--- 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