpecDiff=00.2
+ptmshepherd.glyco_fdr=1.00
+ptmshepherd.glyco_isotope_max=3
+ptmshepherd.glyco_isotope_min=-1
+ptmshepherd.glyco_ppm_tol=50
+ptmshepherd.glycodatabase=
+ptmshepherd.histo_smoothbins=2
+ptmshepherd.iontype_a=false
+ptmshepherd.iontype_b=true
+ptmshepherd.iontype_c=true
+ptmshepherd.iontype_x=false
+ptmshepherd.iontype_y=true
+ptmshepherd.iontype_z=true
+ptmshepherd.iterloc_maxEpoch=100
+ptmshepherd.iterloc_mode=false
+ptmshepherd.localization_allowed_res=
+ptmshepherd.n_glyco=true
+ptmshepherd.normalization-psms=true
+ptmshepherd.normalization-scans=false
+ptmshepherd.output_extended=false
+ptmshepherd.peakpicking_mass_units=0
+ptmshepherd.peakpicking_minPsm=10
+ptmshepherd.peakpicking_promRatio=0.3
+ptmshepherd.peakpicking_width=0.002
+ptmshepherd.precursor_mass_units=0
+ptmshepherd.precursor_tol=0.01
+ptmshepherd.print_decoys=false
+ptmshepherd.print_full_glyco_params=false
+ptmshepherd.prob_mass=0.5
+ptmshepherd.remainder_masses=
+ptmshepherd.remove_glycan_delta_mass=true
+ptmshepherd.run-shepherd=false
+ptmshepherd.run_diagextract_mode=false
+ptmshepherd.run_diagmine_mode=false
+ptmshepherd.run_glyco_mode=false
+ptmshepherd.spectra_condPeaks=150
+ptmshepherd.spectra_condRatio=0.0001
+ptmshepherd.spectra_maxPrecursorCharge=4
+ptmshepherd.spectra_maxfragcharge=2
+ptmshepherd.spectra_ppmtol=20
+ptmshepherd.varmod_masses=
+quantitation.run-label-free-quant=false
+run-psm-validation=true
+run-validation-tab=true
+saintexpress.cmd-opts=
+saintexpress.max-replicates=10
+saintexpress.run-saint-express=false
+saintexpress.virtual-controls=100
+skyline.run-skyline=false
+skyline.skyline=false
+skyline.skyline-custom=false
+skyline.skyline-custom-path=
+skyline.skyline-daily=true
+skyline.skyline-fragment-tolerance=10
+skyline.skyline-mods-mode=Default
+skyline.skyline-precursor-tolerance=10
+skyline.use-ssl=false
+speclibgen.convert-pepxml=true
+speclibgen.convert-psm=false
+speclibgen.easypqp.extras.max_delta_ppm=15
+speclibgen.easypqp.extras.max_delta_unimod=0.02
+speclibgen.easypqp.extras.max_glycan_qval=1
+speclibgen.easypqp.extras.rt_lowess_fraction=0
+speclibgen.easypqp.fragment.a=false
+speclibgen.easypqp.fragment.b=true
+speclibgen.easypqp.fragment.c=false
+speclibgen.easypqp.fragment.x=false
+speclibgen.easypqp.fragment.y=true
+speclibgen.easypqp.fragment.z=false
+speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
+speclibgen.easypqp.labile_mode=Regular (not glyco)
+speclibgen.easypqp.neutral_loss=false
+speclibgen.easypqp.rt-cal=ciRT
+speclibgen.easypqp.select-file.text=
+speclibgen.easypqp.select-im-file.text=
+speclibgen.keep-intermediate-files=false
+speclibgen.run-speclibgen=false
+tab-run.delete_calibrated_mzml=false
+tab-run.delete_temp_files=false
+tab-run.export_matched_fragments=false
+tab-run.sub_mzml_prob_threshold=0.5
+tab-run.write_sub_mzml=false
+tmtintegrator.add_Ref=-1
+tmtintegrator.aggregation_method=0
+tmtintegrator.allow_overlabel=true
+tmtintegrator.allow_unlabeled=true
+tmtintegrator.best_psm=true
+tmtintegrator.channel_num=TMT-6
+tmtintegrator.extraction_tool=IonQuant
+tmtintegrator.glyco_qval=-1
+tmtintegrator.groupby=-1
+tmtintegrator.log2transformed=true
+tmtintegrator.max_pep_prob_thres=0
+tmtintegrator.min_ntt=0
+tmtintegrator.min_pep_prob=0.9
+tmtintegrator.min_percent=0.05
+tmtintegrator.min_purity=0.5
+tmtintegrator.min_resolution=0
+tmtintegrator.min_site_prob=-1
+tmtintegrator.min_snr=0
+tmtintegrator.mod_tag=none
+tmtintegrator.ms1_int=true
+tmtintegrator.outlier_removal=true
+tmtintegrator.philosopher-msstats=false
+tmtintegrator.print_RefInt=false
+tmtintegrator.prot_exclude=none
+tmtintegrator.prot_norm=0
+tmtintegrator.psm_norm=false
+tmtintegrator.quant_level=2
+tmtintegrator.ref_d_tag=Pool
+tmtintegrator.ref_tag=Bridge
+tmtintegrator.run-tmtintegrator=false
+tmtintegrator.tolerance=20
+tmtintegrator.top3_pep=true
+tmtintegrator.unique_gene=0
+tmtintegrator.unique_pep=false
+tmtintegrator.use_glycan_composition=false
+workflow.input.data-type.im-ms=false
+workflow.input.data-type.regular-ms=true
+workflow.misc.save-sdrf=true
+workflow.misc.sdrf-type=Default
+workflow.saved-with-ver=23.0-build14
diff -r 59fec1e2a6c3 -r b4f6df8fa89b workflows/DIA_SpecLib_Quant.workflow
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/workflows/DIA_SpecLib_Quant.workflow	Wed Oct 01 22:20:54 2025 +0000
@@ -0,0 +1,362 @@
+# Workflow: DIA_SpecLib_Quant
+
+crystalc.run-crystalc=false
+database.decoy-tag=rev_
+diann.channel-normalization-strategy=0
+diann.cmd-opts=
+diann.generate-msstats=true
+diann.heavy=
+diann.library=
+diann.light=
+diann.medium=
+diann.min-site-prob=0.75
+diann.mod-tag=
+diann.q-value=0.01
+diann.quantification-strategy=3
+diann.quantification-strategy-2=2
+diann.run-dia-nn=true
+diann.run-dia-plex=false
+diann.run-specific-protein-q-value=false
+diann.unrelated-runs=false
+diann.use-predicted-spectra=false
+diatracer.corr-threshold=0.3
+diatracer.delta-apex-im=0.01
+diatracer.delta-apex-rt=3
+diatracer.mass-defect-filter=true
+diatracer.mass-defect-offset=0.1
+diatracer.rf-max=500
+diatracer.run-diatracer=false
+diatracer.write-intermediate-files=false
+diaumpire.AdjustFragIntensity=true
+diaumpire.BoostComplementaryIon=false
+diaumpire.CorrThreshold=0
+diaumpire.DeltaApex=0.2
+diaumpire.ExportPrecursorPeak=false
+diaumpire.Q1=true
+diaumpire.Q2=true
+diaumpire.Q3=true
+diaumpire.RFmax=500
+diaumpire.RPmax=25
+diaumpire.RTOverlap=0.3
+diaumpire.SE.EstimateBG=false
+diaumpire.SE.IsoPattern=0.3
+diaumpire.SE.MS1PPM=10
+diaumpire.SE.MS2PPM=20
+diaumpire.SE.MS2SN=1.1
+diaumpire.SE.MassDefectFilter=true
+diaumpire.SE.MassDefectOffset=0.1
+diaumpire.SE.NoMissedScan=1
+diaumpire.SE.SN=1.1
+diaumpire.run-diaumpire=false
+fpop.coadaptr.fpop.fpop_masses=
+fpop.coadaptr.fpop.run-fpop-coadaptr=false
+fpop.fragpipe.fpop.fpop-tmt=false
+fpop.fragpipe.fpop.label_control=
+fpop.fragpipe.fpop.label_fpop=
+fpop.fragpipe.fpop.region_size=1
+fpop.fragpipe.fpop.run-fpop=false
+fpop.fragpipe.fpop.subtract-control=false
+freequant.mz-tol=10
+freequant.rt-tol=0.4
+freequant.run-freequant=false
+ionquant.excludemods=
+ionquant.formula=
+ionquant.heavy=
+ionquant.imtol=0.05
+ionquant.ionfdr=0.01
+ionquant.light=
+ionquant.locprob=0.75
+ionquant.maxlfq=1
+ionquant.mbr=0
+ionquant.mbrimtol=0.05
+ionquant.mbrmincorr=0
+ionquant.mbrrttol=1
+ionquant.mbrtoprun=10
+ionquant.medium=
+ionquant.minfreq=0
+ionquant.minions=1
+ionquant.minisotopes=1
+ionquant.minscans=3
+ionquant.mztol=10
+ionquant.normalization=1
+ionquant.peptidefdr=1
+ionquant.proteinfdr=1
+ionquant.requantify=1
+ionquant.rttol=0.4
+ionquant.run-ionquant=true
+ionquant.tp=0
+ionquant.uniqueness=0
+ionquant.use-labeling=false
+ionquant.use-lfq=true
+ionquant.writeindex=0
+msbooster.find-best-im-model=false
+msbooster.find-best-rt-model=false
+msbooster.find-best-spectra-model=false
+msbooster.fragmentation-type=0
+msbooster.im-model=DIA-NN
+msbooster.koina-url=
+msbooster.predict-im=true
+msbooster.predict-rt=true
+msbooster.predict-spectra=true
+msbooster.rt-model=DIA-NN
+msbooster.run-msbooster=true
+msbooster.spectra-model=DIA-NN
+msbooster.spectral-library-path=
+msfragger.Y_type_masses=
+msfragger.activation_types=all
+msfragger.allowed_missed_cleavage_1=1
+msfragger.allowed_missed_cleavage_2=1
+msfragger.analyzer_types=all
+msfragger.calibrate_mass=2
+msfragger.check_spectral_files=false
+msfragger.clip_nTerm_M=true
+msfragger.deisotope=1
+msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
+msfragger.deneutralloss=1
+msfragger.diagnostic_fragments=
+msfragger.diagnostic_intensity_filter=0
+msfragger.digest_max_length=50
+msfragger.digest_min_length=7
+msfragger.fragment_ion_series=b,y
+msfragger.fragment_mass_tolerance=20
+msfragger.fragment_mass_units=1
+msfragger.group_variable=0
+msfragger.intensity_transform=0
+msfragger.ion_series_definitions=
+msfragger.isotope_error=0/1/2
+msfragger.labile_search_mode=off
+msfragger.localize_delta_mass=false
+msfragger.mass_diff_to_variable_mod=0
+msfragger.mass_offsets=0
+msfragger.mass_offsets_detailed=
+msfragger.max_fragment_charge=2
+msfragger.max_variable_mods_combinations=5000
+msfragger.max_variable_mods_per_peptide=3
+msfragger.min_fragments_modelling=2
+msfragger.min_matched_fragments=4
+msfragger.min_sequence_matches=2
+msfragger.minimum_peaks=15
+msfragger.minimum_ratio=0.00
+msfragger.misc.fragger.clear-mz-hi=0
+msfragger.misc.fragger.clear-mz-lo=0
+msfragger.misc.fragger.digest-mass-hi=5000
+msfragger.misc.fragger.digest-mass-lo=500
+msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
+msfragger.misc.fragger.enzyme-dropdown-2=null
+msfragger.misc.fragger.precursor-charge-hi=4
+msfragger.misc.fragger.precursor-charge-lo=2
+msfragger.misc.fragger.remove-precursor-range-hi=1.5
+msfragger.misc.fragger.remove-precursor-range-lo=-1.5
+msfragger.misc.slice-db=1
+msfragger.num_enzyme_termini=2
+msfragger.output_format=pepXML_pin
+msfragger.output_max_expect=50
+msfragger.output_report_topN=1
+msfragger.output_report_topN_dda_plus=5
+msfragger.output_report_topN_dia1=5
+msfragger.override_charge=false
+msfragger.precursor_mass_lower=-20
+msfragger.precursor_mass_mode=selected
+msfragger.precursor_mass_units=1
+msfragger.precursor_mass_upper=20
+msfragger.precursor_true_tolerance=20
+msfragger.precursor_true_units=1
+msfragger.remainder_fragment_masses=
+msfragger.remove_precursor_peak=1
+msfragger.report_alternative_proteins=true
+msfragger.require_precursor=true
+msfragger.restrict_deltamass_to=all
+msfragger.reuse_dia_fragment_peaks=false
+msfragger.run-msfragger=true
+msfragger.search_enzyme_cut_1=KR
+msfragger.search_enzyme_cut_2=
+msfragger.search_enzyme_name_1=stricttrypsin
+msfragger.search_enzyme_name_2=null
+msfragger.search_enzyme_nocut_1=
+msfragger.search_enzyme_nocut_2=
+msfragger.search_enzyme_sense_1=C
+msfragger.search_enzyme_sense_2=C
+msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
+msfragger.table.var-mods=15.9949,M,true,1; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 0.0,site_06,false,1; 0.0,site_07,false,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
+msfragger.track_zero_topN=0
+msfragger.use_all_mods_in_first_search=false
+msfragger.use_detailed_offsets=false
+msfragger.use_topN_peaks=1000
+msfragger.write_calibrated_mzml=false
+msfragger.zero_bin_accept_expect=0
+msfragger.zero_bin_mult_expect=1
+opair.activation1=HCD
+opair.activation2=ETD
+opair.allowed_sites=
+opair.filterOxonium=true
+opair.glyco_db=
+opair.max_glycans=4
+opair.max_isotope_error=2
+opair.min_isotope_error=0
+opair.ms1_tol=20
+opair.ms2_tol=20
+opair.oxonium_filtering_file=
+opair.oxonium_minimum_intensity=0.05
+opair.reverse_scan_order=false
+opair.run-opair=false
+opair.single_scan_type=false
+peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
+peptide-prophet.combine-pepxml=false
+peptide-prophet.run-peptide-prophet=false
+percolator.cmd-opts=--no-terminate --post-processing-tdc --subset-max-train 500000
+percolator.keep-tsv-files=false
+percolator.min-prob=0.7
+percolator.run-percolator=true
+phi-report.dont-use-prot-proph-file=false
+phi-report.filter=--picked --prot 0.01 --minPepLen 8
+phi-report.pep-level-summary=false
+phi-report.print-decoys=false
+phi-report.prot-level-summary=false
+phi-report.remove-contaminants=false
+phi-report.run-report=true
+protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5
+protein-prophet.run-protein-prophet=true
+ptmprophet.cmdline=
+ptmprophet.override-defaults=false
+ptmprophet.run-ptmprophet=false
+ptmshepherd.adv_params=false
+ptmshepherd.annotation-common=false
+ptmshepherd.annotation-custom=false
+ptmshepherd.annotation-glyco=false
+ptmshepherd.annotation-unimod=true
+ptmshepherd.annotation_file=
+ptmshepherd.annotation_tol=0.01
+ptmshepherd.cap_y_ions=
+ptmshepherd.decoy_type=1
+ptmshepherd.diag_ions=
+ptmshepherd.diagmine_diagMinFoldChange=3.0
+ptmshepherd.diagmine_diagMinSpecDiff=25
+ptmshepherd.diagmine_fragMinFoldChange=3.0
+ptmshepherd.diagmine_fragMinPropensity=12.5
+ptmshepherd.diagmine_fragMinSpecDiff=25
+ptmshepherd.diagmine_minIonsPerSpec=2
+ptmshepherd.diagmine_minPeps=25
+ptmshepherd.diagmine_pepMinFoldChange=3.0
+ptmshepherd.diagmine_pepMinSpecDiff=25
+ptmshepherd.glyco_fdr=1.00
+ptmshepherd.glyco_isotope_max=3
+ptmshepherd.glyco_isotope_min=-1
+ptmshepherd.glyco_ppm_tol=50
+ptmshepherd.glycodatabase=
+ptmshepherd.histo_smoothbins=2
+ptmshepherd.iontype_a=false
+ptmshepherd.iontype_b=true
+ptmshepherd.iontype_c=true
+ptmshepherd.iontype_x=false
+ptmshepherd.iontype_y=true
+ptmshepherd.iontype_z=true
+ptmshepherd.iterloc_maxEpoch=100
+ptmshepherd.iterloc_mode=false
+ptmshepherd.localization_allowed_res=
+ptmshepherd.n_glyco=true
+ptmshepherd.normalization-psms=true
+ptmshepherd.normalization-scans=false
+ptmshepherd.output_extended=false
+ptmshepherd.peakpicking_mass_units=0
+ptmshepherd.peakpicking_minPsm=10
+ptmshepherd.peakpicking_promRatio=0.3
+ptmshepherd.peakpicking_width=0.002
+ptmshepherd.precursor_mass_units=0
+ptmshepherd.precursor_tol=0.01
+ptmshepherd.print_decoys=false
+ptmshepherd.print_full_glyco_params=false
+ptmshepherd.prob_mass=0.5
+ptmshepherd.remainder_masses=
+ptmshepherd.remove_glycan_delta_mass=true
+ptmshepherd.run-shepherd=false
+ptmshepherd.run_diagextract_mode=false
+ptmshepherd.run_diagmine_mode=false
+ptmshepherd.run_glyco_mode=false
+ptmshepherd.spectra_condPeaks=150
+ptmshepherd.spectra_condRatio=0.0001
+ptmshepherd.spectra_maxPrecursorCharge=4
+ptmshepherd.spectra_maxfragcharge=2
+ptmshepherd.spectra_ppmtol=20
+ptmshepherd.varmod_masses=
+quantitation.run-label-free-quant=false
+run-psm-validation=true
+run-validation-tab=true
+saintexpress.cmd-opts=
+saintexpress.max-replicates=10
+saintexpress.run-saint-express=false
+saintexpress.virtual-controls=100
+skyline.run-skyline=false
+skyline.skyline=false
+skyline.skyline-custom=false
+skyline.skyline-custom-path=
+skyline.skyline-daily=true
+skyline.skyline-fragment-tolerance=10
+skyline.skyline-mods-mode=Default
+skyline.skyline-precursor-tolerance=10
+skyline.use-ssl=false
+speclibgen.convert-pepxml=true
+speclibgen.convert-psm=false
+speclibgen.easypqp.extras.max_delta_ppm=15
+speclibgen.easypqp.extras.max_delta_unimod=0.02
+speclibgen.easypqp.extras.max_glycan_qval=1
+speclibgen.easypqp.extras.rt_lowess_fraction=0
+speclibgen.easypqp.fragment.a=false
+speclibgen.easypqp.fragment.b=true
+speclibgen.easypqp.fragment.c=false
+speclibgen.easypqp.fragment.x=false
+speclibgen.easypqp.fragment.y=true
+speclibgen.easypqp.fragment.z=false
+speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
+speclibgen.easypqp.labile_mode=Regular (not glyco)
+speclibgen.easypqp.neutral_loss=false
+speclibgen.easypqp.rt-cal=noiRT
+speclibgen.easypqp.select-file.text=
+speclibgen.easypqp.select-im-file.text=
+speclibgen.keep-intermediate-files=false
+speclibgen.run-speclibgen=true
+tab-run.delete_calibrated_mzml=false
+tab-run.delete_temp_files=false
+tab-run.export_matched_fragments=false
+tab-run.sub_mzml_prob_threshold=0.5
+tab-run.write_sub_mzml=false
+tmtintegrator.add_Ref=-1
+tmtintegrator.aggregation_method=0
+tmtintegrator.allow_overlabel=true
+tmtintegrator.allow_unlabeled=true
+tmtintegrator.best_psm=true
+tmtintegrator.channel_num=TMT-6
+tmtintegrator.extraction_tool=IonQuant
+tmtintegrator.glyco_qval=-1
+tmtintegrator.groupby=-1
+tmtintegrator.log2transformed=true
+tmtintegrator.max_pep_prob_thres=0
+tmtintegrator.min_ntt=0
+tmtintegrator.min_pep_prob=0.9
+tmtintegrator.min_percent=0.05
+tmtintegrator.min_purity=0.5
+tmtintegrator.min_resolution=0
+tmtintegrator.min_site_prob=-1
+tmtintegrator.min_snr=0
+tmtintegrator.mod_tag=none
+tmtintegrator.ms1_int=true
+tmtintegrator.outlier_removal=true
+tmtintegrator.philosopher-msstats=false
+tmtintegrator.print_RefInt=false
+tmtintegrator.prot_exclude=none
+tmtintegrator.prot_norm=0
+tmtintegrator.psm_norm=false
+tmtintegrator.quant_level=2
+tmtintegrator.ref_d_tag=Pool
+tmtintegrator.ref_tag=Bridge
+tmtintegrator.run-tmtintegrator=false
+tmtintegrator.tolerance=20
+tmtintegrator.top3_pep=true
+tmtintegrator.unique_gene=0
+tmtintegrator.unique_pep=false
+tmtintegrator.use_glycan_composition=false
+workflow.description=<p style\="margin-top\: 0">Complete workflow for DIA analysis using spectral library building and quantification using DIA-NN.</p>\n<p style\="margin-top\: 0"></p>\n<p style\="margin-top\: 0">Spectral library can be built from DDA data and/or DIA data, with direct identification from DIA data using MSFragger-DIA. All data are processed together using MSFragger (in DDA or DIA mode, respectively) - MSBooster - Percolator - ProteinProphet (Philosopher) - EasyPQP. The library is filtered to 1% FDR at the protein and peptide levels. DIA files annotated as 'DIA-Quant' are used for quantification only (i.e. not used for spectral library building). If building the library from fractionated DDA data only, in EasyPQP tab change RT Calibration option to "ciRT", or "iRT" if using organisms other than yeast or human (requires iRT peptides).</p>\n<p style\="margin-top\: 0"></p>\n<p style\="margin-top\: 0">Supports DDA RAW/.d files, mzML, and MGF files. DIA files with staggered windows should be mzML files demultiplexed using Proteowizard. For quantification using DIA-NN, Thermo/Sciex DIA files should be in mzML format, and .d for Bruker's timsTOF. diaPASEF DIA data will only be used for quantification (i.e. automatically considered as 'DIA-Quant' data type).</p>
+workflow.input.data-type.im-ms=false
+workflow.input.data-type.regular-ms=true
+workflow.misc.save-sdrf=true
+workflow.misc.sdrf-type=Default
+workflow.saved-with-ver=23.0-build14
diff -r 59fec1e2a6c3 -r b4f6df8fa89b workflows/Default.workflow
--- a/workflows/Default.workflow	Sun Mar 30 23:00:45 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,311 +0,0 @@
-# Workflow: Default
-
-crystalc.run-crystalc=false
-database.decoy-tag=rev_
-diann.fragpipe.cmd-opts=
-diann.heavy=
-diann.library=
-diann.light=
-diann.medium=
-diann.q-value=0.01
-diann.quantification-strategy=3
-diann.run-dia-nn=false
-diann.run-dia-plex=false
-diann.run-specific-protein-q-value=false
-diann.unrelated-runs=false
-diann.use-predicted-spectra=true
-diaumpire.AdjustFragIntensity=true
-diaumpire.BoostComplementaryIon=false
-diaumpire.CorrThreshold=0
-diaumpire.DeltaApex=0.2
-diaumpire.ExportPrecursorPeak=false
-diaumpire.Q1=true
-diaumpire.Q2=true
-diaumpire.Q3=true
-diaumpire.RFmax=500
-diaumpire.RPmax=25
-diaumpire.RTOverlap=0.3
-diaumpire.SE.EstimateBG=false
-diaumpire.SE.IsoPattern=0.3
-diaumpire.SE.MS1PPM=10
-diaumpire.SE.MS2PPM=20
-diaumpire.SE.MS2SN=1.1
-diaumpire.SE.MassDefectFilter=true
-diaumpire.SE.MassDefectOffset=0.1
-diaumpire.SE.NoMissedScan=1
-diaumpire.SE.SN=1.1
-diaumpire.run-diaumpire=false
-freequant.mz-tol=10
-freequant.rt-tol=0.4
-freequant.run-freequant=false
-ionquant.excludemods=
-ionquant.heavy=
-ionquant.imtol=0.05
-ionquant.ionfdr=0.01
-ionquant.light=
-ionquant.locprob=0.75
-ionquant.maxlfq=1
-ionquant.mbr=1
-ionquant.mbrimtol=0.05
-ionquant.mbrmincorr=0
-ionquant.mbrrttol=1
-ionquant.mbrtoprun=10
-ionquant.medium=
-ionquant.minfreq=0
-ionquant.minions=2
-ionquant.minisotopes=2
-ionquant.minscans=3
-ionquant.mztol=10
-ionquant.normalization=1
-ionquant.peptidefdr=1
-ionquant.proteinfdr=1
-ionquant.requantify=1
-ionquant.rttol=0.4
-ionquant.run-ionquant=true
-ionquant.tp=0
-ionquant.uniqueness=0
-ionquant.use-labeling=false
-ionquant.use-lfq=true
-ionquant.writeindex=0
-msbooster.predict-rt=true
-msbooster.predict-spectra=true
-msbooster.run-msbooster=true
-msbooster.use-correlated-features=false
-msfragger.Y_type_masses=
-msfragger.activation_types=all
-msfragger.add_topN_complementary=0
-msfragger.allowed_missed_cleavage_1=2
-msfragger.allowed_missed_cleavage_2=2
-msfragger.calibrate_mass=2
-msfragger.check_spectral_files=true
-msfragger.clip_nTerm_M=true
-msfragger.deisotope=1
-msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
-msfragger.deneutralloss=1
-msfragger.diagnostic_fragments=
-msfragger.diagnostic_intensity_filter=0
-msfragger.digest_max_length=50
-msfragger.digest_min_length=7
-msfragger.fragment_ion_series=b,y
-msfragger.fragment_mass_tolerance=20
-msfragger.fragment_mass_units=1
-msfragger.group_variable=0
-msfragger.intensity_transform=0
-msfragger.ion_series_definitions=
-msfragger.isotope_error=0/1/2/3
-msfragger.labile_search_mode=off
-msfragger.localize_delta_mass=false
-msfragger.mass_diff_to_variable_mod=0
-msfragger.mass_offsets=0
-msfragger.max_fragment_charge=2
-msfragger.max_variable_mods_combinations=5000
-msfragger.max_variable_mods_per_peptide=3
-msfragger.min_fragments_modelling=2
-msfragger.min_matched_fragments=4
-msfragger.min_sequence_matches=2
-msfragger.minimum_peaks=15
-msfragger.minimum_ratio=0.01
-msfragger.misc.fragger.clear-mz-hi=0
-msfragger.misc.fragger.clear-mz-lo=0
-msfragger.misc.fragger.digest-mass-hi=5000
-msfragger.misc.fragger.digest-mass-lo=500
-msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
-msfragger.misc.fragger.enzyme-dropdown-2=null
-msfragger.misc.fragger.precursor-charge-hi=4
-msfragger.misc.fragger.precursor-charge-lo=1
-msfragger.misc.fragger.remove-precursor-range-hi=1.5
-msfragger.misc.fragger.remove-precursor-range-lo=-1.5
-msfragger.misc.slice-db=1
-msfragger.num_enzyme_termini=2
-msfragger.output_format=pepXML_pin
-msfragger.output_max_expect=50
-msfragger.output_report_topN=1
-msfragger.output_report_topN_dia1=5
-msfragger.output_report_topN_dia2=3
-msfragger.override_charge=false
-msfragger.precursor_mass_lower=-20
-msfragger.precursor_mass_mode=selected
-msfragger.precursor_mass_units=1
-msfragger.precursor_mass_upper=20
-msfragger.precursor_true_tolerance=20
-msfragger.precursor_true_units=1
-msfragger.remainder_fragment_masses=
-msfragger.remove_precursor_peak=1
-msfragger.report_alternative_proteins=true
-msfragger.require_precursor=true
-msfragger.restrict_deltamass_to=all
-msfragger.reuse_dia_fragment_peaks=false
-msfragger.run-msfragger=true
-msfragger.search_enzyme_cut_1=KR
-msfragger.search_enzyme_cut_2=
-msfragger.search_enzyme_name_1=stricttrypsin
-msfragger.search_enzyme_name_2=null
-msfragger.search_enzyme_nocut_1=
-msfragger.search_enzyme_nocut_2=
-msfragger.search_enzyme_sense_1=C
-msfragger.search_enzyme_sense_2=C
-msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
-msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
-msfragger.track_zero_topN=0
-msfragger.use_all_mods_in_first_search=false
-msfragger.use_topN_peaks=150
-msfragger.write_calibrated_mzml=false
-msfragger.write_uncalibrated_mgf=false
-msfragger.zero_bin_accept_expect=0
-msfragger.zero_bin_mult_expect=1
-opair.activation1=HCD
-opair.activation2=ETD
-opair.filterOxonium=true
-opair.glyco_db=
-opair.max_glycans=4
-opair.max_isotope_error=2
-opair.min_isotope_error=0
-opair.ms1_tol=20
-opair.ms2_tol=20
-opair.oxonium_filtering_file=
-opair.oxonium_minimum_intensity=0.05
-opair.reverse_scan_order=false
-opair.run-opair=false
-opair.single_scan_type=false
-peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
-peptide-prophet.combine-pepxml=false
-peptide-prophet.run-peptide-prophet=false
-percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
-percolator.keep-tsv-files=false
-percolator.min-prob=0.5
-percolator.run-percolator=true
-phi-report.dont-use-prot-proph-file=false
-phi-report.filter=--sequential --picked --prot 0.01
-phi-report.pep-level-summary=false
-phi-report.philosoher-msstats=false
-phi-report.print-decoys=false
-phi-report.prot-level-summary=true
-phi-report.remove-contaminants=false
-phi-report.run-report=true
-protein-prophet.cmd-opts=--maxppmdiff 2000000
-protein-prophet.run-protein-prophet=true
-ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
-ptmprophet.run-ptmprophet=false
-ptmshepherd.adv_params=false
-ptmshepherd.annotation-common=false
-ptmshepherd.annotation-custom=false
-ptmshepherd.annotation-glyco=false
-ptmshepherd.annotation-unimod=true
-ptmshepherd.annotation_file=
-ptmshepherd.annotation_tol=0.01
-ptmshepherd.cap_y_ions=
-ptmshepherd.decoy_type=1
-ptmshepherd.diag_ions=
-ptmshepherd.diagextract_mode=false
-ptmshepherd.diagmine_diagMinFoldChange=3.0
-ptmshepherd.diagmine_diagMinSpecDiff=00.2
-ptmshepherd.diagmine_fragMinFoldChange=3.0
-ptmshepherd.diagmine_fragMinPropensity=00.1
-ptmshepherd.diagmine_fragMinSpecDiff=00.1
-ptmshepherd.diagmine_minIonsPerSpec=2
-ptmshepherd.diagmine_minPeps=25
-ptmshepherd.diagmine_mode=false
-ptmshepherd.diagmine_pepMinFoldChange=3.0
-ptmshepherd.diagmine_pepMinSpecDiff=00.2
-ptmshepherd.glyco_adducts=
-ptmshepherd.glyco_fdr=1.00
-ptmshepherd.glyco_isotope_max=3
-ptmshepherd.glyco_isotope_min=-1
-ptmshepherd.glyco_mode=false
-ptmshepherd.glyco_ppm_tol=50
-ptmshepherd.glycodatabase=
-ptmshepherd.histo_smoothbins=2
-ptmshepherd.iontype_a=false
-ptmshepherd.iontype_b=true
-ptmshepherd.iontype_c=true
-ptmshepherd.iontype_x=false
-ptmshepherd.iontype_y=true
-ptmshepherd.iontype_z=true
-ptmshepherd.localization_allowed_res=
-ptmshepherd.localization_background=4
-ptmshepherd.max_adducts=0
-ptmshepherd.n_glyco=true
-ptmshepherd.normalization-psms=true
-ptmshepherd.normalization-scans=false
-ptmshepherd.output_extended=false
-ptmshepherd.peakpicking_mass_units=0
-ptmshepherd.peakpicking_minPsm=10
-ptmshepherd.peakpicking_promRatio=0.3
-ptmshepherd.peakpicking_width=0.002
-ptmshepherd.precursor_mass_units=0
-ptmshepherd.precursor_tol=0.01
-ptmshepherd.print_decoys=false
-ptmshepherd.prob_dhexOx=2,0.5,0.1
-ptmshepherd.prob_dhexY=2,0.5
-ptmshepherd.prob_neuacOx=2,0.05,0.2
-ptmshepherd.prob_neugcOx=2,0.05,0.2
-ptmshepherd.prob_phosphoOx=2,0.05,0.2
-ptmshepherd.prob_regY=5,0.5
-ptmshepherd.prob_sulfoOx=2,0.05,0.2
-ptmshepherd.remainder_masses=
-ptmshepherd.remove_glycan_delta_mass=true
-ptmshepherd.run-shepherd=false
-ptmshepherd.spectra_maxfragcharge=2
-ptmshepherd.spectra_ppmtol=20
-ptmshepherd.varmod_masses=
-quantitation.run-label-free-quant=false
-run-psm-validation=true
-run-validation-tab=true
-saintexpress.fragpipe.cmd-opts=
-saintexpress.max-replicates=10
-saintexpress.run-saint-express=false
-saintexpress.virtual-controls=100
-speclibgen.easypqp.extras.max_delta_ppm=15
-speclibgen.easypqp.extras.max_delta_unimod=0.02
-speclibgen.easypqp.extras.rt_lowess_fraction=0
-speclibgen.easypqp.fragment.a=false
-speclibgen.easypqp.fragment.b=true
-speclibgen.easypqp.fragment.c=false
-speclibgen.easypqp.fragment.x=false
-speclibgen.easypqp.fragment.y=true
-speclibgen.easypqp.fragment.z=false
-speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
-speclibgen.easypqp.neutral_loss=false
-speclibgen.easypqp.rt-cal=ciRT
-speclibgen.easypqp.select-file.text=
-speclibgen.easypqp.select-im-file.text=
-speclibgen.keep-intermediate-files=false
-speclibgen.run-speclibgen=false
-tab-run.delete_calibrated_mzml=false
-tab-run.delete_temp_files=false
-tab-run.sub_mzml_prob_threshold=0.5
-tab-run.write_sub_mzml=false
-tmtintegrator.add_Ref=-1
-tmtintegrator.aggregation_method=0
-tmtintegrator.allow_overlabel=true
-tmtintegrator.allow_unlabeled=true
-tmtintegrator.best_psm=true
-tmtintegrator.channel_num=TMT-6
-tmtintegrator.dont-run-fq-lq=false
-tmtintegrator.glyco_qval=-1
-tmtintegrator.groupby=0
-tmtintegrator.log2transformed=true
-tmtintegrator.max_pep_prob_thres=0
-tmtintegrator.min_ntt=0
-tmtintegrator.min_pep_prob=0.9
-tmtintegrator.min_percent=0.05
-tmtintegrator.min_purity=0.5
-tmtintegrator.min_site_prob=-1
-tmtintegrator.mod_tag=none
-tmtintegrator.ms1_int=true
-tmtintegrator.outlier_removal=true
-tmtintegrator.print_RefInt=false
-tmtintegrator.prot_exclude=none
-tmtintegrator.prot_norm=0
-tmtintegrator.psm_norm=false
-tmtintegrator.quant_level=2
-tmtintegrator.ref_tag=Bridge
-tmtintegrator.run-tmtintegrator=false
-tmtintegrator.tolerance=20
-tmtintegrator.top3_pep=true
-tmtintegrator.unique_gene=0
-tmtintegrator.unique_pep=false
-tmtintegrator.use_glycan_composition=false
-workflow.input.data-type.im-ms=false
-workflow.input.data-type.regular-ms=true
-workflow.saved-with-ver=20.0-build5
diff -r 59fec1e2a6c3 -r b4f6df8fa89b workflows/LFQ-MBR.workflow
--- a/workflows/LFQ-MBR.workflow	Sun Mar 30 23:00:45 2025 +0000
+++ b/workflows/LFQ-MBR.workflow	Wed Oct 01 22:20:54 2025 +0000
@@ -2,18 +2,31 @@
 
 crystalc.run-crystalc=false
 database.decoy-tag=rev_
-diann.fragpipe.cmd-opts=
+diann.channel-normalization-strategy=0
+diann.cmd-opts=
+diann.generate-msstats=true
 diann.heavy=
 diann.library=
 diann.light=
 diann.medium=
+diann.min-site-prob=0.75
+diann.mod-tag=
 diann.q-value=0.01
 diann.quantification-strategy=3
+diann.quantification-strategy-2=2
 diann.run-dia-nn=false
 diann.run-dia-plex=false
 diann.run-specific-protein-q-value=false
 diann.unrelated-runs=false
-diann.use-predicted-spectra=true
+diann.use-predicted-spectra=false
+diatracer.corr-threshold=0.3
+diatracer.delta-apex-im=0.01
+diatracer.delta-apex-rt=3
+diatracer.mass-defect-filter=true
+diatracer.mass-defect-offset=0.1
+diatracer.rf-max=500
+diatracer.run-diatracer=false
+diatracer.write-intermediate-files=false
 diaumpire.AdjustFragIntensity=true
 diaumpire.BoostComplementaryIon=false
 diaumpire.CorrThreshold=0
@@ -35,10 +48,19 @@
 diaumpire.SE.NoMissedScan=1
 diaumpire.SE.SN=1.1
 diaumpire.run-diaumpire=false
+fpop.coadaptr.fpop.fpop_masses=
+fpop.coadaptr.fpop.run-fpop-coadaptr=false
+fpop.fragpipe.fpop.fpop-tmt=false
+fpop.fragpipe.fpop.label_control=
+fpop.fragpipe.fpop.label_fpop=
+fpop.fragpipe.fpop.region_size=1
+fpop.fragpipe.fpop.run-fpop=false
+fpop.fragpipe.fpop.subtract-control=false
 freequant.mz-tol=10
 freequant.rt-tol=0.4
 freequant.run-freequant=false
 ionquant.excludemods=
+ionquant.formula=
 ionquant.heavy=
 ionquant.imtol=0.05
 ionquant.ionfdr=0.01
@@ -52,7 +74,7 @@
 ionquant.mbrtoprun=10
 ionquant.medium=
 ionquant.minfreq=0
-ionquant.minions=2
+ionquant.minions=1
 ionquant.minisotopes=2
 ionquant.minscans=3
 ionquant.mztol=10
@@ -67,15 +89,24 @@
 ionquant.use-labeling=false
 ionquant.use-lfq=true
 ionquant.writeindex=0
+msbooster.find-best-im-model=false
+msbooster.find-best-rt-model=false
+msbooster.find-best-spectra-model=false
+msbooster.fragmentation-type=0
+msbooster.im-model=DIA-NN
+msbooster.koina-url=
+msbooster.predict-im=true
 msbooster.predict-rt=true
 msbooster.predict-spectra=true
+msbooster.rt-model=DIA-NN
 msbooster.run-msbooster=true
-msbooster.use-correlated-features=false
+msbooster.spectra-model=DIA-NN
+msbooster.spectral-library-path=
 msfragger.Y_type_masses=
 msfragger.activation_types=all
-msfragger.add_topN_complementary=0
 msfragger.allowed_missed_cleavage_1=2
 msfragger.allowed_missed_cleavage_2=2
+msfragger.analyzer_types=all
 msfragger.calibrate_mass=2
 msfragger.check_spectral_files=true
 msfragger.clip_nTerm_M=true
@@ -97,6 +128,7 @@
 msfragger.localize_delta_mass=false
 msfragger.mass_diff_to_variable_mod=0
 msfragger.mass_offsets=0
+msfragger.mass_offsets_detailed=
 msfragger.max_fragment_charge=2
 msfragger.max_variable_mods_combinations=5000
 msfragger.max_variable_mods_per_peptide=3
@@ -120,8 +152,8 @@
 msfragger.output_format=pepXML_pin
 msfragger.output_max_expect=50
 msfragger.output_report_topN=1
+msfragger.output_report_topN_dda_plus=5
 msfragger.output_report_topN_dia1=5
-msfragger.output_report_topN_dia2=3
 msfragger.override_charge=false
 msfragger.precursor_mass_lower=-20
 msfragger.precursor_mass_mode=selected
@@ -148,13 +180,14 @@
 msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
 msfragger.track_zero_topN=0
 msfragger.use_all_mods_in_first_search=false
+msfragger.use_detailed_offsets=false
 msfragger.use_topN_peaks=150
 msfragger.write_calibrated_mzml=false
-msfragger.write_uncalibrated_mgf=false
 msfragger.zero_bin_accept_expect=0
 msfragger.zero_bin_mult_expect=1
 opair.activation1=HCD
 opair.activation2=ETD
+opair.allowed_sites=
 opair.filterOxonium=true
 opair.glyco_db=
 opair.max_glycans=4
@@ -175,16 +208,16 @@
 percolator.min-prob=0.5
 percolator.run-percolator=true
 phi-report.dont-use-prot-proph-file=false
-phi-report.filter=--sequential --prot 0.01
+phi-report.filter=--sequential --prot 0.01 --picked
 phi-report.pep-level-summary=false
-phi-report.philosoher-msstats=false
 phi-report.print-decoys=false
 phi-report.prot-level-summary=false
 phi-report.remove-contaminants=false
 phi-report.run-report=true
 protein-prophet.cmd-opts=--maxppmdiff 2000000
 protein-prophet.run-protein-prophet=true
-ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
+ptmprophet.cmdline=NOSTACK KEEPOLD STATIC FRAGPPMTOL\=10 EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5
+ptmprophet.override-defaults=false
 ptmprophet.run-ptmprophet=false
 ptmshepherd.adv_params=false
 ptmshepherd.annotation-common=false
@@ -196,7 +229,6 @@
 ptmshepherd.cap_y_ions=
 ptmshepherd.decoy_type=1
 ptmshepherd.diag_ions=
-ptmshepherd.diagextract_mode=false
 ptmshepherd.diagmine_diagMinFoldChange=3.0
 ptmshepherd.diagmine_diagMinSpecDiff=00.2
 ptmshepherd.diagmine_fragMinFoldChange=3.0
@@ -204,14 +236,11 @@
 ptmshepherd.diagmine_fragMinSpecDiff=00.1
 ptmshepherd.diagmine_minIonsPerSpec=2
 ptmshepherd.diagmine_minPeps=25
-ptmshepherd.diagmine_mode=false
 ptmshepherd.diagmine_pepMinFoldChange=3.0
 ptmshepherd.diagmine_pepMinSpecDiff=00.2
-ptmshepherd.glyco_adducts=
 ptmshepherd.glyco_fdr=1.00
 ptmshepherd.glyco_isotope_max=3
 ptmshepherd.glyco_isotope_min=-1
-ptmshepherd.glyco_mode=false
 ptmshepherd.glyco_ppm_tol=50
 ptmshepherd.glycodatabase=
 ptmshepherd.histo_smoothbins=2
@@ -221,9 +250,9 @@
 ptmshepherd.iontype_x=false
 ptmshepherd.iontype_y=true
 ptmshepherd.iontype_z=false
+ptmshepherd.iterloc_maxEpoch=100
+ptmshepherd.iterloc_mode=false
 ptmshepherd.localization_allowed_res=
-ptmshepherd.localization_background=4
-ptmshepherd.max_adducts=0
 ptmshepherd.n_glyco=true
 ptmshepherd.normalization-psms=true
 ptmshepherd.normalization-scans=false
@@ -235,28 +264,41 @@
 ptmshepherd.precursor_mass_units=0
 ptmshepherd.precursor_tol=0.01
 ptmshepherd.print_decoys=false
-ptmshepherd.prob_dhexOx=2,0.5,0.1
-ptmshepherd.prob_dhexY=2,0.5
-ptmshepherd.prob_neuacOx=2,0.05,0.2
-ptmshepherd.prob_neugcOx=2,0.05,0.2
-ptmshepherd.prob_phosphoOx=2,0.05,0.2
-ptmshepherd.prob_regY=5,0.5
-ptmshepherd.prob_sulfoOx=2,0.05,0.2
+ptmshepherd.print_full_glyco_params=false
+ptmshepherd.prob_mass=0.5
 ptmshepherd.remainder_masses=
 ptmshepherd.remove_glycan_delta_mass=true
 ptmshepherd.run-shepherd=false
+ptmshepherd.run_diagextract_mode=false
+ptmshepherd.run_diagmine_mode=false
+ptmshepherd.run_glyco_mode=false
+ptmshepherd.spectra_condPeaks=150
+ptmshepherd.spectra_condRatio=0.0001
+ptmshepherd.spectra_maxPrecursorCharge=4
 ptmshepherd.spectra_maxfragcharge=2
 ptmshepherd.spectra_ppmtol=20
 ptmshepherd.varmod_masses=
 quantitation.run-label-free-quant=true
 run-psm-validation=true
 run-validation-tab=true
-saintexpress.fragpipe.cmd-opts=
+saintexpress.cmd-opts=
 saintexpress.max-replicates=10
 saintexpress.run-saint-express=false
 saintexpress.virtual-controls=100
+skyline.run-skyline=false
+skyline.skyline=false
+skyline.skyline-custom=false
+skyline.skyline-custom-path=
+skyline.skyline-daily=true
+skyline.skyline-fragment-tolerance=10
+skyline.skyline-mods-mode=Default
+skyline.skyline-precursor-tolerance=10
+skyline.use-ssl=false
+speclibgen.convert-pepxml=true
+speclibgen.convert-psm=false
 speclibgen.easypqp.extras.max_delta_ppm=15
 speclibgen.easypqp.extras.max_delta_unimod=0.02
+speclibgen.easypqp.extras.max_glycan_qval=1
 speclibgen.easypqp.extras.rt_lowess_fraction=0
 speclibgen.easypqp.fragment.a=false
 speclibgen.easypqp.fragment.b=true
@@ -265,6 +307,7 @@
 speclibgen.easypqp.fragment.y=true
 speclibgen.easypqp.fragment.z=false
 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
+speclibgen.easypqp.labile_mode=Regular (not glyco)
 speclibgen.easypqp.neutral_loss=false
 speclibgen.easypqp.rt-cal=noiRT
 speclibgen.easypqp.select-file.text=
@@ -273,6 +316,7 @@
 speclibgen.run-speclibgen=false
 tab-run.delete_calibrated_mzml=false
 tab-run.delete_temp_files=false
+tab-run.export_matched_fragments=false
 tab-run.sub_mzml_prob_threshold=0.5
 tab-run.write_sub_mzml=false
 tmtintegrator.add_Ref=-1
@@ -281,24 +325,28 @@
 tmtintegrator.allow_unlabeled=true
 tmtintegrator.best_psm=true
 tmtintegrator.channel_num=TMT-6
-tmtintegrator.dont-run-fq-lq=false
+tmtintegrator.extraction_tool=IonQuant
 tmtintegrator.glyco_qval=-1
-tmtintegrator.groupby=0
+tmtintegrator.groupby=-1
 tmtintegrator.log2transformed=true
 tmtintegrator.max_pep_prob_thres=0
 tmtintegrator.min_ntt=0
 tmtintegrator.min_pep_prob=0.9
 tmtintegrator.min_percent=0.05
 tmtintegrator.min_purity=0.5
+tmtintegrator.min_resolution=0
 tmtintegrator.min_site_prob=-1
+tmtintegrator.min_snr=0
 tmtintegrator.mod_tag=none
 tmtintegrator.ms1_int=true
 tmtintegrator.outlier_removal=true
+tmtintegrator.philosopher-msstats=false
 tmtintegrator.print_RefInt=false
 tmtintegrator.prot_exclude=none
 tmtintegrator.prot_norm=0
 tmtintegrator.psm_norm=false
 tmtintegrator.quant_level=2
+tmtintegrator.ref_d_tag=Pool
 tmtintegrator.ref_tag=Bridge
 tmtintegrator.run-tmtintegrator=false
 tmtintegrator.tolerance=20
@@ -309,4 +357,6 @@
 workflow.description=Perform closed search, followed by label free quantification with match-between-runs using IonQuant. If using mzML files, need to choose the right MS data type (Regular MS vs IM-MS). Need to assign runs to experiments.
 workflow.input.data-type.im-ms=false
 workflow.input.data-type.regular-ms=true
-workflow.saved-with-ver=20.0-build5
+workflow.misc.save-sdrf=true
+workflow.misc.sdrf-type=Default
+workflow.saved-with-ver=23.0-build14
diff -r 59fec1e2a6c3 -r b4f6df8fa89b workflows/Nonspecific-HLA.workflow
--- a/workflows/Nonspecific-HLA.workflow	Sun Mar 30 23:00:45 2025 +0000
+++ b/workflows/Nonspecific-HLA.workflow	Wed Oct 01 22:20:54 2025 +0000
@@ -2,18 +2,31 @@
 
 crystalc.run-crystalc=false
 database.decoy-tag=rev_
-diann.fragpipe.cmd-opts=
+diann.channel-normalization-strategy=0
+diann.cmd-opts=
+diann.generate-msstats=true
 diann.heavy=
 diann.library=
 diann.light=
 diann.medium=
+diann.min-site-prob=0.75
+diann.mod-tag=
 diann.q-value=0.01
 diann.quantification-strategy=3
+diann.quantification-strategy-2=2
 diann.run-dia-nn=false
 diann.run-dia-plex=false
 diann.run-specific-protein-q-value=false
 diann.unrelated-runs=false
 diann.use-predicted-spectra=false
+diatracer.corr-threshold=0.3
+diatracer.delta-apex-im=0.01
+diatracer.delta-apex-rt=3
+diatracer.mass-defect-filter=true
+diatracer.mass-defect-offset=0.1
+diatracer.rf-max=500
+diatracer.run-diatracer=false
+diatracer.write-intermediate-files=false
 diaumpire.AdjustFragIntensity=true
 diaumpire.BoostComplementaryIon=false
 diaumpire.CorrThreshold=0
@@ -35,10 +48,19 @@
 diaumpire.SE.NoMissedScan=1
 diaumpire.SE.SN=1.1
 diaumpire.run-diaumpire=false
+fpop.coadaptr.fpop.fpop_masses=
+fpop.coadaptr.fpop.run-fpop-coadaptr=false
+fpop.fragpipe.fpop.fpop-tmt=false
+fpop.fragpipe.fpop.label_control=
+fpop.fragpipe.fpop.label_fpop=
+fpop.fragpipe.fpop.region_size=1
+fpop.fragpipe.fpop.run-fpop=false
+fpop.fragpipe.fpop.subtract-control=false
 freequant.mz-tol=10
 freequant.rt-tol=0.4
 freequant.run-freequant=false
 ionquant.excludemods=
+ionquant.formula=
 ionquant.heavy=
 ionquant.imtol=0.05
 ionquant.ionfdr=0.01
@@ -52,7 +74,7 @@
 ionquant.mbrtoprun=10
 ionquant.medium=
 ionquant.minfreq=0
-ionquant.minions=2
+ionquant.minions=1
 ionquant.minisotopes=2
 ionquant.minscans=3
 ionquant.mztol=10
@@ -67,15 +89,24 @@
 ionquant.use-labeling=false
 ionquant.use-lfq=true
 ionquant.writeindex=0
+msbooster.find-best-im-model=false
+msbooster.find-best-rt-model=false
+msbooster.find-best-spectra-model=false
+msbooster.fragmentation-type=0
+msbooster.im-model=DIA-NN
+msbooster.koina-url=
+msbooster.predict-im=true
 msbooster.predict-rt=true
 msbooster.predict-spectra=true
+msbooster.rt-model=DIA-NN
 msbooster.run-msbooster=true
-msbooster.use-correlated-features=false
+msbooster.spectra-model=DIA-NN
+msbooster.spectral-library-path=
 msfragger.Y_type_masses=
 msfragger.activation_types=all
-msfragger.add_topN_complementary=0
 msfragger.allowed_missed_cleavage_1=2
 msfragger.allowed_missed_cleavage_2=2
+msfragger.analyzer_types=all
 msfragger.calibrate_mass=2
 msfragger.check_spectral_files=true
 msfragger.clip_nTerm_M=true
@@ -97,6 +128,7 @@
 msfragger.localize_delta_mass=false
 msfragger.mass_diff_to_variable_mod=0
 msfragger.mass_offsets=0
+msfragger.mass_offsets_detailed=
 msfragger.max_fragment_charge=2
 msfragger.max_variable_mods_combinations=5000
 msfragger.max_variable_mods_per_peptide=3
@@ -120,8 +152,8 @@
 msfragger.output_format=pepXML_pin
 msfragger.output_max_expect=50
 msfragger.output_report_topN=1
+msfragger.output_report_topN_dda_plus=5
 msfragger.output_report_topN_dia1=5
-msfragger.output_report_topN_dia2=3
 msfragger.override_charge=false
 msfragger.precursor_mass_lower=-20
 msfragger.precursor_mass_mode=selected
@@ -136,8 +168,8 @@
 msfragger.restrict_deltamass_to=all
 msfragger.reuse_dia_fragment_peaks=false
 msfragger.run-msfragger=true
-msfragger.search_enzyme_cut_1=-
-msfragger.search_enzyme_cut_2=-
+msfragger.search_enzyme_cut_1=@
+msfragger.search_enzyme_cut_2=@
 msfragger.search_enzyme_name_1=nonspecific
 msfragger.search_enzyme_name_2=null
 msfragger.search_enzyme_nocut_1=
@@ -148,13 +180,14 @@
 msfragger.table.var-mods=15.9949,M,true,2; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQ,true,1; -18.0106,nE,true,1; 119.0041,C,true,1; 0.98402,N,false,1; 8.014199,K,false,1; 10.008269,R,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
 msfragger.track_zero_topN=0
 msfragger.use_all_mods_in_first_search=false
+msfragger.use_detailed_offsets=false
 msfragger.use_topN_peaks=300
 msfragger.write_calibrated_mzml=false
-msfragger.write_uncalibrated_mgf=false
 msfragger.zero_bin_accept_expect=0
 msfragger.zero_bin_mult_expect=1
 opair.activation1=HCD
 opair.activation2=ETD
+opair.allowed_sites=
 opair.filterOxonium=true
 opair.glyco_db=
 opair.max_glycans=4
@@ -177,7 +210,6 @@
 phi-report.dont-use-prot-proph-file=false
 phi-report.filter=--sequential --prot 1
 phi-report.pep-level-summary=true
-phi-report.philosoher-msstats=false
 phi-report.print-decoys=false
 phi-report.prot-level-summary=true
 phi-report.remove-contaminants=false
@@ -185,6 +217,7 @@
 protein-prophet.cmd-opts=--maxppmdiff 2000000
 protein-prophet.run-protein-prophet=true
 ptmprophet.cmdline=
+ptmprophet.override-defaults=false
 ptmprophet.run-ptmprophet=false
 ptmshepherd.adv_params=false
 ptmshepherd.annotation-common=false
@@ -196,7 +229,6 @@
 ptmshepherd.cap_y_ions=
 ptmshepherd.decoy_type=1
 ptmshepherd.diag_ions=
-ptmshepherd.diagextract_mode=false
 ptmshepherd.diagmine_diagMinFoldChange=3.0
 ptmshepherd.diagmine_diagMinSpecDiff=00.2
 ptmshepherd.diagmine_fragMinFoldChange=3.0
@@ -204,14 +236,11 @@
 ptmshepherd.diagmine_fragMinSpecDiff=00.1
 ptmshepherd.diagmine_minIonsPerSpec=2
 ptmshepherd.diagmine_minPeps=25
-ptmshepherd.diagmine_mode=false
 ptmshepherd.diagmine_pepMinFoldChange=3.0
 ptmshepherd.diagmine_pepMinSpecDiff=00.2
-ptmshepherd.glyco_adducts=
 ptmshepherd.glyco_fdr=1.00
 ptmshepherd.glyco_isotope_max=3
 ptmshepherd.glyco_isotope_min=-1
-ptmshepherd.glyco_mode=false
 ptmshepherd.glyco_ppm_tol=50
 ptmshepherd.glycodatabase=
 ptmshepherd.histo_smoothbins=2
@@ -221,9 +250,9 @@
 ptmshepherd.iontype_x=false
 ptmshepherd.iontype_y=true
 ptmshepherd.iontype_z=false
+ptmshepherd.iterloc_maxEpoch=100
+ptmshepherd.iterloc_mode=false
 ptmshepherd.localization_allowed_res=
-ptmshepherd.localization_background=4
-ptmshepherd.max_adducts=0
 ptmshepherd.n_glyco=true
 ptmshepherd.normalization-psms=true
 ptmshepherd.normalization-scans=false
@@ -235,28 +264,41 @@
 ptmshepherd.precursor_mass_units=0
 ptmshepherd.precursor_tol=0.01
 ptmshepherd.print_decoys=false
-ptmshepherd.prob_dhexOx=2,0.5,0.1
-ptmshepherd.prob_dhexY=2,0.5
-ptmshepherd.prob_neuacOx=2,0.05,0.2
-ptmshepherd.prob_neugcOx=2,0.05,0.2
-ptmshepherd.prob_phosphoOx=2,0.05,0.2
-ptmshepherd.prob_regY=5,0.5
-ptmshepherd.prob_sulfoOx=2,0.05,0.2
+ptmshepherd.print_full_glyco_params=false
+ptmshepherd.prob_mass=0.5
 ptmshepherd.remainder_masses=
 ptmshepherd.remove_glycan_delta_mass=true
 ptmshepherd.run-shepherd=false
+ptmshepherd.run_diagextract_mode=false
+ptmshepherd.run_diagmine_mode=false
+ptmshepherd.run_glyco_mode=false
+ptmshepherd.spectra_condPeaks=150
+ptmshepherd.spectra_condRatio=0.0001
+ptmshepherd.spectra_maxPrecursorCharge=4
 ptmshepherd.spectra_maxfragcharge=2
 ptmshepherd.spectra_ppmtol=20
 ptmshepherd.varmod_masses=
 quantitation.run-label-free-quant=false
 run-psm-validation=true
 run-validation-tab=true
-saintexpress.fragpipe.cmd-opts=
+saintexpress.cmd-opts=
 saintexpress.max-replicates=10
 saintexpress.run-saint-express=false
 saintexpress.virtual-controls=100
+skyline.run-skyline=false
+skyline.skyline=false
+skyline.skyline-custom=false
+skyline.skyline-custom-path=
+skyline.skyline-daily=true
+skyline.skyline-fragment-tolerance=10
+skyline.skyline-mods-mode=Default
+skyline.skyline-precursor-tolerance=10
+skyline.use-ssl=false
+speclibgen.convert-pepxml=true
+speclibgen.convert-psm=false
 speclibgen.easypqp.extras.max_delta_ppm=15
 speclibgen.easypqp.extras.max_delta_unimod=0.02
+speclibgen.easypqp.extras.max_glycan_qval=1
 speclibgen.easypqp.extras.rt_lowess_fraction=0
 speclibgen.easypqp.fragment.a=false
 speclibgen.easypqp.fragment.b=true
@@ -265,6 +307,7 @@
 speclibgen.easypqp.fragment.y=true
 speclibgen.easypqp.fragment.z=false
 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
+speclibgen.easypqp.labile_mode=Regular (not glyco)
 speclibgen.easypqp.neutral_loss=false
 speclibgen.easypqp.rt-cal=noiRT
 speclibgen.easypqp.select-file.text=
@@ -273,6 +316,7 @@
 speclibgen.run-speclibgen=false
 tab-run.delete_calibrated_mzml=false
 tab-run.delete_temp_files=false
+tab-run.export_matched_fragments=false
 tab-run.sub_mzml_prob_threshold=0.5
 tab-run.write_sub_mzml=false
 tmtintegrator.add_Ref=-1
@@ -281,24 +325,28 @@
 tmtintegrator.allow_unlabeled=true
 tmtintegrator.best_psm=true
 tmtintegrator.channel_num=TMT-6
-tmtintegrator.dont-run-fq-lq=false
+tmtintegrator.extraction_tool=IonQuant
 tmtintegrator.glyco_qval=-1
-tmtintegrator.groupby=0
+tmtintegrator.groupby=-1
 tmtintegrator.log2transformed=true
 tmtintegrator.max_pep_prob_thres=0
 tmtintegrator.min_ntt=0
 tmtintegrator.min_pep_prob=0.9
 tmtintegrator.min_percent=0.05
 tmtintegrator.min_purity=0.5
+tmtintegrator.min_resolution=0
 tmtintegrator.min_site_prob=-1
+tmtintegrator.min_snr=0
 tmtintegrator.mod_tag=none
 tmtintegrator.ms1_int=true
 tmtintegrator.outlier_removal=true
+tmtintegrator.philosopher-msstats=false
 tmtintegrator.print_RefInt=false
 tmtintegrator.prot_exclude=none
 tmtintegrator.prot_norm=0
 tmtintegrator.psm_norm=false
 tmtintegrator.quant_level=2
+tmtintegrator.ref_d_tag=Pool
 tmtintegrator.ref_tag=Bridge
 tmtintegrator.run-tmtintegrator=false
 tmtintegrator.tolerance=20
@@ -309,4 +357,6 @@
 workflow.description=<p style\="margin-top\: 0in">Nonspecific search, with recommended settings for HLA peptides. Peptide length 7-25. MSFragger search assumes cysteines were not alkylated (i.e. samples were not treated with iodoacetamide). Cysteinylation (C+119) is specified as variable modification. MSFragger rescoring with MSBooster. PSM validation with Percolator. Protein FDR filter is not applied, so each output file (PSM, ion, peptide) is filtered to 1% FDR at that level. If needed, extend to add label-free quantifcation (using IonQuant) or spectral library building with EasyPQP.</p>
 workflow.input.data-type.im-ms=false
 workflow.input.data-type.regular-ms=true
-workflow.saved-with-ver=20.0-build5
+workflow.misc.save-sdrf=true
+workflow.misc.sdrf-type=Default
+workflow.saved-with-ver=23.0-build14
diff -r 59fec1e2a6c3 -r b4f6df8fa89b workflows/Open.workflow
--- a/workflows/Open.workflow	Sun Mar 30 23:00:45 2025 +0000
+++ b/workflows/Open.workflow	Wed Oct 01 22:20:54 2025 +0000
@@ -2,18 +2,31 @@
 
 crystalc.run-crystalc=true
 database.decoy-tag=rev_
-diann.fragpipe.cmd-opts=
+diann.channel-normalization-strategy=0
+diann.cmd-opts=
+diann.generate-msstats=true
 diann.heavy=
 diann.library=
 diann.light=
 diann.medium=
+diann.min-site-prob=0.75
+diann.mod-tag=
 diann.q-value=0.01
 diann.quantification-strategy=3
+diann.quantification-strategy-2=2
 diann.run-dia-nn=false
 diann.run-dia-plex=false
 diann.run-specific-protein-q-value=false
 diann.unrelated-runs=false
-diann.use-predicted-spectra=true
+diann.use-predicted-spectra=false
+diatracer.corr-threshold=0.3
+diatracer.delta-apex-im=0.01
+diatracer.delta-apex-rt=3
+diatracer.mass-defect-filter=true
+diatracer.mass-defect-offset=0.1
+diatracer.rf-max=500
+diatracer.run-diatracer=false
+diatracer.write-intermediate-files=false
 diaumpire.AdjustFragIntensity=true
 diaumpire.BoostComplementaryIon=false
 diaumpire.CorrThreshold=0
@@ -35,10 +48,19 @@
 diaumpire.SE.NoMissedScan=1
 diaumpire.SE.SN=1.1
 diaumpire.run-diaumpire=false
+fpop.coadaptr.fpop.fpop_masses=
+fpop.coadaptr.fpop.run-fpop-coadaptr=false
+fpop.fragpipe.fpop.fpop-tmt=false
+fpop.fragpipe.fpop.label_control=
+fpop.fragpipe.fpop.label_fpop=
+fpop.fragpipe.fpop.region_size=1
+fpop.fragpipe.fpop.run-fpop=false
+fpop.fragpipe.fpop.subtract-control=false
 freequant.mz-tol=10
 freequant.rt-tol=0.4
 freequant.run-freequant=true
 ionquant.excludemods=
+ionquant.formula=
 ionquant.heavy=
 ionquant.imtol=0.05
 ionquant.ionfdr=0.01
@@ -52,7 +74,7 @@
 ionquant.mbrtoprun=10
 ionquant.medium=
 ionquant.minfreq=0
-ionquant.minions=2
+ionquant.minions=1
 ionquant.minisotopes=2
 ionquant.minscans=3
 ionquant.mztol=10
@@ -67,15 +89,24 @@
 ionquant.use-labeling=false
 ionquant.use-lfq=true
 ionquant.writeindex=0
+msbooster.find-best-im-model=false
+msbooster.find-best-rt-model=false
+msbooster.find-best-spectra-model=false
+msbooster.fragmentation-type=0
+msbooster.im-model=DIA-NN
+msbooster.koina-url=
+msbooster.predict-im=true
 msbooster.predict-rt=true
 msbooster.predict-spectra=true
+msbooster.rt-model=DIA-NN
 msbooster.run-msbooster=false
-msbooster.use-correlated-features=false
+msbooster.spectra-model=DIA-NN
+msbooster.spectral-library-path=
 msfragger.Y_type_masses=
 msfragger.activation_types=all
-msfragger.add_topN_complementary=0
 msfragger.allowed_missed_cleavage_1=2
 msfragger.allowed_missed_cleavage_2=2
+msfragger.analyzer_types=all
 msfragger.calibrate_mass=2
 msfragger.check_spectral_files=true
 msfragger.clip_nTerm_M=true
@@ -97,6 +128,7 @@
 msfragger.localize_delta_mass=true
 msfragger.mass_diff_to_variable_mod=0
 msfragger.mass_offsets=0
+msfragger.mass_offsets_detailed=
 msfragger.max_fragment_charge=2
 msfragger.max_variable_mods_combinations=5000
 msfragger.max_variable_mods_per_peptide=3
@@ -120,8 +152,8 @@
 msfragger.output_format=pepXML_pin
 msfragger.output_max_expect=50
 msfragger.output_report_topN=1
+msfragger.output_report_topN_dda_plus=5
 msfragger.output_report_topN_dia1=5
-msfragger.output_report_topN_dia2=3
 msfragger.override_charge=false
 msfragger.precursor_mass_lower=-150
 msfragger.precursor_mass_mode=corrected
@@ -148,13 +180,14 @@
 msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
 msfragger.track_zero_topN=0
 msfragger.use_all_mods_in_first_search=false
+msfragger.use_detailed_offsets=false
 msfragger.use_topN_peaks=150
 msfragger.write_calibrated_mzml=false
-msfragger.write_uncalibrated_mgf=false
 msfragger.zero_bin_accept_expect=0
 msfragger.zero_bin_mult_expect=1
 opair.activation1=HCD
 opair.activation2=ETD
+opair.allowed_sites=
 opair.filterOxonium=true
 opair.glyco_db=
 opair.max_glycans=4
@@ -177,7 +210,6 @@
 phi-report.dont-use-prot-proph-file=false
 phi-report.filter=--sequential --prot 0.01 --mapmods
 phi-report.pep-level-summary=false
-phi-report.philosoher-msstats=false
 phi-report.print-decoys=false
 phi-report.prot-level-summary=true
 phi-report.remove-contaminants=false
@@ -185,6 +217,7 @@
 protein-prophet.cmd-opts=--maxppmdiff 2000000
 protein-prophet.run-protein-prophet=true
 ptmprophet.cmdline=
+ptmprophet.override-defaults=false
 ptmprophet.run-ptmprophet=false
 ptmshepherd.adv_params=false
 ptmshepherd.annotation-common=false
@@ -196,7 +229,6 @@
 ptmshepherd.cap_y_ions=
 ptmshepherd.decoy_type=1
 ptmshepherd.diag_ions=
-ptmshepherd.diagextract_mode=false
 ptmshepherd.diagmine_diagMinFoldChange=3.0
 ptmshepherd.diagmine_diagMinSpecDiff=25
 ptmshepherd.diagmine_fragMinFoldChange=3.0
@@ -204,14 +236,11 @@
 ptmshepherd.diagmine_fragMinSpecDiff=25
 ptmshepherd.diagmine_minIonsPerSpec=2
 ptmshepherd.diagmine_minPeps=25
-ptmshepherd.diagmine_mode=false
 ptmshepherd.diagmine_pepMinFoldChange=3.0
 ptmshepherd.diagmine_pepMinSpecDiff=25
-ptmshepherd.glyco_adducts=
 ptmshepherd.glyco_fdr=1.00
 ptmshepherd.glyco_isotope_max=3
 ptmshepherd.glyco_isotope_min=-1
-ptmshepherd.glyco_mode=false
 ptmshepherd.glyco_ppm_tol=50
 ptmshepherd.glycodatabase=
 ptmshepherd.histo_smoothbins=2
@@ -221,9 +250,9 @@
 ptmshepherd.iontype_x=false
 ptmshepherd.iontype_y=true
 ptmshepherd.iontype_z=false
+ptmshepherd.iterloc_maxEpoch=100
+ptmshepherd.iterloc_mode=false
 ptmshepherd.localization_allowed_res=
-ptmshepherd.localization_background=4
-ptmshepherd.max_adducts=0
 ptmshepherd.n_glyco=true
 ptmshepherd.normalization-psms=true
 ptmshepherd.normalization-scans=false
@@ -235,28 +264,41 @@
 ptmshepherd.precursor_mass_units=0
 ptmshepherd.precursor_tol=0.01
 ptmshepherd.print_decoys=false
-ptmshepherd.prob_dhexOx=2,0.5,0.1
-ptmshepherd.prob_dhexY=2,0.5
-ptmshepherd.prob_neuacOx=2,0.05,0.2
-ptmshepherd.prob_neugcOx=2,0.05,0.2
-ptmshepherd.prob_phosphoOx=2,0.05,0.2
-ptmshepherd.prob_regY=5,0.5
-ptmshepherd.prob_sulfoOx=2,0.05,0.2
+ptmshepherd.print_full_glyco_params=false
+ptmshepherd.prob_mass=0.5
 ptmshepherd.remainder_masses=
 ptmshepherd.remove_glycan_delta_mass=true
 ptmshepherd.run-shepherd=true
+ptmshepherd.run_diagextract_mode=false
+ptmshepherd.run_diagmine_mode=false
+ptmshepherd.run_glyco_mode=false
+ptmshepherd.spectra_condPeaks=150
+ptmshepherd.spectra_condRatio=0.0001
+ptmshepherd.spectra_maxPrecursorCharge=4
 ptmshepherd.spectra_maxfragcharge=1
 ptmshepherd.spectra_ppmtol=20
 ptmshepherd.varmod_masses=
 quantitation.run-label-free-quant=false
 run-psm-validation=true
 run-validation-tab=true
-saintexpress.fragpipe.cmd-opts=
+saintexpress.cmd-opts=
 saintexpress.max-replicates=10
 saintexpress.run-saint-express=false
 saintexpress.virtual-controls=100
+skyline.run-skyline=false
+skyline.skyline=false
+skyline.skyline-custom=false
+skyline.skyline-custom-path=
+skyline.skyline-daily=true
+skyline.skyline-fragment-tolerance=10
+skyline.skyline-mods-mode=Default
+skyline.skyline-precursor-tolerance=10
+skyline.use-ssl=false
+speclibgen.convert-pepxml=true
+speclibgen.convert-psm=false
 speclibgen.easypqp.extras.max_delta_ppm=15
 speclibgen.easypqp.extras.max_delta_unimod=0.02
+speclibgen.easypqp.extras.max_glycan_qval=1
 speclibgen.easypqp.extras.rt_lowess_fraction=0
 speclibgen.easypqp.fragment.a=false
 speclibgen.easypqp.fragment.b=true
@@ -265,6 +307,7 @@
 speclibgen.easypqp.fragment.y=true
 speclibgen.easypqp.fragment.z=false
 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
+speclibgen.easypqp.labile_mode=Regular (not glyco)
 speclibgen.easypqp.neutral_loss=false
 speclibgen.easypqp.rt-cal=ciRT
 speclibgen.easypqp.select-file.text=
@@ -273,6 +316,7 @@
 speclibgen.run-speclibgen=false
 tab-run.delete_calibrated_mzml=false
 tab-run.delete_temp_files=false
+tab-run.export_matched_fragments=false
 tab-run.sub_mzml_prob_threshold=0.5
 tab-run.write_sub_mzml=false
 tmtintegrator.add_Ref=-1
@@ -281,7 +325,7 @@
 tmtintegrator.allow_unlabeled=false
 tmtintegrator.best_psm=true
 tmtintegrator.channel_num=TMT-10
-tmtintegrator.dont-run-fq-lq=false
+tmtintegrator.extraction_tool=IonQuant
 tmtintegrator.glyco_qval=-1
 tmtintegrator.groupby=-1
 tmtintegrator.log2transformed=true
@@ -290,15 +334,19 @@
 tmtintegrator.min_pep_prob=0.9
 tmtintegrator.min_percent=0.05
 tmtintegrator.min_purity=0.5
+tmtintegrator.min_resolution=0
 tmtintegrator.min_site_prob=-1
+tmtintegrator.min_snr=0
 tmtintegrator.mod_tag=none
 tmtintegrator.ms1_int=true
 tmtintegrator.outlier_removal=true
+tmtintegrator.philosopher-msstats=false
 tmtintegrator.print_RefInt=false
 tmtintegrator.prot_exclude=none
 tmtintegrator.prot_norm=-1
 tmtintegrator.psm_norm=false
 tmtintegrator.quant_level=2
+tmtintegrator.ref_d_tag=Pool
 tmtintegrator.ref_tag=pool
 tmtintegrator.run-tmtintegrator=false
 tmtintegrator.tolerance=20
@@ -309,4 +357,6 @@
 workflow.description=<p style\="margin-top\: 0in">Open search workflow for PTM analysis. MSFragger localization-aware open search (LOS) algorithm, with deisotoping, mass calibration, parameter optimization, and monoisotope correction enabled. Mass range -150 to 500 Da. PeptideProphet with extended mass model. Crystal-C for artifact removal. Precursor ion quantification using Freequant. PTM-Shepherd for mass shift summarization. For faster run time, in MSFragger change the number of allowed missed cleavages to 1.</p>
 workflow.input.data-type.im-ms=false
 workflow.input.data-type.regular-ms=true
-workflow.saved-with-ver=20.0-build5
+workflow.misc.save-sdrf=true
+workflow.misc.sdrf-type=Default
+workflow.saved-with-ver=23.0-build14
diff -r 59fec1e2a6c3 -r b4f6df8fa89b workflows/TMT10.workflow
--- a/workflows/TMT10.workflow	Sun Mar 30 23:00:45 2025 +0000
+++ b/workflows/TMT10.workflow	Wed Oct 01 22:20:54 2025 +0000
@@ -2,18 +2,31 @@
 
 crystalc.run-crystalc=false
 database.decoy-tag=rev_
-diann.fragpipe.cmd-opts=
+diann.channel-normalization-strategy=0
+diann.cmd-opts=
+diann.generate-msstats=true
 diann.heavy=
 diann.library=
 diann.light=
 diann.medium=
+diann.min-site-prob=0.75
+diann.mod-tag=
 diann.q-value=0.01
 diann.quantification-strategy=3
+diann.quantification-strategy-2=2
 diann.run-dia-nn=false
 diann.run-dia-plex=false
 diann.run-specific-protein-q-value=false
 diann.unrelated-runs=false
-diann.use-predicted-spectra=true
+diann.use-predicted-spectra=false
+diatracer.corr-threshold=0.3
+diatracer.delta-apex-im=0.01
+diatracer.delta-apex-rt=3
+diatracer.mass-defect-filter=true
+diatracer.mass-defect-offset=0.1
+diatracer.rf-max=500
+diatracer.run-diatracer=false
+diatracer.write-intermediate-files=false
 diaumpire.AdjustFragIntensity=true
 diaumpire.BoostComplementaryIon=false
 diaumpire.CorrThreshold=0
@@ -35,10 +48,19 @@
 diaumpire.SE.NoMissedScan=1
 diaumpire.SE.SN=1.1
 diaumpire.run-diaumpire=false
+fpop.coadaptr.fpop.fpop_masses=
+fpop.coadaptr.fpop.run-fpop-coadaptr=false
+fpop.fragpipe.fpop.fpop-tmt=false
+fpop.fragpipe.fpop.label_control=
+fpop.fragpipe.fpop.label_fpop=
+fpop.fragpipe.fpop.region_size=1
+fpop.fragpipe.fpop.run-fpop=false
+fpop.fragpipe.fpop.subtract-control=false
 freequant.mz-tol=10
 freequant.rt-tol=0.4
 freequant.run-freequant=false
 ionquant.excludemods=
+ionquant.formula=
 ionquant.heavy=
 ionquant.imtol=0.05
 ionquant.ionfdr=0.01
@@ -52,7 +74,7 @@
 ionquant.mbrtoprun=10
 ionquant.medium=
 ionquant.minfreq=0
-ionquant.minions=2
+ionquant.minions=1
 ionquant.minisotopes=2
 ionquant.minscans=3
 ionquant.mztol=10
@@ -67,15 +89,24 @@
 ionquant.use-labeling=false
 ionquant.use-lfq=true
 ionquant.writeindex=0
+msbooster.find-best-im-model=false
+msbooster.find-best-rt-model=false
+msbooster.find-best-spectra-model=false
+msbooster.fragmentation-type=0
+msbooster.im-model=DIA-NN
+msbooster.koina-url=
+msbooster.predict-im=true
 msbooster.predict-rt=true
 msbooster.predict-spectra=true
+msbooster.rt-model=DIA-NN
 msbooster.run-msbooster=true
-msbooster.use-correlated-features=false
+msbooster.spectra-model=DIA-NN
+msbooster.spectral-library-path=
 msfragger.Y_type_masses=
 msfragger.activation_types=all
-msfragger.add_topN_complementary=0
 msfragger.allowed_missed_cleavage_1=2
 msfragger.allowed_missed_cleavage_2=2
+msfragger.analyzer_types=all
 msfragger.calibrate_mass=2
 msfragger.check_spectral_files=true
 msfragger.clip_nTerm_M=true
@@ -97,6 +128,7 @@
 msfragger.localize_delta_mass=false
 msfragger.mass_diff_to_variable_mod=0
 msfragger.mass_offsets=0
+msfragger.mass_offsets_detailed=
 msfragger.max_fragment_charge=2
 msfragger.max_variable_mods_combinations=5000
 msfragger.max_variable_mods_per_peptide=3
@@ -120,8 +152,8 @@
 msfragger.output_format=pepXML_pin
 msfragger.output_max_expect=50
 msfragger.output_report_topN=1
+msfragger.output_report_topN_dda_plus=5
 msfragger.output_report_topN_dia1=5
-msfragger.output_report_topN_dia2=3
 msfragger.override_charge=false
 msfragger.precursor_mass_lower=-20
 msfragger.precursor_mass_mode=selected
@@ -148,13 +180,14 @@
 msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.16293,n^,true,1; 229.16293,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
 msfragger.track_zero_topN=0
 msfragger.use_all_mods_in_first_search=false
+msfragger.use_detailed_offsets=false
 msfragger.use_topN_peaks=150
 msfragger.write_calibrated_mzml=false
-msfragger.write_uncalibrated_mgf=false
 msfragger.zero_bin_accept_expect=0
 msfragger.zero_bin_mult_expect=1
 opair.activation1=HCD
 opair.activation2=ETD
+opair.allowed_sites=
 opair.filterOxonium=true
 opair.glyco_db=
 opair.max_glycans=4
@@ -177,7 +210,6 @@
 phi-report.dont-use-prot-proph-file=false
 phi-report.filter=--sequential --picked --prot 0.01
 phi-report.pep-level-summary=false
-phi-report.philosoher-msstats=false
 phi-report.print-decoys=false
 phi-report.prot-level-summary=false
 phi-report.remove-contaminants=false
@@ -185,6 +217,7 @@
 protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5
 protein-prophet.run-protein-prophet=true
 ptmprophet.cmdline=
+ptmprophet.override-defaults=false
 ptmprophet.run-ptmprophet=false
 ptmshepherd.adv_params=false
 ptmshepherd.annotation-common=true
@@ -196,7 +229,6 @@
 ptmshepherd.cap_y_ions=
 ptmshepherd.decoy_type=1
 ptmshepherd.diag_ions=
-ptmshepherd.diagextract_mode=false
 ptmshepherd.diagmine_diagMinFoldChange=3.0
 ptmshepherd.diagmine_diagMinSpecDiff=00.2
 ptmshepherd.diagmine_fragMinFoldChange=3.0
@@ -204,14 +236,11 @@
 ptmshepherd.diagmine_fragMinSpecDiff=00.1
 ptmshepherd.diagmine_minIonsPerSpec=2
 ptmshepherd.diagmine_minPeps=25
-ptmshepherd.diagmine_mode=false
 ptmshepherd.diagmine_pepMinFoldChange=3.0
 ptmshepherd.diagmine_pepMinSpecDiff=00.2
-ptmshepherd.glyco_adducts=
 ptmshepherd.glyco_fdr=1.00
 ptmshepherd.glyco_isotope_max=3
 ptmshepherd.glyco_isotope_min=-1
-ptmshepherd.glyco_mode=false
 ptmshepherd.glyco_ppm_tol=50
 ptmshepherd.glycodatabase=
 ptmshepherd.histo_smoothbins=2
@@ -221,9 +250,9 @@
 ptmshepherd.iontype_x=false
 ptmshepherd.iontype_y=true
 ptmshepherd.iontype_z=false
+ptmshepherd.iterloc_maxEpoch=100
+ptmshepherd.iterloc_mode=false
 ptmshepherd.localization_allowed_res=
-ptmshepherd.localization_background=4
-ptmshepherd.max_adducts=0
 ptmshepherd.n_glyco=true
 ptmshepherd.normalization-psms=true
 ptmshepherd.normalization-scans=false
@@ -235,28 +264,41 @@
 ptmshepherd.precursor_mass_units=0
 ptmshepherd.precursor_tol=0.01
 ptmshepherd.print_decoys=false
-ptmshepherd.prob_dhexOx=2,0.5,0.1
-ptmshepherd.prob_dhexY=2,0.5
-ptmshepherd.prob_neuacOx=2,0.05,0.2
-ptmshepherd.prob_neugcOx=2,0.05,0.2
-ptmshepherd.prob_phosphoOx=2,0.05,0.2
-ptmshepherd.prob_regY=5,0.5
-ptmshepherd.prob_sulfoOx=2,0.05,0.2
+ptmshepherd.print_full_glyco_params=false
+ptmshepherd.prob_mass=0.5
 ptmshepherd.remainder_masses=
 ptmshepherd.remove_glycan_delta_mass=true
 ptmshepherd.run-shepherd=false
+ptmshepherd.run_diagextract_mode=false
+ptmshepherd.run_diagmine_mode=false
+ptmshepherd.run_glyco_mode=false
+ptmshepherd.spectra_condPeaks=150
+ptmshepherd.spectra_condRatio=0.0001
+ptmshepherd.spectra_maxPrecursorCharge=4
 ptmshepherd.spectra_maxfragcharge=2
 ptmshepherd.spectra_ppmtol=20
 ptmshepherd.varmod_masses=
 quantitation.run-label-free-quant=false
 run-psm-validation=true
 run-validation-tab=true
-saintexpress.fragpipe.cmd-opts=
+saintexpress.cmd-opts=
 saintexpress.max-replicates=3
 saintexpress.run-saint-express=true
 saintexpress.virtual-controls=100
+skyline.run-skyline=false
+skyline.skyline=false
+skyline.skyline-custom=false
+skyline.skyline-custom-path=
+skyline.skyline-daily=true
+skyline.skyline-fragment-tolerance=10
+skyline.skyline-mods-mode=Default
+skyline.skyline-precursor-tolerance=10
+skyline.use-ssl=false
+speclibgen.convert-pepxml=true
+speclibgen.convert-psm=false
 speclibgen.easypqp.extras.max_delta_ppm=15
 speclibgen.easypqp.extras.max_delta_unimod=0.02
+speclibgen.easypqp.extras.max_glycan_qval=1
 speclibgen.easypqp.extras.rt_lowess_fraction=0
 speclibgen.easypqp.fragment.a=false
 speclibgen.easypqp.fragment.b=true
@@ -265,6 +307,7 @@
 speclibgen.easypqp.fragment.y=true
 speclibgen.easypqp.fragment.z=false
 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
+speclibgen.easypqp.labile_mode=Regular (not glyco)
 speclibgen.easypqp.neutral_loss=false
 speclibgen.easypqp.rt-cal=noiRT
 speclibgen.easypqp.select-file.text=
@@ -273,6 +316,7 @@
 speclibgen.run-speclibgen=false
 tab-run.delete_calibrated_mzml=false
 tab-run.delete_temp_files=false
+tab-run.export_matched_fragments=false
 tab-run.sub_mzml_prob_threshold=0.5
 tab-run.write_sub_mzml=false
 tmtintegrator.add_Ref=1
@@ -281,24 +325,28 @@
 tmtintegrator.allow_unlabeled=false
 tmtintegrator.best_psm=true
 tmtintegrator.channel_num=TMT-10
-tmtintegrator.dont-run-fq-lq=false
+tmtintegrator.extraction_tool=IonQuant
 tmtintegrator.glyco_qval=-1
-tmtintegrator.groupby=0
+tmtintegrator.groupby=-1
 tmtintegrator.log2transformed=true
 tmtintegrator.max_pep_prob_thres=0.9
 tmtintegrator.min_ntt=0
 tmtintegrator.min_pep_prob=0.9
 tmtintegrator.min_percent=0.05
 tmtintegrator.min_purity=0.5
+tmtintegrator.min_resolution=0
 tmtintegrator.min_site_prob=-1
+tmtintegrator.min_snr=0
 tmtintegrator.mod_tag=none
 tmtintegrator.ms1_int=true
 tmtintegrator.outlier_removal=true
+tmtintegrator.philosopher-msstats=false
 tmtintegrator.print_RefInt=false
 tmtintegrator.prot_exclude=none
 tmtintegrator.prot_norm=1
 tmtintegrator.psm_norm=false
 tmtintegrator.quant_level=2
+tmtintegrator.ref_d_tag=Pool
 tmtintegrator.ref_tag=Bridge
 tmtintegrator.run-tmtintegrator=true
 tmtintegrator.tolerance=20
@@ -309,4 +357,6 @@
 workflow.description=<p style\="margin-top\: 0">Basic TMT 10-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.</p>
 workflow.input.data-type.im-ms=false
 workflow.input.data-type.regular-ms=true
-workflow.saved-with-ver=20.0-build5
+workflow.misc.save-sdrf=true
+workflow.misc.sdrf-type=Default
+workflow.saved-with-ver=23.0-build14
diff -r 59fec1e2a6c3 -r b4f6df8fa89b workflows/TMT11.workflow
--- a/workflows/TMT11.workflow	Sun Mar 30 23:00:45 2025 +0000
+++ b/workflows/TMT11.workflow	Wed Oct 01 22:20:54 2025 +0000
@@ -2,18 +2,31 @@
 
 crystalc.run-crystalc=false
 database.decoy-tag=rev_
-diann.fragpipe.cmd-opts=
+diann.channel-normalization-strategy=0
+diann.cmd-opts=
+diann.generate-msstats=true
 diann.heavy=
 diann.library=
 diann.light=
 diann.medium=
+diann.min-site-prob=0.75
+diann.mod-tag=
 diann.q-value=0.01
 diann.quantification-strategy=3
+diann.quantification-strategy-2=2
 diann.run-dia-nn=false
 diann.run-dia-plex=false
 diann.run-specific-protein-q-value=false
 diann.unrelated-runs=false
-diann.use-predicted-spectra=true
+diann.use-predicted-spectra=false
+diatracer.corr-threshold=0.3
+diatracer.delta-apex-im=0.01
+diatracer.delta-apex-rt=3
+diatracer.mass-defect-filter=true
+diatracer.mass-defect-offset=0.1
+diatracer.rf-max=500
+diatracer.run-diatracer=false
+diatracer.write-intermediate-files=false
 diaumpire.AdjustFragIntensity=true
 diaumpire.BoostComplementaryIon=false
 diaumpire.CorrThreshold=0
@@ -35,10 +48,19 @@
 diaumpire.SE.NoMissedScan=1
 diaumpire.SE.SN=1.1
 diaumpire.run-diaumpire=false
+fpop.coadaptr.fpop.fpop_masses=
+fpop.coadaptr.fpop.run-fpop-coadaptr=false
+fpop.fragpipe.fpop.fpop-tmt=false
+fpop.fragpipe.fpop.label_control=
+fpop.fragpipe.fpop.label_fpop=
+fpop.fragpipe.fpop.region_size=1
+fpop.fragpipe.fpop.run-fpop=false
+fpop.fragpipe.fpop.subtract-control=false
 freequant.mz-tol=10
 freequant.rt-tol=0.4
 freequant.run-freequant=false
 ionquant.excludemods=
+ionquant.formula=
 ionquant.heavy=
 ionquant.imtol=0.05
 ionquant.ionfdr=0.01
@@ -52,7 +74,7 @@
 ionquant.mbrtoprun=10
 ionquant.medium=
 ionquant.minfreq=0
-ionquant.minions=2
+ionquant.minions=1
 ionquant.minisotopes=2
 ionquant.minscans=3
 ionquant.mztol=10
@@ -67,15 +89,24 @@
 ionquant.use-labeling=false
 ionquant.use-lfq=true
 ionquant.writeindex=0
+msbooster.find-best-im-model=false
+msbooster.find-best-rt-model=false
+msbooster.find-best-spectra-model=false
+msbooster.fragmentation-type=0
+msbooster.im-model=DIA-NN
+msbooster.koina-url=
+msbooster.predict-im=true
 msbooster.predict-rt=true
 msbooster.predict-spectra=true
+msbooster.rt-model=DIA-NN
 msbooster.run-msbooster=true
-msbooster.use-correlated-features=false
+msbooster.spectra-model=DIA-NN
+msbooster.spectral-library-path=
 msfragger.Y_type_masses=
 msfragger.activation_types=all
-msfragger.add_topN_complementary=0
 msfragger.allowed_missed_cleavage_1=2
 msfragger.allowed_missed_cleavage_2=2
+msfragger.analyzer_types=all
 msfragger.calibrate_mass=2
 msfragger.check_spectral_files=true
 msfragger.clip_nTerm_M=true
@@ -97,6 +128,7 @@
 msfragger.localize_delta_mass=false
 msfragger.mass_diff_to_variable_mod=0
 msfragger.mass_offsets=0
+msfragger.mass_offsets_detailed=
 msfragger.max_fragment_charge=2
 msfragger.max_variable_mods_combinations=5000
 msfragger.max_variable_mods_per_peptide=3
@@ -120,8 +152,8 @@
 msfragger.output_format=pepXML_pin
 msfragger.output_max_expect=50
 msfragger.output_report_topN=1
+msfragger.output_report_topN_dda_plus=5
 msfragger.output_report_topN_dia1=5
-msfragger.output_report_topN_dia2=3
 msfragger.override_charge=false
 msfragger.precursor_mass_lower=-20
 msfragger.precursor_mass_mode=selected
@@ -145,16 +177,17 @@
 msfragger.search_enzyme_sense_1=C
 msfragger.search_enzyme_sense_2=C
 msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 229.16293,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
-msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.16293,n^,true,1; 229.16293,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
+msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.169252,n^,true,1; 229.169252,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
 msfragger.track_zero_topN=0
 msfragger.use_all_mods_in_first_search=false
+msfragger.use_detailed_offsets=false
 msfragger.use_topN_peaks=150
 msfragger.write_calibrated_mzml=false
-msfragger.write_uncalibrated_mgf=false
 msfragger.zero_bin_accept_expect=0
 msfragger.zero_bin_mult_expect=1
 opair.activation1=HCD
 opair.activation2=ETD
+opair.allowed_sites=
 opair.filterOxonium=true
 opair.glyco_db=
 opair.max_glycans=4
@@ -177,7 +210,6 @@
 phi-report.dont-use-prot-proph-file=false
 phi-report.filter=--sequential --picked --prot 0.01
 phi-report.pep-level-summary=false
-phi-report.philosoher-msstats=false
 phi-report.print-decoys=false
 phi-report.prot-level-summary=false
 phi-report.remove-contaminants=false
@@ -185,6 +217,7 @@
 protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5
 protein-prophet.run-protein-prophet=true
 ptmprophet.cmdline=
+ptmprophet.override-defaults=false
 ptmprophet.run-ptmprophet=false
 ptmshepherd.adv_params=false
 ptmshepherd.annotation-common=true
@@ -196,7 +229,6 @@
 ptmshepherd.cap_y_ions=
 ptmshepherd.decoy_type=1
 ptmshepherd.diag_ions=
-ptmshepherd.diagextract_mode=false
 ptmshepherd.diagmine_diagMinFoldChange=3.0
 ptmshepherd.diagmine_diagMinSpecDiff=00.2
 ptmshepherd.diagmine_fragMinFoldChange=3.0
@@ -204,14 +236,11 @@
 ptmshepherd.diagmine_fragMinSpecDiff=00.1
 ptmshepherd.diagmine_minIonsPerSpec=2
 ptmshepherd.diagmine_minPeps=25
-ptmshepherd.diagmine_mode=false
 ptmshepherd.diagmine_pepMinFoldChange=3.0
 ptmshepherd.diagmine_pepMinSpecDiff=00.2
-ptmshepherd.glyco_adducts=
 ptmshepherd.glyco_fdr=1.00
 ptmshepherd.glyco_isotope_max=3
 ptmshepherd.glyco_isotope_min=-1
-ptmshepherd.glyco_mode=false
 ptmshepherd.glyco_ppm_tol=50
 ptmshepherd.glycodatabase=
 ptmshepherd.histo_smoothbins=2
@@ -221,9 +250,9 @@
 ptmshepherd.iontype_x=false
 ptmshepherd.iontype_y=true
 ptmshepherd.iontype_z=false
+ptmshepherd.iterloc_maxEpoch=100
+ptmshepherd.iterloc_mode=false
 ptmshepherd.localization_allowed_res=
-ptmshepherd.localization_background=4
-ptmshepherd.max_adducts=0
 ptmshepherd.n_glyco=true
 ptmshepherd.normalization-psms=true
 ptmshepherd.normalization-scans=false
@@ -235,28 +264,41 @@
 ptmshepherd.precursor_mass_units=0
 ptmshepherd.precursor_tol=0.01
 ptmshepherd.print_decoys=false
-ptmshepherd.prob_dhexOx=2,0.5,0.1
-ptmshepherd.prob_dhexY=2,0.5
-ptmshepherd.prob_neuacOx=2,0.05,0.2
-ptmshepherd.prob_neugcOx=2,0.05,0.2
-ptmshepherd.prob_phosphoOx=2,0.05,0.2
-ptmshepherd.prob_regY=5,0.5
-ptmshepherd.prob_sulfoOx=2,0.05,0.2
+ptmshepherd.print_full_glyco_params=false
+ptmshepherd.prob_mass=0.5
 ptmshepherd.remainder_masses=
 ptmshepherd.remove_glycan_delta_mass=true
 ptmshepherd.run-shepherd=false
+ptmshepherd.run_diagextract_mode=false
+ptmshepherd.run_diagmine_mode=false
+ptmshepherd.run_glyco_mode=false
+ptmshepherd.spectra_condPeaks=150
+ptmshepherd.spectra_condRatio=0.0001
+ptmshepherd.spectra_maxPrecursorCharge=4
 ptmshepherd.spectra_maxfragcharge=2
 ptmshepherd.spectra_ppmtol=20
 ptmshepherd.varmod_masses=
 quantitation.run-label-free-quant=false
 run-psm-validation=true
 run-validation-tab=true
-saintexpress.fragpipe.cmd-opts=
+saintexpress.cmd-opts=
 saintexpress.max-replicates=3
 saintexpress.run-saint-express=true
 saintexpress.virtual-controls=100
+skyline.run-skyline=false
+skyline.skyline=false
+skyline.skyline-custom=false
+skyline.skyline-custom-path=
+skyline.skyline-daily=true
+skyline.skyline-fragment-tolerance=10
+skyline.skyline-mods-mode=Default
+skyline.skyline-precursor-tolerance=10
+skyline.use-ssl=false
+speclibgen.convert-pepxml=true
+speclibgen.convert-psm=false
 speclibgen.easypqp.extras.max_delta_ppm=15
 speclibgen.easypqp.extras.max_delta_unimod=0.02
+speclibgen.easypqp.extras.max_glycan_qval=1
 speclibgen.easypqp.extras.rt_lowess_fraction=0
 speclibgen.easypqp.fragment.a=false
 speclibgen.easypqp.fragment.b=true
@@ -265,6 +307,7 @@
 speclibgen.easypqp.fragment.y=true
 speclibgen.easypqp.fragment.z=false
 speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
+speclibgen.easypqp.labile_mode=Regular (not glyco)
 speclibgen.easypqp.neutral_loss=false
 speclibgen.easypqp.rt-cal=noiRT
 speclibgen.easypqp.select-file.text=
@@ -273,6 +316,7 @@
 speclibgen.run-speclibgen=false
 tab-run.delete_calibrated_mzml=false
 tab-run.delete_temp_files=false
+tab-run.export_matched_fragments=false
 tab-run.sub_mzml_prob_threshold=0.5
 tab-run.write_sub_mzml=false
 tmtintegrator.add_Ref=1
@@ -281,24 +325,28 @@
 tmtintegrator.allow_unlabeled=false
 tmtintegrator.best_psm=true
 tmtintegrator.channel_num=TMT-11
-tmtintegrator.dont-run-fq-lq=false
+tmtintegrator.extraction_tool=IonQuant
 tmtintegrator.glyco_qval=-1
-tmtintegrator.groupby=0
+tmtintegrator.groupby=-1
 tmtintegrator.log2transformed=true
 tmtintegrator.max_pep_prob_thres=0.9
 tmtintegrator.min_ntt=0
 tmtintegrator.min_pep_prob=0.9
 tmtintegrator.min_percent=0.05
 tmtintegrator.min_purity=0.5
+tmtintegrator.min_resolution=0
 tmtintegrator.min_site_prob=-1
+tmtintegrator.min_snr=0
 tmtintegrator.mod_tag=none
 tmtintegrator.ms1_int=true
 tmtintegrator.outlier_removal=true
+tmtintegrator.philosopher-msstats=false
 tmtintegrator.print_RefInt=false
 tmtintegrator.prot_exclude=none
 tmtintegrator.prot_norm=1
 tmtintegrator.psm_norm=false
 tmtintegrator.quant_level=2
+tmtintegrator.ref_d_tag=Pool
 tmtintegrator.ref_tag=Bridge
 tmtintegrator.run-tmtintegrator=true
 tmtintegrator.tolerance=20
@@ -309,4 +357,6 @@
 workflow.description=<p style\="margin-top\: 0">Basic TMT 11-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.</p>
 workflow.input.data-type.im-ms=false
 workflow.input.data-type.regular-ms=true
-workflow.saved-with-ver=20.0-build5
+workflow.misc.save-sdrf=true
+workflow.misc.sdrf-type=Default
+workflow.saved-with-ver=23.0-build14