--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bsa.mzid	Wed Mar 05 01:16:36 2014 -0500
@@ -0,0 +1,123 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<MzIdentML id="MS-GF+" version="1.1.0" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2013-06-05T16:52:19" >
+<cvList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
+    <cv id="PSI-MS" uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.30.0" fullName="PSI-MS"/>
+    <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/>
+    <cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" fullName="UNIT-ONTOLOGY"/>
+</cvList>
+<AnalysisSoftwareList xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
+    <AnalysisSoftware version="Beta (v9517)" name="MS-GF+" id="ID_software">
+        <SoftwareName>
+            <cvParam accession="MS:1002048" cvRef="PSI-MS" name="MS-GF+"/>
+        </SoftwareName>
+    </AnalysisSoftware>
+</AnalysisSoftwareList>
+<SequenceCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
+    <DBSequence accession="sp|ALBU_BOVIN|" searchDatabase_ref="SearchDB_1" length="607" id="DBSeq1">
+        <cvParam accession="MS:1001088" cvRef="PSI-MS" value="sp|ALBU_BOVIN|" name="protein description"/>
+    </DBSequence>
+    <Peptide id="Pep1">
+        <PeptideSequence>YICDNQDTISSK</PeptideSequence>
+        <Modification monoisotopicMassDelta="57.021463735" location="3">
+            <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/>
+        </Modification>
+    </Peptide>
+    <PeptideEvidence isDecoy="false" post="L" pre="K" end="297" start="286" peptide_ref="Pep1" dBSequence_ref="DBSeq1" id="PepEv_286_1_286"/>
+</SequenceCollection>
+<AnalysisCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
+    <SpectrumIdentification spectrumIdentificationList_ref="SI_LIST_1" spectrumIdentificationProtocol_ref="SearchProtocol_1" id="SpecIdent_1">
+        <InputSpectra spectraData_ref="SID_1"/>
+        <SearchDatabaseRef searchDatabase_ref="SearchDB_1"/>
+    </SpectrumIdentification>
+</AnalysisCollection>
+<AnalysisProtocolCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
+    <SpectrumIdentificationProtocol analysisSoftware_ref="ID_software" id="SearchProtocol_1">
+        <SearchType>
+            <cvParam accession="MS:1001083" cvRef="PSI-MS" name="ms-ms search"/>
+        </SearchType>
+        <AdditionalSearchParams>
+            <cvParam accession="MS:1001211" cvRef="PSI-MS" name="parent mass type mono"/>
+            <cvParam accession="MS:1001256" cvRef="PSI-MS" name="fragment mass type mono"/>
+            <userParam value="false" name="TargetDecoyApproach"/>
+            <userParam value="0" name="MinIsotopeError"/>
+            <userParam value="1" name="MaxIsotopeError"/>
+            <userParam value="As written in the spectrum or CID if no info" name="FragmentMethod"/>
+            <userParam value="LowRes" name="Instrument"/>
+            <userParam value="NoProtocol" name="Protocol"/>
+            <userParam value="2" name="NumTolerableTermini"/>
+            <userParam value="1" name="NumMatchesPerSpec"/>
+            <userParam value="6" name="MinPepLength"/>
+            <userParam value="40" name="MaxPepLength"/>
+            <userParam value="2" name="MinCharge"/>
+            <userParam value="3" name="MaxCharge"/>
+        </AdditionalSearchParams>
+        <ModificationParams>
+            <SearchModification residues="C" massDelta="57.021465" fixedMod="true">
+                <cvParam accession="UNIMOD:4" cvRef="UNIMOD" name="Carbamidomethyl"/>
+            </SearchModification>
+        </ModificationParams>
+        <Enzymes>
+            <Enzyme missedCleavages="1000" semiSpecific="false" id="Tryp">
+                <EnzymeName>
+                    <cvParam accession="MS:1001251" cvRef="PSI-MS" name="Trypsin"/>
+                </EnzymeName>
+            </Enzyme>
+        </Enzymes>
+        <ParentTolerance>
+            <cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="200.0" name="search tolerance plus value"/>
+            <cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="200.0" name="search tolerance minus value"/>
+        </ParentTolerance>
+        <Threshold>
+            <cvParam accession="MS:1001494" cvRef="PSI-MS" name="no threshold"/>
+        </Threshold>
+    </SpectrumIdentificationProtocol>
+</AnalysisProtocolCollection>
+<DataCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.1">
+    <Inputs>
+        <SearchDatabase numDatabaseSequences="2" location="/Users/iracooke/Sources/protk-wk/bsa.fasta" id="SearchDB_1">
+            <FileFormat>
+                <cvParam accession="MS:1001348" cvRef="PSI-MS" name="FASTA format"/>
+            </FileFormat>
+            <DatabaseName>
+                <userParam name="bsa.fasta"/>
+            </DatabaseName>
+        </SearchDatabase>
+        <SpectraData location="/Users/iracooke/Sources/protk-wk/bsa.mzML" name="bsa.mzML" id="SID_1">
+            <FileFormat>
+                <cvParam accession="MS:1000584" cvRef="PSI-MS" name="mzML file"/>
+            </FileFormat>
+            <SpectrumIDFormat>
+                <cvParam accession="MS:1000774" cvRef="PSI-MS" name="multiple peak list nativeID format"/>
+            </SpectrumIDFormat>
+        </SpectraData>
+    </Inputs>
+    <AnalysisData>
+        <SpectrumIdentificationList id="SI_LIST_1">
+            <FragmentationTable>
+                <Measure id="Measure_MZ">
+                    <cvParam accession="MS:1001225" cvRef="PSI-MS" unitCvRef="PSI-MS" unitName="m/z" unitAccession="MS:1000040" name="product ion m/z"/>
+                </Measure>
+            </FragmentationTable>
+            <SpectrumIdentificationResult spectraData_ref="SID_1" spectrumID="index=0" id="SIR_1">
+                <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="Pep1" calculatedMassToCharge="722.3251953125" experimentalMassToCharge="722.3522338867188" chargeState="2" id="SII_1_1">
+                    <PeptideEvidenceRef peptideEvidence_ref="PepEv_286_1_286"/>
+                    <cvParam accession="MS:1002049" cvRef="PSI-MS" value="21" name="MS-GF:RawScore"/>
+                    <cvParam accession="MS:1002050" cvRef="PSI-MS" value="71" name="MS-GF:DeNovoScore"/>
+                    <cvParam accession="MS:1002052" cvRef="PSI-MS" value="2.0246382E-9" name="MS-GF:SpecEValue"/>
+                    <cvParam accession="MS:1002053" cvRef="PSI-MS" value="2.2635456E-6" name="MS-GF:EValue"/>
+                    <userParam value="0" name="IsotopeError"/>
+                    <userParam value="CID" name="AssumedDissociationMethod"/>
+                    <userParam value="0.5818614" name="ExplainedIonCurrentRatio"/>
+                    <userParam value="0.12558742" name="NTermIonCurrentRatio"/>
+                    <userParam value="0.45627397" name="CTermIonCurrentRatio"/>
+                    <userParam value="18513.0" name="MS2IonCurrent"/>
+                    <userParam value="61.02686" name="MeanErrorAll"/>
+                    <userParam value="64.35494" name="StdevErrorAll"/>
+                    <userParam value="88.56576" name="MeanErrorTop7"/>
+                    <userParam value="86.03032" name="StdevErrorTop7"/>
+                </SpectrumIdentificationItem>
+            </SpectrumIdentificationResult>
+        </SpectrumIdentificationList>
+    </AnalysisData>
+</DataCollection>
+</MzIdentML>