Element <mzIdentML>

Definition: The upper-most hierarchy level of mzIdentML with sub-containers for example describing software, protocols and search results (spectrum identifications or protein detection results).
Type: PSI-PI.Main.mzIdentMLType
Attributes:
Attribute NameData TypeUseDefinition
creationDatexsd:dateTimeoptionalThe date on which the file was produced.
idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance.
versionpsi-pi:versionRegexrequiredThe version of the schema this instance document refers to, in the format x.y.z. Changes to z should not affect prevent instance documents from validating.
Subelements:
Subelement NameminOccursmaxOccursDefinition
cvList11 The list of CVs used within the file
AnalysisSoftwareList01 The software used to perform the analyses (specify at least name, manufacturer, version, URL).
Provider01The Provider of the mzIdentML record in terms of the contact and software.
AuditCollection01The complete set of Contacts (people and organisations) for this file.
AnalysisSampleCollection01The samples analysed can optionally be recorded using CV terms for descriptions. If a composite...
SequenceCollection01The collection of sequences (DBSequence or Peptide) identified to be referenced in the results.
AnalysisCollection11 The analyses performed to get the results, which map the input and output data sets. Analyses are for example: SpectrumIdentification (resulting in peptides) or ProteinDetection (assemble proteins from peptides).
AnalysisProtocolCollection11 The collection of protocols which include the parameters and settings of the performed analyses.
DataCollection11The collection of input and output data sets of the analyses.
BibliographicReference0unboundedAny bibliographic references associated with the file
Example Context: 
<mzIdentML id="MPC_use_case" creationDate="2008-11-28T13:56:00" xmlns="http://psidev.info/psi/pi/mzIdentML/1.0" xmlns:pf="http://psidev.info/fuge-light/1.0" xmlns:PSI-MS="http://psidev.info/psi/pi/mzIdentML/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.0 ../schema/mzIdentML_working.xsd" version="0.9.9">
  <!-- CAUTION: ALL experimentalMassToCharge, peptide scores, protein scores and sequence coverage values are only placeholders for the real values, because file is handcrafted and shows only principle structure of AnalysisXML! -->
  <cvList>
    <cv id="PSI-MS" fullName="Proteomics Standards Initiative Mass Spectrometry Vocabularies" URI="http://www.psidev.info/PSI-MS" version="2.0.0"/>
    <cv id="BTO" fullName="BRENDA tissue 7 enzyme source" URI="http://www.brenda-enzymes.info/" version="12/2007"/>
    <cv id="UNIMOD" fullName="UNIMOD CV for modifications" URI="http://www.unimod.org/obo/unimod.obo"/>
    <cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
  ...
</mzIdentML>

Element <cvList>

Definition: The list of CVs used within the file
Type: cvListType
Attributes: none
Subelements:
Subelement NameminOccursmaxOccursDefinition
cv1unbounded-
Example Context: 
  <cvList>
    <cv id="PSI-MS" fullName="Proteomics Standards Initiative Mass Spectrometry Vocabularies" URI="http://www.psidev.info/PSI-MS" version="2.0.0"/>
    <cv id="BTO" fullName="BRENDA tissue 7 enzyme source" URI="http://www.brenda-enzymes.info/" version="12/2007"/>
    <cv id="UNIMOD" fullName="UNIMOD CV for modifications" URI="http://www.unimod.org/obo/unimod.obo"/>
    <cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
  </cvList>

Element <AnalysisSoftwareList>

Definition: The software used to perform the analyses (specify at least name, manufacturer, version, URL).
Type: AnalysisSoftwareListType
Attributes: none
Subelements:
Subelement NameminOccursmaxOccursDefinition
AnalysisSoftware1unbounded The software used for performing the analyses.
Example Context: 
  <AnalysisSoftwareList>
    <AnalysisSoftware id="SEQUEST_SW" name="ThermoFisher TurboSequest" version="PVM Slave v.27 (rev. 12)" URI="http://www.thermo.com/com/cda/product/detail/1,,16483,00.html">
      <ContactRole Contact_ref="THERMO">
        <role>
          <cvParam accession="MS:1001267" name="software vendor" cvRef="PSI-MS"/>
        </role>
      </ContactRole>
  ...
</AnalysisSoftwareList>

Element <Provider>

Definition: The Provider of the mzIdentML record in terms of the contact and software.
Attributes: none
Subelements: none
Example Context: 
<Provider id="PROVIDER">
  <ContactRole Contact_ref="PERSON_DOC_OWNER">
    <role>
      <cvParam accession="MS:1001271" name="researcher" cvRef="PSI-MS" />
    </role>
  </ContactRole>
</Provider>

Element <AuditCollection>

Definition: The complete set of Contacts (people and organisations) for this file.
Attributes: none
Subelements: none
Example Context: 
  <AuditCollection>
    <Organization id="BRUKER" name="Bruker Daltonics GmbH" address="Bremen, Germany"/>
    <Organization id="MATRIXSCIENCE" name="MatrixScience" address="UK"/>
    <Organization id="THERMO" name="Thermo Corp." address="USA"/>
    <Person id="MPCMEYER" name="Prof. Dr. Helmut E. Meyer" address="Universitaetsstr. 150, D-44795 Bochum, Germany" email="helmut.e.meyer@rub.de">
      <affiliations Organization_ref="MPCINSTITUTE"/>
    </Person>
  ...
</AuditCollection>

Element <AnalysisSampleCollection>

Definition: The samples analysed can optionally be recorded using CV terms for descriptions. If a composite...
Type: AnalysisSampleCollectionType
Attributes: none
Subelements:
Subelement NameminOccursmaxOccursDefinition
Sample1unboundedA description of the sample analysed by mass spectrometry using CVParams or UserParams. If a composite sample has been analysed, a parent sample should be defined, which references subsamples.
Example Context: 
  <AnalysisSampleCollection>
    <Sample id="sample1">
      <cvParam accession="MS:1001467" name="taxonomy: NCBI TaxID" cvRef="PSI-MS" value="9606"/>
      <cvParam accession="BTO:0000255" name="brain cell line" cvRef="BTO"/>
    </Sample>
  </AnalysisSampleCollection>

Element <SequenceCollection>

Definition: The collection of sequences (DBSequence or Peptide) identified to be referenced in the results.
Type: SequenceCollectionType
Attributes: none
Subelements:
Subelement NameminOccursmaxOccursDefinition
DBSequence0unboundedA database sequence from the specified SearchDatabase (nucleic acid or amino acid). If the sequence is nucleic acid, the source nucleic acid sequence should be given in the seq attribute rather than a translated sequence.
Peptide0unbounded One (poly)peptide (a sequence with modifications).
Graphical Context:
Example Context: 
  <SequenceCollection>
    <DBSequence id="prot1_IPI" accession="IPI00013808.1" SearchDatabase_ref="ipi.HUMAN_decoy">
      <seq>MVDYHAANQSYQYGPSSAGNGAGGGGSMGDYMAQEDDWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIDEDFRDGLKLMLLLEVISGERLPKPERGKMRVHKINNVNKALDFIASKGVKLVSIGAEEIVDGNAKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYKNVNVQNFHISWKDGLAFNALIHRHRPELIEYDKLRKDDPVTNLNNAFEVAEKYLDIPKMLDAEDIVNTARPDEKAIMTYVSSFYHAFSGAQKAETAANRICKVLAVNQENEHLMEDYEKLASDLLEWIRRTIPWLEDRVPQKTIQEMQQKLEDFRDYRRVHKPPKVQEKCQLEINFNTLQTKLRLSNRPAFMPSEGKMVSDINNGWQHLEQAEKGYEEWLLNEIRRLERLDHLAEKFRQKASIHEAWTDGKEAMLKHRDYETATLSDIKALIRKHEAFESDLAAHQDRVEQIAAIAQELNELDYYDSHNVNTRCQKICDQWDALGSLTHSRREALEKTEKQLEAIDQLHLEYAKRAAPFNNWMESAMEDLQDMFIVHTIEEIEGLISAHDQFKSTLPDADREREAILAIHKEAQRIAESNHIKLSGSNPYTTVTPQIINSKWEKVQQLVPKRDHALLEEQSKQQSNEHLRRQFASQANVVGPWIQTKMEEIGRISIEMNGTLEDQLSHLKQYERSIVDYKPNLDLLEQQHQLIQEALIFDNKHTNYTMEHIRVGWEQLLTTIARTINEVENQILTRDAKGISQEQMQEFRASFNHFDKDHGGALGPEEFKACLISLGYDVENDRQGEAEFNRIMSLVDPNHSGLVTFQAFIDFMSRETTDTDTADQVIASFKVLAGDKNFITAEELRRELPPDQAEYCIARMAPYQGPDAVPGALDYKSFSTALYGESDL</seq>
      <cvParam accession="MS:1001088" name="protein description" cvRef="PSI-MS" value="IPI:IPI00013808.1|SWISS-PROT:O43707|TREMBL:Q96BG6|ENSEMBL:ENSP00000252699|REFSEQ:NP_004915|H-INV:HIT000032172|VEGA:OTTHUMP00000076071;OTTHUMP00000174445 Tax_Id=9606 Gene_Symbol=ACTN4 Alpha-actinin-4"/>
    </DBSequence>
    <DBSequence id="prot2_IPI" accession="IPI00554648.1" SearchDatabase_ref="ipi.HUMAN_decoy">
      <seq>SIRVTQKSYKVSTSGPRAFSSRSYTSGPGSRISSSSFSRVGSSNFRGGLGGGYGGASGMGGITAVTVNQSLLSPLVLEVDPNIQAVRTQEKEQIKTLNNKFASFIDKVRFLEQQNKMLETKWSLLQQQKTARSNMDNMFESYINNLRRQLETLGQEKLKLEAELGNMQGLVEDFKNKYEDEINKRTEMENEFVLIKKDVDEAYMNKVELESRLEGLTDEINFLRQLYEEEIRELQSQISDTSVVLSMDNSRSLDMDSIIAEVKAQYEDIANRSRAEAESMYQIKYEELQSLAGKHGDDLRRTKTEISEMNRNISRLQAEIEGLKGQRASLEAAIADAEQRGELAIKDANAKLSELEAALQRAKQDMARQLREYQELMNVKLALDIEIATYRKLLEGEESRLESGMQNMSIHTKTTGGYAGGLSSAYGGLTSPGLSYSLGSSFGSGAGSSSFSRTSSSRAVVVKKIETRDGKLVSESSDVLPK</seq>
  ...
</SequenceCollection>

Element <AnalysisCollection>

Definition: The analyses performed to get the results, which map the input and output data sets. Analyses are for example: SpectrumIdentification (resulting in peptides) or ProteinDetection (assemble proteins from peptides).
Type: AnalysisCollectionType
Attributes: none
Subelements:
Subelement NameminOccursmaxOccursDefinition
SpectrumIdentification1unbounded An Analysis which tries to identify peptides in input spectra, referencing the database searched, the input spectra, the output results and the protocol that is run.
ProteinDetection01 An Analysis which assembles a set of peptides (e.g. from a spectra search analysis) to proteins.
Example Context: 
  <AnalysisCollection>
    <SpectrumIdentification id="SEQUEST_analysis" SpectrumIdentificationProtocol_ref="SEQUEST_proto" SpectrumIdentificationList_ref="SEQUEST_results" activityDate="2007-05-12T13:00:00">
      <InputSpectra SpectraData_ref="LCMALDI_spectra"/>
      <SearchDatabase SearchDatabase_ref="ipi.HUMAN_decoy"/>
    </SpectrumIdentification>
    <SpectrumIdentification id="Mascot_analysis" SpectrumIdentificationProtocol_ref="Mascot_proto" SpectrumIdentificationList_ref="Mascot_results" activityDate="2007-05-12T14:00:00">
      <InputSpectra SpectraData_ref="LCMALDI_spectra"/>
  ...
</AnalysisCollection>

Element <AnalysisProtocolCollection>

Definition: The collection of protocols which include the parameters and settings of the performed analyses.
Type: AnalysisProtocolCollectionType
Attributes: none
Subelements:
Subelement NameminOccursmaxOccursDefinition
SpectrumIdentificationProtocol1unbounded The parameters and settings of a SpectrumIdentification analysis.
ProteinDetectionProtocol01 The parameters and settings of a ProteinDetection process.
Example Context: 
<AnalysisProtocolCollection>
  <SpectrumIdentificationProtocol id="SIP" AnalysisSoftware_ref="AS_mascot_server">
    <SearchType>
      <cvParam accession="MS:1001081" name="pmf search" cvRef="PSI-MS" value=""/>
    </SearchType>
    <AdditionalSearchParams>
      <userParam name="Mascot User Comment" value="Figure 8. MALDI-TOF spectrum of an in-gel tryptic digest of a protein isolated from a thermophilic bacterium"/>
  ...
</AnalysisProtocolCollection>

Element <DataCollection>

Definition: The collection of input and output data sets of the analyses.
Type: DataCollectionType
Attributes: none
Subelements:
Subelement NameminOccursmaxOccursDefinition
Inputs11The inputs to the analyses including the databases searched, the spectral data and the source file converted to mzIdentML.
AnalysisData11Data sets generated by the analyses, including peptide and protein lists.
Graphical Context:
Example Context: 
  <DataCollection>
    <Inputs>
      <SourceFile id="SF1" location="proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X/SpectraData/Results1">
        <fileFormat>
          <cvParam accession="MS:1001275" name="ProteinScape SearchEvent" cvRef="PSI-MS"/>
        </fileFormat>
      </SourceFile>
  ...
</DataCollection>

Element <BibliographicReference>

Definition: Any bibliographic references associated with the file
Attributes: none
Subelements: none
Example Context: 
<BibliographicReference authors="David N. Perkins, Darryl J. C. Pappin, David M. Creasy, John S. Cottrell" editor="" id="10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2" name="Probability-based protein identification by searching sequence databases using mass spectrometry data" issue="18" pages="3551-3567" publication="Electrophoresis" volume="20" year="1999" publisher="Wiley VCH" title="Probability-based protein identification by searching sequence databases using mass spectrometry data"/>

Element <cv>

Definition: -
Attributes: none
Subelements: none
Example Context: 
<cv id="PSI-MS" fullName="Proteomics Standards Initiative Mass Spectrometry Vocabularies"   URI="http://www.psidev.info/PSI-MS" version="2.0.0"></cv>

Element <AnalysisSoftware>

Definition: The software used for performing the analyses.
Type: PSI-PI.analysis.search.AnalysisSoftwareType
Attributes:
Attribute NameData TypeUseDefinition
URIxsd:anyURIoptionalURI of the analysis software e.g. manufacturer's website
idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance.
versionxsd:stringoptional The version of Software used.
Subelements:
Subelement NameminOccursmaxOccursDefinition
pf:ContactRole01 The Contact that provided the document instance.
SoftwareName11The name of the analysis software package, sourced from a CV if available.
Customizations01Any customizations to the software, such as alternative scoring mechanisms implemented, should be documented here as free text.
Example Context: 
    <AnalysisSoftware id="SEQUEST_SW" name="ThermoFisher TurboSequest" version="PVM Slave v.27 (rev. 12)" URI="http://www.thermo.com/com/cda/product/detail/1,,16483,00.html">
      <ContactRole Contact_ref="THERMO">
        <role>
          <cvParam accession="MS:1001267" name="software vendor" cvRef="PSI-MS"/>
        </role>
      </ContactRole>
      <SoftwareName>
  ...
</AnalysisSoftware>

Element <Sample>

Definition: A description of the sample analysed by mass spectrometry using CVParams or UserParams. If a composite sample has been analysed, a parent sample should be defined, which references subsamples.
Type: SampleType
Attributes:
Attribute NameData TypeUseDefinition
idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance.
Subelements:
Subelement NameminOccursmaxOccursDefinition
pf:ContactRole0unbounded The Contact that provided the document instance.
subSample0unboundedReferences to the individual component samples within a mixed parent sample.
Example Context: 
    <Sample id="sample1">
      <cvParam accession="MS:1001467" name="taxonomy: NCBI TaxID" cvRef="PSI-MS" value="9606"/>
      <cvParam accession="BTO:0000255" name="brain cell line" cvRef="BTO"/>
    </Sample>
cvParam Mapping Rules: 
Path /mzIdentML/AnalysisSampleCollection/Sample
SHOULD supply a *child* term of MS:1001089 (molecule taxonomy) one or more times
  e.g.: MS:1001090 (taxonomy nomenclature)
  e.g.: MS:1001467 (taxonomy: NCBI TaxID)
  e.g.: MS:1001468 (taxonomy: common name)
  e.g.: MS:1001469 (taxonomy: scientific name)
  e.g.: MS:1001470 (taxonomy: Swiss-Prot ID)
SHOULD supply a *child* term of BTO:0000000 (brenda source tissue ontology) one or more times

Element <DBSequence>

Definition: A database sequence from the specified SearchDatabase (nucleic acid or amino acid). If the sequence is nucleic acid, the source nucleic acid sequence should be given in the seq attribute rather than a translated sequence.
Type: PSI-PI.analysis.search.DBSequenceType
Attributes:
Attribute NameData TypeUseDefinition
SearchDatabase_refxsd:stringrequiredThe source database of this sequence.
accessionxsd:stringrequiredThe unique accession of this sequence.
idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
lengthxsd:intoptionalThe length of the sequence as a number of bases or residues.
namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance.
Subelements:
Subelement NameminOccursmaxOccursDefinition
seq01The actual sequence of amino acids or nucleic acid.
Example Context: 
    <DBSequence id="prot5_IPI" accession="IPI00398776.3" SearchDatabase_ref="ipi.HUMAN_decoy">
      <seq>MKIVPDERDRVQKKTFTKWVNKHLIKAQRHISDLYEDLRDGHNLISLLEVLSGDSLPREKGRMRFHKLQNVQIALDYLRHRQVKLVNIRNDDIADGNPKLTLGLIWTIILHFQISDIQVSGQSEDMTAKEKLLLWSQRMVEGYQGLRCDNFTSSWRDGRLFNAIIHRHKPLLIDMNKVYRQTNLENLDQAFSVAERDLGVTRLLDPEDVDVPQPDEKSIITYVSSLYDAMPRVPDVQDGVRANELQLRWQEYRELVLLLLQWMRHHTAAFEERRFPSSFEEIEILWSQFLKFKEMELPAKEADKNRSKGIYQSLEGAVQAGQLKVPPGYHPLDVEKEWGKLHVAILEREKQLRSEFERLECLQRIVTKLQMEAGLCEEQLNQADALLQSDVRLLAAGKVPQRAGEVERDLDKADSMIRLLFNDVQTLKDGRHPQGEQMYRRVYRLHERLVAIRTEYNLRLKAGVAAPATQVAQVTLQSVQRRPELEDSTLRYLQDLLAWVEENQHRVDGAEWGVDLPSVEAQLGSHRGLHQSIEEFRAKIERARSDEGQLSPATRGAYRDCLGRLDLQYAKLLNSSKARLRSLESLHSFVAAATKELMWLNEKEEEEVGFDWSDRNTNMTAKKESYSALMRELELKEKKIKELQNAGDRLLREDHPARPTVESFQAALQTQWSWMLQLCCCIEAHLKENAAYFQFFSDVREAEGQLQKLQEALRRKYSCDRSATVTRLEDLLQDAQDEKEQLNEYKGHLSGLAKRAKAVVQLKPRHPAHPMRGRLPLLAVCDYKQVEVTVHKGDECQLVGPAQPSHWKVLSSSGSEAAVPSVCFLVPPPNQEAQEAVTRLEAQHQALVTLWHQLHVDMKSLLAWQSLRRDVQLIRSWSLATFRTLKPEEQRQALHSLELHYQAFLRDSQDAGGFGPEDRLMAEREYGSCSHHYQQLLQSLEQGAQEESRCQRCISELKDIRLQLEACETRTVHRLRLPLDKEPARECAQRIAEQQKAQAEVEGLGKGVARLSAEAEKVLALPEPSPAAPTLRSELELTLGKLEQVRSLSAIYLEKLKTISLVIRGTQGAEEVLRAHEEQLKEAQAVPATLPELEATKASLKKLRAQAEAQQPTFDALRDELRGAQEVGERLQQRHGERDVEVERWRERVAQLLERWQAVLAQTDVRQRELEQLGRQLRYYRESADPLGAWLQDARRRQEQIQAMPLADSQAVREQLRQEQALLEEIERHGEKVEECQRFAKQYINAIKDYELQLVTYKAQLEPVASPAKKPKVQSGSESVIQEYVDLRTHYSELTTLTSQYIKFISETLRRMEEEERLAEQQRAEERERLAEVEAALEKQRQLAEAHAQAKAQAEREAKELQQRMQEEVVRREEAAVDAQQQKRSIQEELQQLRQSSEAEIQAKARQAEAAERSRLRIEEEIRVVRLQLEATERQRGGAEGELQALRARAEEAEAQKRQAQEEAERLRRQVQDESQRKRQAEVELASRVKAEAEAAREKQRALQALEELRLQAEEAERRLRQAEVERARQVQVALETAQRSAEAELQSKRASFAEKTAQLERSLQEEHVAVAQLREEAERRAQQQAEAERAREEAERELERWQLKANEALRLRLQAEEVAQQKSLAQAEAEKQKEEAEREARRRGKAEEQAVRQRELAEQELEKQRQLAEGTAQQRLAAEQELIRLRAETEQGEQQRQLLEEELARLQREAAAATQKRQELEAELAKVRAEMEVLLASKARAEEESRSTSEKSKQRLEAEAGRFRELAEEAARLRALAEEAKRQRQLAEEDAARQRAEAERVLAEKLAAIGEATRLKTEAEIALKEKEAENERLRRLAEDEAFQRRRLEEQAAQHKADIEERLAQLRKASDSELERQKGLVEDTLRQRRQVEEEILALKASFEKAAAGKAELELELGRIRSNAEDTLRSKEQAELEAARQRQLAAEEERRRREAEERVQKSLAAEEEAARQRKAALEEVERLKAKVEEARRLRERAEQESARQLQLAQEAAQKRLQAEEKAHAFAVQQKEQELQQTLQQEQSVLDQLRGEAEAARRAAEEAEEARVQAEREAAQSRRQVEEAERLKQSAEEQAQARAQAQAAAEKLRKEAEQEAARRAQAEQAALRQKQAADAEMEKHKKFAEQTLRQKAQVEQELTTLRLQLEETDHQKNLLDEELQRLKAEATEAARQRSQVEEELFSVRVQMEELSKLKARIEAENRALILRDKDNTQRFLQEEAEKMKQVAEEAARLSVAAQEAARLRQLAEEDLAQQRALAEKMLKEKMQAVQEATRLKAEAELLQQQKELAQEQARRLQEDKEQMAQQLAEETQGFQRTLEAERQRQLEMSAEAERLKLRVAEMSRAQARAEEDAQRFRKQAEEIGEKLHRTELATQEKVTLVQTLEIQRQQSDHDAERLREAIAELEREKEKLQQEAKLLQLKSEEMQTVQQEQLLQETQALQQSFLSEKDSLLQRERFIEQEKAKLEQLFQDEVAKAQQLREEQQRQQQQMEQERQRLVASMEEARRRQHEAEEGVRRKQEELQQLEQQRRQQEELLAEENQRLREQLQLLEEQHRAALAHSEEVTASQVAATKTLPNGRDALDGPAAEAEPEHSFDGLRRKVSAQRLQEAGILSAEELQRLAQGHTTVDELARREDVRHYLQGRSSIAGLLLKATNEKLSVYAALQRQLLSPGTALILLEAQAASGFLLDPVRNRRLTVNEAVKEGVVGPELHHKLLSAERAVTGYKDPYTGQQISLFQAMQKGLIVREHGIRLLEAQIATGGVIDPVHSHRVPVDVAYRRGYFDEEMNRVLADPSDDTKGFFDPNTHENLTYLQLLERCVEDPETGLCLLPLTDKAAKGGELVYTDSEARDVFEKATVSAPFGKFQGKTVTIWEIINSEYFTAEQRRDLLRQFRTGRITVEKIIKIIITVVEEQEQKGRLCFEGLRSLVPAAELLESRVIDRELYQQLQRGERSVRDVAEVDTVRRALRGANVIAGVWLEEAGQKLSIYNALKKDLLPSDMAVALLEAQAGTGHIIDPATSARLTVDEAVRAGLVGPEFHEKLLSAEKAVTGYRDPYTGQSVSLFQALKKGLIPREQGLRLLDAQLSTGGIVDPSKSHRVPLDVACARGCLDEETSRALSAPRADAKAYSDPSTGEPATYGELQQRCRPDQLTGLSLLPLSEKAARARQEELYSELQARETFEKTPVEVPVGGFKGRTVTVWELISSEYFTAEQRQELLRQFRTGKVTVEKVIKILITIVEEVETLRQERLSFSGLRAPVPASELLASGVLSRAQFEQLKDGKTTVKDLSELGSVRTLLQGSGCLAGIYLEDTKEKVSIYEAMRRGLLRATTAALLLEAQAATGFLVDPVRNQRLYVHEAVKAGVVGPELHEQLLSAEKAVTGYRDPYSGSTISLFQAMQKGLVLRQHGIRLLEAQIATGGIIDPVHSHRVPVDVAYQRGYFSEEMNRVLADPSDDTKGFFDPNTHENLTYRQLLERCVEDPETGLRLLPLKGAEKAEVVETTQVYTEEETRRAFEETQIDIPGGGSHGGSTMSLWEVMQSDLIPEEQRAQLMADFQAGRVTKERMIIIIIEIIEKTEIIRQQGLASYDYVRRRLTAEDLFEARIISLETYNLLREGTRSLREALEAESAWCYLYGTGSVAGVYLPGSRQTLSIYQALKKGLLSAEVARLLLEAQAATGFLLDPVKGERLTVDEAVRKGLVGPELHDRLLSAERAVTGYRDPYTEQTISLFQAMKKELIPTEEALRLLDAQLATGGIVDPRLGFHLPLEVAYQRGYLNKDTHDQLSEPSEVRSYVDPSTDERLSYTQLLRRCRRDDGTGQLLLPLSDARKLTFRGLRKQITMEELVRSQVMDEATALQLREGLTSIEEVTKNLQKFLEGTSCIAGVFVDATKERLSVYQAMKKGIIRPGTAFELLEAQAATGYVIDPIKGLKLTVEEAVRMGIVGPEFKDKLLSAERAVTGYKDPYSGKLISLFQAMKKGLILKDHGIRLLEAQIATGGIIDPEESHRLPVEVAYKRGLFDEEMNEILTDPSDDTKGFFDPNTEENLTYLQLMERCITDPQTGLCLLPLKEKKRERKTSSKSSVRKRRVVIVDPETGKEMSVYEAYRKGLIDHQTYLELSEQECEWEEITISSSDGVVKSMIIDRRSGRQYDIDDAIAKNLIDRSALDQYRAGTLSITEFADMLSGNAGGFRSRSSSVGSSSSYPISPAVSRTQLASWSDPTEETGPVAGILDTETLEKVSITEAMHRNLVDNITGQRLLEAQACTGGIIDPSTGERFPVTDAVNKGLVDKIMVDRINLAQKAFCGFEDPRTKTKMSAAQALKKGWLYYEAGQRFLEVQYLTGGLIEPDTPGRVPLDEALQRGTVDARTAQKLRDVGAYSKYLTCPKTKLKISYKDALDRSMVEEGTGLRLLEAAAQSTKGYYSPYSVSGSGSTAGSRTGSRTGSRAGSRRGSFDATGSGFSMTFSSSSYSSSGYGRRYASGSSASLGGPESAVA</seq>
      <cvParam accession="MS:1001088" name="protein description" cvRef="PSI-MS" value=">IPI:IPI00398776.3|TREMBL:Q6S379;Q96IE3|REFSEQ:NP_958783 Tax_Id=9606 plectin 1 isoform 7"/>
    </DBSequence>
cvParam Mapping Rules: 
Path /mzIdentML/SequenceCollection/DBSequence
MAY supply a *child* term of MS:1001342 (database sequence details) one or more times
  e.g.: MS:1001088 (protein description)
  e.g.: MS:1001090 (taxonomy nomenclature)
  e.g.: MS:1001343 (NA sequence)
  e.g.: MS:1001344 (AA sequence)
  e.g.: MS:1001467 (taxonomy: NCBI TaxID)
  e.g.: MS:1001468 (taxonomy: common name)
  e.g.: MS:1001469 (taxonomy: scientific name)
  e.g.: MS:1001470 (taxonomy: Swiss-Prot ID)
MAY supply a *child* term of MS:1001089 (molecule taxonomy) one or more times
  e.g.: MS:1001090 (taxonomy nomenclature)
  e.g.: MS:1001467 (taxonomy: NCBI TaxID)
  e.g.: MS:1001468 (taxonomy: common name)
  e.g.: MS:1001469 (taxonomy: scientific name)
  e.g.: MS:1001470 (taxonomy: Swiss-Prot ID)

Element <Peptide>

Definition: One (poly)peptide (a sequence with modifications).
Type: PSI-PI.polypeptide.PeptideType
Attributes:
Attribute NameData TypeUseDefinition
idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance.
Subelements:
Subelement NameminOccursmaxOccursDefinition
peptideSequence11 The amino acid sequence of the (poly)peptide. If a substitution modification has been found, the original sequence should be reported.
Modification0unboundedA molecule modification specification. If n modifications have been found on a peptide, there should be n instances of Modification. If multiple modifications are provided as cvParams, it is assumed that the modification is ambiguous i.e. one modification or another. If no CVParams are provided it is assumed that the delta has not been matched to a known modification. A neutral loss should be defined as an additional CVParam within Modification. If more complex information should be given about neutral losses (such as presence/absence on particular product ions), this can additionally be encoded within the FragmentationArray.
SubstitutionModification0unbounded A modification where one residue is substituted by another (amino acid change).
Example Context: 
<Peptide id="peptide_176_4">
  <peptideSequence>EMMYKIAAMQSVDIDPATVK</peptideSequence>
  <Modification location="2" residues="M" monoisotopicMassDelta="15.994919">
    <cvParam accession="UNIMOD:35" name="Oxidation" cvRef="UNIMOD" />
    <cvParam accession="MS:1001524" name="fragment neutral loss" cvRef="PSI-MS" value="63.998285" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"/>
  </Modification>
  <Modification location="3" residues="M" monoisotopicMassDelta="15.994919">
  ...
</Peptide>
cvParam Mapping Rules: 
Path /mzIdentML/SequenceCollection/Peptide
MAY supply a *child* term of MS:1001355 (peptide descriptions) one or more times

Element <SpectrumIdentification>

Definition: An Analysis which tries to identify peptides in input spectra, referencing the database searched, the input spectra, the output results and the protocol that is run.
Type: PSI-PI.analysis.search.SpectrumIdentificationType
Attributes:
Attribute NameData TypeUseDefinition
SpectrumIdentificationList_refxsd:stringrequired A reference to the SpectrumIdentificationList produced by this analysis in the DataCollection section.
SpectrumIdentificationProtocol_refxsd:stringrequired A reference to the search protocol used for this SpectrumIdentification.
activityDatexsd:dateTimeoptional When the protocol was applied.
idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance.
Subelements:
Subelement NameminOccursmaxOccursDefinition
InputSpectra1unbounded One of the spectra data sets used (can be several).
SearchDatabase1unbounded One of the search databases used (can be several).
Example Context: 
    <SpectrumIdentification id="SEQUEST_analysis" SpectrumIdentificationProtocol_ref="SEQUEST_proto" SpectrumIdentificationList_ref="SEQUEST_results" activityDate="2007-05-12T13:00:00">
      <InputSpectra SpectraData_ref="LCMALDI_spectra"/>
      <SearchDatabase SearchDatabase_ref="ipi.HUMAN_decoy"/>
    </SpectrumIdentification>

Element <ProteinDetection>

Definition: An Analysis which assembles a set of peptides (e.g. from a spectra search analysis) to proteins.
Type: PSI-PI.analysis.process.ProteinDetectionType
Attributes:
Attribute NameData TypeUseDefinition
ProteinDetectionList_refxsd:stringrequired A reference to the ProteinDetectionList in the DataCollection section.
ProteinDetectionProtocol_refxsd:stringrequired A reference to the detection protocol used for this ProteinDetection.
activityDatexsd:dateTimeoptional When the protocol was applied.
idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance.
Subelements:
Subelement NameminOccursmaxOccursDefinition
InputSpectrumIdentifications1unboundedThe lists of spectrum identifications that are input to the protein detection process.
Example Context: 
    <ProteinDetection id="ProteinExtractor_analysis" ProteinDetectionProtocol_ref="ProteinExtractor_proto" ProteinDetectionList_ref="ProteinExtractor_results" activityDate="2007-05-12T15:30:00">
      <InputSpectrumIdentifications SpectrumIdentificationList_ref="SEQUEST_results"/>
      <InputSpectrumIdentifications SpectrumIdentificationList_ref="Mascot_results"/>
    </ProteinDetection>

Element <SpectrumIdentificationProtocol>

Definition: The parameters and settings of a SpectrumIdentification analysis.
Type: PSI-PI.analysis.search.SpectrumIdentificationProtocolType
Attributes:
Attribute NameData TypeUseDefinition
AnalysisSoftware_refxsd:stringrequired The search algorithm used, given as a reference to the SoftwareCollection section.
idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance.
Subelements:
Subelement NameminOccursmaxOccursDefinition
SearchType11The type of search performed e.g. PMF, Tag searches, MS-MS
AdditionalSearchParams01The search parameters other than the modifications searched.
ModificationParams01 The specification of static/variable modifications (e.g. Oxidation of Methionine) that are to be considered in the spectra search.
Enzymes01The list of enzymes used in experiment
MassTable0unboundedThe masses of residues used in the search.
FragmentTolerance01The tolerance of the search given as a plus and minus value with units.
ParentTolerance01The tolerance of the search given as a plus and minus value with units.
Threshold11The threshold(s) applied to determine that a result is significant. If multiple terms are used it is assumed that all conditions are satisfied by the passing results.
DatabaseFilters01The specification of filters applied to the database searched.
DatabaseTranslation01A specification of how a nucleic acid sequence database was translated for searching.
Graphical Context:
Example Context: 
<SpectrumIdentificationProtocol id="SIP" AnalysisSoftware_ref="AS_mascot_server">
  <SearchType>
    <cvParam accession="MS:1001081" name="pmf search" cvRef="PSI-MS" value=""/>
  </SearchType>
  <AdditionalSearchParams>
    <userParam name="Mascot User Comment" value="Figure 8. MALDI-TOF spectrum of an in-gel tryptic digest of a protein isolated from a thermophilic bacterium"/>
    <cvParam accession="MS:1001211" name="parent mass type mono"    cvRef="PSI-MS"/>
  ...
</SpectrumIdentificationProtocol>

Element <ProteinDetectionProtocol>

Definition: The parameters and settings of a ProteinDetection process.
Type: PSI-PI.analysis.process.ProteinDetectionProtocolType
Attributes:
Attribute NameData TypeUseDefinition
AnalysisSoftware_refxsd:stringrequired The protein detection software used, given as a reference to the SoftwareCollection section.
idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance.
Subelements:
Subelement NameminOccursmaxOccursDefinition
AnalysisParams01The parameters and settings for the protein detection given as CV terms.
Threshold11The threshold(s) applied to determine that a result is significant. If multiple terms are used it is assumed that all conditions are satisfied by the passing results.
Graphical Context:
Example Context: 
<ProteinDetectionProtocol id="PDP_MascotParser_1"  AnalysisSoftware_ref="AS_mascot_parser">
  <AnalysisParams>
    <cvParam accession="MS:1001316" name="mascot:SigThreshold"                               cvRef="PSI-MS" value="0.05"/>
    <cvParam accession="MS:1001317" name="mascot:MaxProteinHits"                             cvRef="PSI-MS" value="Auto"/>
    <cvParam accession="MS:1001318" name="mascot:ProteinScoringMethod"                       cvRef="PSI-MS" value="Standard"/>
    <cvParam accession="MS:1001319" name="mascot:MinMSMSThreshold"                           cvRef="PSI-MS" value="0"/>
    <cvParam accession="MS:1001320" name="mascot:ShowHomologousProteinsWithSamePeptides"     cvRef="PSI-MS" value="1"/>
  ...
</ProteinDetectionProtocol>

Element <Inputs>

Definition: The inputs to the analyses including the databases searched, the spectral data and the source file converted to mzIdentML.
Type: InputsType
Attributes: none
Subelements:
Subelement NameminOccursmaxOccursDefinition
SourceFile0unbounded A file from which this mzIdentML instance was created.
SearchDatabase0unbounded One of the search databases used (can be several).
SpectraData0unbounded A data set containing spectra data (consisting of one or more spectra).
Example Context: 
    <Inputs>
      <SourceFile id="SF1" location="proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X/SpectraData/Results1">
        <fileFormat>
          <cvParam accession="MS:1001275" name="ProteinScape SearchEvent" cvRef="PSI-MS"/>
        </fileFormat>
      </SourceFile>
      <SearchDatabase id="ipi.HUMAN_decoy" location="uri://www.medizinisches-proteom-center.de/ipi.HUMAN_decoy/3.15" version="3.15" releaseDate="22 February, 2006" numDatabaseSequences="58099">
  ...
</Inputs>

Element <AnalysisData>

Definition: Data sets generated by the analyses, including peptide and protein lists.
Type: AnalysisDataType
Attributes: none
Subelements:
Subelement NameminOccursmaxOccursDefinition
SpectrumIdentificationList1unbounded Represents the set of all search results from SpectrumIdentification.
ProteinDetectionList01 The protein list resulting from a protein detection process.
Example Context: 
<AnalysisData>
  <SpectrumIdentificationList id="SIL_1" numSequencesSearched="257964">
    <SpectrumIdentificationResult id="SIR_1" spectrumID="1" SpectraData_ref="SD_1">
      <SpectrumIdentificationItem id="SII_1_1"  calculatedMassToCharge="1107.534897" chargeState="1" experimentalMassToCharge="1108.53" Peptide_ref="peptide_1_1" rank="0" passThreshold="true">
        <PeptideEvidence id="PE_1_1_UVRB_THET8" start="542" end="550" pre="R" post="V" missedCleavages="0" isDecoy="false" DBSequence_Ref="DBSeq_UVRB_THET8" />
      </SpectrumIdentificationItem>
      <SpectrumIdentificationItem id="SII_1_8"  calculatedMassToCharge="1107.617584" chargeState="1" experimentalMassToCharge="1108.53" Peptide_ref="peptide_1_8" rank="0" passThreshold="true">
  ...
</AnalysisData>

Element <pf:ContactRole>

Definition: The Contact that provided the document instance.
Type: FuGE.Common.Audit.ContactRoleType
Attributes:
Attribute NameData TypeUseDefinition
Contact_refxsd:stringrequired When a ContactRole is used, it specifies which Contact the role is associated with.
Subelements:
Subelement NameminOccursmaxOccursDefinition
pf:role11 The roles (lab equipment sales, contractor, etc.) the Contact fills.
Example Context: 









Element <SoftwareName>






Definition:
The name of the analysis software package, sourced from a CV if available.





Type:
ParamType





Attributes:
none






Subelements:
none






Example Context:

      <SoftwareName>
        <cvParam accession="MS:1000734" name="ProteinScape" cvRef="PSI-MS"/>
      </SoftwareName>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisSoftwareList/AnalysisSoftware/SoftwareName
MUST supply a *child* term of MS:1001456 (analysis software) one or more times
  e.g.: MS:1000532 (Xcalibur)
  e.g.: MS:1000533 (Bioworks)
  e.g.: MS:1000534 (MassLynx)
  e.g.: MS:1000535 (FlexAnalysis)
  e.g.: MS:1000536 (Data Explorer)
  e.g.: MS:1000537 (4700 Explorer)
  e.g.: MS:1000539 (Voyager Biospectrometry Workstation System)
  e.g.: MS:1000551 (Analyst)
  e.g.: MS:1000600 (Proteios)
  e.g.: MS:1000601 (ProteinLynx Global Server)
  et al.










Element <Customizations>






Definition:
Any customizations to the software, such as alternative scoring mechanisms implemented, should be documented here as free text.





Type:
xsd:string





Attributes:
none






Subelements:
none






Example Context:

<Customizations>
  No customisations
</Customizations>










Element <subSample>






Definition:
References to the individual component samples within a mixed parent sample.





Type:
subSampleType





Attributes:



Attribute NameData TypeUseDefinition


Sample_refxsd:stringrequired








Subelements:
none






Example Context:

<subSample Sample_ref="Sample_light"/>










Element <seq>






Definition:
The actual sequence of amino acids or nucleic acid.





Type:
sequence





Attributes:
none






Subelements:
none






Example Context:

      <seq>MKIVPDERDRVQKKTFTKWVNKHLIKAQRHISDLYEDLRDGHNLISLLEVLSGDSLPREKGRMRFHKLQNVQIALDYLRHRQVKLVNIRNDDIADGNPKLTLGLIWTIILHFQISDIQVSGQSEDMTAKEKLLLWSQRMVEGYQGLRCDNFTSSWRDGRLFNAIIHRHKPLLIDMNKVYRQTNLENLDQAFSVAERDLGVTRLLDPEDVDVPQPDEKSIITYVSSLYDAMPRVPDVQDGVRANELQLRWQEYRELVLLLLQWMRHHTAAFEERRFPSSFEEIEILWSQFLKFKEMELPAKEADKNRSKGIYQSLEGAVQAGQLKVPPGYHPLDVEKEWGKLHVAILEREKQLRSEFERLECLQRIVTKLQMEAGLCEEQLNQADALLQSDVRLLAAGKVPQRAGEVERDLDKADSMIRLLFNDVQTLKDGRHPQGEQMYRRVYRLHERLVAIRTEYNLRLKAGVAAPATQVAQVTLQSVQRRPELEDSTLRYLQDLLAWVEENQHRVDGAEWGVDLPSVEAQLGSHRGLHQSIEEFRAKIERARSDEGQLSPATRGAYRDCLGRLDLQYAKLLNSSKARLRSLESLHSFVAAATKELMWLNEKEEEEVGFDWSDRNTNMTAKKESYSALMRELELKEKKIKELQNAGDRLLREDHPARPTVESFQAALQTQWSWMLQLCCCIEAHLKENAAYFQFFSDVREAEGQLQKLQEALRRKYSCDRSATVTRLEDLLQDAQDEKEQLNEYKGHLSGLAKRAKAVVQLKPRHPAHPMRGRLPLLAVCDYKQVEVTVHKGDECQLVGPAQPSHWKVLSSSGSEAAVPSVCFLVPPPNQEAQEAVTRLEAQHQALVTLWHQLHVDMKSLLAWQSLRRDVQLIRSWSLATFRTLKPEEQRQALHSLELHYQAFLRDSQDAGGFGPEDRLMAEREYGSCSHHYQQLLQSLEQGAQEESRCQRCISELKDIRLQLEACETRTVHRLRLPLDKEPARECAQRIAEQQKAQAEVEGLGKGVARLSAEAEKVLALPEPSPAAPTLRSELELTLGKLEQVRSLSAIYLEKLKTISLVIRGTQGAEEVLRAHEEQLKEAQAVPATLPELEATKASLKKLRAQAEAQQPTFDALRDELRGAQEVGERLQQRHGERDVEVERWRERVAQLLERWQAVLAQTDVRQRELEQLGRQLRYYRESADPLGAWLQDARRRQEQIQAMPLADSQAVREQLRQEQALLEEIERHGEKVEECQRFAKQYINAIKDYELQLVTYKAQLEPVASPAKKPKVQSGSESVIQEYVDLRTHYSELTTLTSQYIKFISETLRRMEEEERLAEQQRAEERERLAEVEAALEKQRQLAEAHAQAKAQAEREAKELQQRMQEEVVRREEAAVDAQQQKRSIQEELQQLRQSSEAEIQAKARQAEAAERSRLRIEEEIRVVRLQLEATERQRGGAEGELQALRARAEEAEAQKRQAQEEAERLRRQVQDESQRKRQAEVELASRVKAEAEAAREKQRALQALEELRLQAEEAERRLRQAEVERARQVQVALETAQRSAEAELQSKRASFAEKTAQLERSLQEEHVAVAQLREEAERRAQQQAEAERAREEAERELERWQLKANEALRLRLQAEEVAQQKSLAQAEAEKQKEEAEREARRRGKAEEQAVRQRELAEQELEKQRQLAEGTAQQRLAAEQELIRLRAETEQGEQQRQLLEEELARLQREAAAATQKRQELEAELAKVRAEMEVLLASKARAEEESRSTSEKSKQRLEAEAGRFRELAEEAARLRALAEEAKRQRQLAEEDAARQRAEAERVLAEKLAAIGEATRLKTEAEIALKEKEAENERLRRLAEDEAFQRRRLEEQAAQHKADIEERLAQLRKASDSELERQKGLVEDTLRQRRQVEEEILALKASFEKAAAGKAELELELGRIRSNAEDTLRSKEQAELEAARQRQLAAEEERRRREAEERVQKSLAAEEEAARQRKAALEEVERLKAKVEEARRLRERAEQESARQLQLAQEAAQKRLQAEEKAHAFAVQQKEQELQQTLQQEQSVLDQLRGEAEAARRAAEEAEEARVQAEREAAQSRRQVEEAERLKQSAEEQAQARAQAQAAAEKLRKEAEQEAARRAQAEQAALRQKQAADAEMEKHKKFAEQTLRQKAQVEQELTTLRLQLEETDHQKNLLDEELQRLKAEATEAARQRSQVEEELFSVRVQMEELSKLKARIEAENRALILRDKDNTQRFLQEEAEKMKQVAEEAARLSVAAQEAARLRQLAEEDLAQQRALAEKMLKEKMQAVQEATRLKAEAELLQQQKELAQEQARRLQEDKEQMAQQLAEETQGFQRTLEAERQRQLEMSAEAERLKLRVAEMSRAQARAEEDAQRFRKQAEEIGEKLHRTELATQEKVTLVQTLEIQRQQSDHDAERLREAIAELEREKEKLQQEAKLLQLKSEEMQTVQQEQLLQETQALQQSFLSEKDSLLQRERFIEQEKAKLEQLFQDEVAKAQQLREEQQRQQQQMEQERQRLVASMEEARRRQHEAEEGVRRKQEELQQLEQQRRQQEELLAEENQRLREQLQLLEEQHRAALAHSEEVTASQVAATKTLPNGRDALDGPAAEAEPEHSFDGLRRKVSAQRLQEAGILSAEELQRLAQGHTTVDELARREDVRHYLQGRSSIAGLLLKATNEKLSVYAALQRQLLSPGTALILLEAQAASGFLLDPVRNRRLTVNEAVKEGVVGPELHHKLLSAERAVTGYKDPYTGQQISLFQAMQKGLIVREHGIRLLEAQIATGGVIDPVHSHRVPVDVAYRRGYFDEEMNRVLADPSDDTKGFFDPNTHENLTYLQLLERCVEDPETGLCLLPLTDKAAKGGELVYTDSEARDVFEKATVSAPFGKFQGKTVTIWEIINSEYFTAEQRRDLLRQFRTGRITVEKIIKIIITVVEEQEQKGRLCFEGLRSLVPAAELLESRVIDRELYQQLQRGERSVRDVAEVDTVRRALRGANVIAGVWLEEAGQKLSIYNALKKDLLPSDMAVALLEAQAGTGHIIDPATSARLTVDEAVRAGLVGPEFHEKLLSAEKAVTGYRDPYTGQSVSLFQALKKGLIPREQGLRLLDAQLSTGGIVDPSKSHRVPLDVACARGCLDEETSRALSAPRADAKAYSDPSTGEPATYGELQQRCRPDQLTGLSLLPLSEKAARARQEELYSELQARETFEKTPVEVPVGGFKGRTVTVWELISSEYFTAEQRQELLRQFRTGKVTVEKVIKILITIVEEVETLRQERLSFSGLRAPVPASELLASGVLSRAQFEQLKDGKTTVKDLSELGSVRTLLQGSGCLAGIYLEDTKEKVSIYEAMRRGLLRATTAALLLEAQAATGFLVDPVRNQRLYVHEAVKAGVVGPELHEQLLSAEKAVTGYRDPYSGSTISLFQAMQKGLVLRQHGIRLLEAQIATGGIIDPVHSHRVPVDVAYQRGYFSEEMNRVLADPSDDTKGFFDPNTHENLTYRQLLERCVEDPETGLRLLPLKGAEKAEVVETTQVYTEEETRRAFEETQIDIPGGGSHGGSTMSLWEVMQSDLIPEEQRAQLMADFQAGRVTKERMIIIIIEIIEKTEIIRQQGLASYDYVRRRLTAEDLFEARIISLETYNLLREGTRSLREALEAESAWCYLYGTGSVAGVYLPGSRQTLSIYQALKKGLLSAEVARLLLEAQAATGFLLDPVKGERLTVDEAVRKGLVGPELHDRLLSAERAVTGYRDPYTEQTISLFQAMKKELIPTEEALRLLDAQLATGGIVDPRLGFHLPLEVAYQRGYLNKDTHDQLSEPSEVRSYVDPSTDERLSYTQLLRRCRRDDGTGQLLLPLSDARKLTFRGLRKQITMEELVRSQVMDEATALQLREGLTSIEEVTKNLQKFLEGTSCIAGVFVDATKERLSVYQAMKKGIIRPGTAFELLEAQAATGYVIDPIKGLKLTVEEAVRMGIVGPEFKDKLLSAERAVTGYKDPYSGKLISLFQAMKKGLILKDHGIRLLEAQIATGGIIDPEESHRLPVEVAYKRGLFDEEMNEILTDPSDDTKGFFDPNTEENLTYLQLMERCITDPQTGLCLLPLKEKKRERKTSSKSSVRKRRVVIVDPETGKEMSVYEAYRKGLIDHQTYLELSEQECEWEEITISSSDGVVKSMIIDRRSGRQYDIDDAIAKNLIDRSALDQYRAGTLSITEFADMLSGNAGGFRSRSSSVGSSSSYPISPAVSRTQLASWSDPTEETGPVAGILDTETLEKVSITEAMHRNLVDNITGQRLLEAQACTGGIIDPSTGERFPVTDAVNKGLVDKIMVDRINLAQKAFCGFEDPRTKTKMSAAQALKKGWLYYEAGQRFLEVQYLTGGLIEPDTPGRVPLDEALQRGTVDARTAQKLRDVGAYSKYLTCPKTKLKISYKDALDRSMVEEGTGLRLLEAAAQSTKGYYSPYSVSGSGSTAGSRTGSRTGSRAGSRRGSFDATGSGFSMTFSSSSYSSSGYGRRYASGSSASLGGPESAVA</seq>










Element <peptideSequence>






Definition:
 The amino acid sequence of the (poly)peptide. If a substitution modification has been found, the original sequence should be reported. 





Type:
sequence





Attributes:
none






Subelements:
none






Example Context:

<peptideSequence>GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG</peptideSequence>










Element <Modification>






Definition:
A molecule modification specification. If n modifications have been found on a peptide, there should be n instances of Modification. If multiple modifications are provided as cvParams, it is assumed that the modification is ambiguous i.e. one modification or another. If no CVParams are provided it is assumed that the delta has not been matched to a known modification. A neutral loss should be defined as an additional CVParam within Modification. If more complex information should be given about neutral losses (such as presence/absence on particular product ions), this can additionally be encoded within the FragmentationArray.





Type:
PSI-PI.polypeptide.ModificationType





Attributes:



Attribute NameData TypeUseDefinition


avgMassDeltaxsd:doubleoptional Atomic mass delta considering the natural distribution of isotopes in Daltons. 


locationxsd:intoptionalLocation of the modification within the peptide - position in peptide sequence, counted from the N-terminus residue, starting at position 1. Specific modifications to the N-terminus should be given the location 0. Modification to the C-terminus should be given as peptide length + 1.


monoisotopicMassDeltaxsd:doubleoptional Atomic mass delta when assuming only the most common isotope of elements in Daltons. 


residueslistOfCharsoptionalSpecification of the residue (amino acid) on which the modification occurs. If multiple values are given, it is assumed that the exact residue modified is unknown i.e. the modification is to ONE of the residues listed. Multiple residues would usually only be specified for PMF data.








Subelements:
none






Example Context:

<Modification location="10" residues="M" monoisotopicMassDelta="15.994919">
  <cvParam accession="UNIMOD:35" name="Oxidation" cvRef="UNIMOD" />
  <cvParam accession="MS:1001524" name="fragment neutral loss" cvRef="PSI-MS" value="63.998285" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"/>
</Modification>







cvParam Mapping Rules:

Path /mzIdentML/SequenceCollection/Peptide/Modification
MUST supply a *child* term of UNIMOD:0 (UNIMOD root) one or more times
MUST supply a *child* term of MS:1001471 (peptide modification details) one or more times
  e.g.: MS:1001460 (unknown modification)
  e.g.: MS:1001524 (fragment neutral loss)
  e.g.: MS:1001525 (precursor neutral loss )
MUST supply a *child* term of MOD:00000 (protein modification) one or more times










Element <SubstitutionModification>






Definition:
 A modification where one residue is substituted by another (amino acid change). 





Type:
PSI-PI.polypeptide.SubstitutionModificationType





Attributes:



Attribute NameData TypeUseDefinition


avgMassDeltaxsd:doubleoptional Atomic mass delta considering the natural distribution of isotopes in Daltons. This should only be reported if the original amino acid is known i.e. it is not "X" 


locationxsd:intoptionalLocation of the modification within the peptide - position in peptide sequence, counted from the N-terminus residue, starting at position 1. Specific modifications to the N-terminus should be given the location 0. Modification to the C-terminus should be given as peptide length + 1.


monoisotopicMassDeltaxsd:doubleoptional Atomic mass delta when assuming only the most common isotope of elements in Daltons. This should only be reported if the original amino acid is known i.e. it is not "X" 


originalResiduerequired The original residue before replacement. 


replacementResiduerequired The residue that replaced the originalResidue. 








Subelements:
none






Example Context:

<SubstitutionModification location="7" originalResidue="X" replacementResidue="N"/>










Element <InputSpectra>






Definition:
 One of the spectra data sets used (can be several).





Type:
InputSpectraType





Attributes:



Attribute NameData TypeUseDefinition


SpectraData_refxsd:stringoptionalA reference to the SpectraData element which locates the input spectra to an external file.








Subelements:
none






Example Context:

      <InputSpectra SpectraData_ref="LCMALDI_spectra"/>










Element <SearchDatabase>






Definition:
 One of the search databases used (can be several).





Type:
SearchDatabaseType





Attributes:



Attribute NameData TypeUseDefinition


SearchDatabase_refxsd:stringoptionalA reference to the database searched.








Subelements:
none






Example Context:

      <SearchDatabase id="ipi.HUMAN_decoy" location="uri://www.medizinisches-proteom-center.de/ipi.HUMAN_decoy/3.15" version="3.15" releaseDate="22 February, 2006" numDatabaseSequences="58099">
        <DatabaseName>
          <userParam name="MPC ipi.HUMAN_decoy"/>
        </DatabaseName>
        <cvParam accession="MS:1001300" name="decoy DB from IPI_human" cvRef="PSI-MS"/>
        <cvParam accession="MS:1001197" name="DB composition target+decoy" cvRef="PSI-MS"/>
        <cvParam accession="MS:1001452" name="decoy DB type shuffle" cvRef="PSI-MS"/>
  ...
</SearchDatabase>







cvParam Mapping Rules:

Path /mzIdentML/DataCollection/Inputs/SearchDatabase
MAY supply a *child* term of MS:1000561 (data file checksum type) one or more times
  e.g.: MS:1000568 (MD5)
  e.g.: MS:1000569 (SHA-1)
MAY supply a *child* term of MS:1001011 (search database details) one or more times
  e.g.: MS:1001014 (database local file path)
  e.g.: MS:1001015 (database original uri)
  e.g.: MS:1001016 (database version)
  e.g.: MS:1001017 (database release date)
  e.g.: MS:1001020 (DB filter taxonomy)
  e.g.: MS:1001021 (DB filter on accession numbers)
  e.g.: MS:1001022 (DB MW filter)
  e.g.: MS:1001023 (DB PI filter)
  e.g.: MS:1001024 (translation frame)
  e.g.: MS:1001025 (translation table)
  et al.










Element <InputSpectrumIdentifications>






Definition:
The lists of spectrum identifications that are input to the protein detection process.





Type:
InputSpectrumIdentificationsType





Attributes:



Attribute NameData TypeUseDefinition


SpectrumIdentificationList_refxsd:stringrequiredA reference to the list of spectrum identifications that were input to the process.








Subelements:
none






Example Context:

      <InputSpectrumIdentifications SpectrumIdentificationList_ref="SEQUEST_results"/>










Element <SearchType>






Definition:
The type of search performed e.g. PMF, Tag searches, MS-MS





Type:
ParamType





Attributes:
none






Subelements:
none






Example Context:

<SearchType>
  <cvParam accession="MS:1001083" name="ms-ms search" cvRef="PSI-MS" value=""/>
</SearchType>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/SearchType
MUST supply a *child* term of MS:1001080 (search type) one or more times
  e.g.: MS:1001010 (de novo search)
  e.g.: MS:1001031 (spectral library search)
  e.g.: MS:1001081 (pmf search)
  e.g.: MS:1001082 (tag search)
  e.g.: MS:1001083 (ms-ms search)










Element <AdditionalSearchParams>






Definition:
The search parameters other than the modifications searched.





Type:
ParamListType





Attributes:
none






Subelements:
none






Example Context:

      <AdditionalSearchParams>
        <cvParam accession="MS:1001211" name="parent mass type mono" cvRef="PSI-MS"/>
        <cvParam accession="MS:1001256" name="fragment mass type mono" cvRef="PSI-MS"/>
        <cvParam accession="MS:1001259" name="param: immonium ion" cvRef="PSI-MS"/>
        <cvParam accession="MS:1001108" name="param: a ion" cvRef="PSI-MS"/>
        <cvParam accession="MS:1001146" name="param: a ion-NH3" cvRef="PSI-MS"/>
        <cvParam accession="MS:1001148" name="param: a ion-H2O" cvRef="PSI-MS"/>
  ...
</AdditionalSearchParams>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/AdditionalSearchParams
MAY supply a *child* term of MS:1001302 (search engine specific input parameter) one or more times
  e.g.: MS:1001005 (sequest:CleavesAt)
  e.g.: MS:1001007 (sequest:OutputLines)
  e.g.: MS:1001009 (sequest:DescriptionLines)
  e.g.: MS:1001026 (sequest:NormalizeXCorrValues)
  e.g.: MS:1001028 (sequest:SequenceHeaderFilter)
  e.g.: MS:1001032 (sequest:SequencePartialFilter)
  e.g.: MS:1001037 (sequest:ShowFragmentIons)
  e.g.: MS:1001038 (sequest:Consensus)
  e.g.: MS:1001042 (sequest:LimitTo)
  e.g.: MS:1001046 (sequest:sort_by_dCn)
  et al.
MAY supply a *child* term of MS:1001066 (ions series considered in search) one or more times
  e.g.: MS:1001108 (param: a ion)
  e.g.: MS:1001118 (param: b ion)
  e.g.: MS:1001119 (param: c ion)
  e.g.: MS:1001146 (param: a ion-NH3)
  e.g.: MS:1001148 (param: a ion-H2O)
  e.g.: MS:1001149 (param: b ion-NH3)
  e.g.: MS:1001150 (param: b ion-H2O)
  e.g.: MS:1001151 (param: y ion-NH3)
  e.g.: MS:1001152 (param: y ion-H2O)
  e.g.: MS:1001257 (param: v ion)
  et al.
MAY supply a *child* term of MS:1001210 (mass type settings) one or more times
  e.g.: MS:1001211 (parent mass type mono)
  e.g.: MS:1001212 (parent mass type average)
  e.g.: MS:1001255 (fragment mass type average)
  e.g.: MS:1001256 (fragment mass type mono)










Element <ModificationParams>






Definition:
 The specification of static/variable modifications (e.g. Oxidation of Methionine) that are to be considered in the spectra search. 





Type:
ModificationParamsType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


SearchModification1unbounded Specification of a search modification as parameter for a spectra search. Contains the name of the modification, the mass, the specificity and whether it is a static modification. 








Example Context:

<ModificationParams>
  <SearchModification fixedMod="false" >
    <ModParam massDelta="57.021469" residues="C">
      <cvParam accession="UNIMOD:4" name="Carbamidomethyl" cvRef="UNIMOD"/>
    </ModParam>
  </SearchModification>
  <SearchModification fixedMod="false" >
  ...
</ModificationParams>










Element <Enzymes>






Definition:
The list of enzymes used in experiment





Type:
PSI-PI.analysis.search.EnzymesType





Attributes:



Attribute NameData TypeUseDefinition


independentxsd:booleanoptionalIf there are multiple enzymes specified, this attribute is set to true if cleavage with different enzymes is performed independently








Subelements:



Subelement NameminOccursmaxOccursDefinition


Enzyme1unboundedThe details of an individual cleavage enzyme should be provided by giving a regular expression or a CV term if a "standard" enzyme cleavage has been performed.








Example Context:

<Enzymes independent="0">
  <Enzyme id="ENZ_0" CTermGain="OH" NTermGain="H" missedCleavages="1" semiSpecific="0">
    <SiteRegexp><![CDATA[(?<=M)]]></SiteRegexp>
    <EnzymeName>
      <cvParam accession="MS:1001307" name="CNBr" cvRef="PSI-MS" />
    </EnzymeName>
  </Enzyme>
  ...
</Enzymes>










Element <MassTable>






Definition:
The masses of residues used in the search.





Type:
PSI-PI.analysis.search.MassTableType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use. 


msLevellistOfIntegersrequiredThe MS spectrum that the MassTable refers to e.g. "1" for MS1 "2" for MS2 or "1 2" for MS1 or MS2


namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


Residue0unboundedThe specification of a single residue within the mass table.


AmbiguousResidue0unboundedAmbiguous residues e.g. X can be specified by the Code attribute and a set of parameters for example giving the different masses that will be used in the search.








Example Context:

<MassTable id="MT_light" msLevel="1 2">
  <Residue Code="A" Mass="71.037113805"/>
  <Residue Code="C" Mass="103.009184505"/>
  <Residue Code="D" Mass="115.026943065"/>
  <Residue Code="E" Mass="129.042593135"/>
  <Residue Code="F" Mass="147.068413945"/>
  <Residue Code="G" Mass="57.021463735"/>
  ...
</MassTable>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/MassTable
MAY supply a *child* term of MS:1001354 (mass table options) one or more times
  e.g.: MS:1001346 (AAIndex mass table)










Element <FragmentTolerance>






Definition:
The tolerance of the search given as a plus and minus value with units.





Type:
ToleranceType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam1unbounded-








Example Context:

      <FragmentTolerance>
        <cvParam accession="MS:1001412" name="search tolerance plus value" cvRef="PSI-MS" value="0.9" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"/>
        <cvParam accession="MS:1001413" name="search tolerance minus value" cvRef="PSI-MS" value="0.9" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"/>
      </FragmentTolerance>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance
MUST supply term MS:1001412 (search tolerance plus value) only once
MUST supply term MS:1001413 (search tolerance minus value) only once










Element <ParentTolerance>






Definition:
The tolerance of the search given as a plus and minus value with units.





Type:
ToleranceType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam1unbounded-








Example Context:

      <ParentTolerance>
        <cvParam accession="MS:1001412" name="search tolerance plus value" cvRef="PSI-MS" value="75.0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO"/>
        <cvParam accession="MS:1001413" name="search tolerance minus value" cvRef="PSI-MS" value="75.0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO"/>
      </ParentTolerance>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance
MUST supply term MS:1001412 (search tolerance plus value) only once
MUST supply term MS:1001413 (search tolerance minus value) only once










Element <Threshold>






Definition:
The threshold(s) applied to determine that a result is significant. If multiple terms are used it is assumed that all conditions are satisfied by the passing results.





Type:
ParamListType





Attributes:
none






Subelements:
none






Example Context:

<Threshold>
  <cvParam accession="MS:1001316" name="mascot:SigThreshold"                               cvRef="PSI-MS" value="0.05"/>
</Threshold>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/Threshold
MUST supply a *child* term of MS:1001302 (search engine specific input parameter) only once
  e.g.: MS:1001005 (sequest:CleavesAt)
  e.g.: MS:1001007 (sequest:OutputLines)
  e.g.: MS:1001009 (sequest:DescriptionLines)
  e.g.: MS:1001026 (sequest:NormalizeXCorrValues)
  e.g.: MS:1001028 (sequest:SequenceHeaderFilter)
  e.g.: MS:1001032 (sequest:SequencePartialFilter)
  e.g.: MS:1001037 (sequest:ShowFragmentIons)
  e.g.: MS:1001038 (sequest:Consensus)
  e.g.: MS:1001042 (sequest:LimitTo)
  e.g.: MS:1001046 (sequest:sort_by_dCn)
  et al.
MUST supply a *child* term of MS:1001153 (search engine specific score) only once
  e.g.: MS:1001154 (sequest:probability)
  e.g.: MS:1001155 (sequest:xcorr)
  e.g.: MS:1001156 (sequest:deltacn)
  e.g.: MS:1001157 (sequest:sp)
  e.g.: MS:1001158 (sequest:Uniq)
  e.g.: MS:1001159 (sequest:expectation value)
  e.g.: MS:1001160 (sequest:sf)
  e.g.: MS:1001161 (sequest:matched ions)
  e.g.: MS:1001162 (sequest:total ions)
  e.g.: MS:1001163 (sequest:consensus score)
  et al.
MUST supply term MS:1001494 (no threshold) only once
MUST supply term MS:1001448 (pep:FDR threshold) only once



Path /mzIdentML/AnalysisProtocolCollection/ProteinDetectionProtocol/Threshold
MUST supply a *child* term of MS:1001302 (search engine specific input parameter) only once
  e.g.: MS:1001005 (sequest:CleavesAt)
  e.g.: MS:1001007 (sequest:OutputLines)
  e.g.: MS:1001009 (sequest:DescriptionLines)
  e.g.: MS:1001026 (sequest:NormalizeXCorrValues)
  e.g.: MS:1001028 (sequest:SequenceHeaderFilter)
  e.g.: MS:1001032 (sequest:SequencePartialFilter)
  e.g.: MS:1001037 (sequest:ShowFragmentIons)
  e.g.: MS:1001038 (sequest:Consensus)
  e.g.: MS:1001042 (sequest:LimitTo)
  e.g.: MS:1001046 (sequest:sort_by_dCn)
  et al.
MUST supply a *child* term of MS:1001153 (search engine specific score) only once
  e.g.: MS:1001154 (sequest:probability)
  e.g.: MS:1001155 (sequest:xcorr)
  e.g.: MS:1001156 (sequest:deltacn)
  e.g.: MS:1001157 (sequest:sp)
  e.g.: MS:1001158 (sequest:Uniq)
  e.g.: MS:1001159 (sequest:expectation value)
  e.g.: MS:1001160 (sequest:sf)
  e.g.: MS:1001161 (sequest:matched ions)
  e.g.: MS:1001162 (sequest:total ions)
  e.g.: MS:1001163 (sequest:consensus score)
  et al.
MUST supply term MS:1001447 (prot:FDR threshold) only once
MUST supply term MS:1001494 (no threshold) only once










Element <DatabaseFilters>






Definition:
The specification of filters applied to the database searched.





Type:
DatabaseFiltersType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


Filter1unboundedThe filter MUST include at least one of Include and Exclude. If both are used, it is assumed that inclusion is performed first.








Example Context:

<DatabaseFilters>
  <Filter>
    <FilterType>
      <cvParam accession="MS:1001020" name="DB filter taxonomy" cvRef="PSI-MS" />
    </FilterType>
    <Include>
      <cvParam accession="MS:1001467" name="taxonomy: NCBI TaxID" cvRef="PSI-MS" value="33208"/>
  ...
</DatabaseFilters>










Element <DatabaseTranslation>






Definition:
A specification of how a nucleic acid sequence database was translated for searching.





Type:
DatabaseTranslationType





Attributes:



Attribute NameData TypeUseDefinition


frameslistOfAllowedFramesoptionalThe frames in which the nucleic acid sequence has been translated as a space separated list








Subelements:



Subelement NameminOccursmaxOccursDefinition


TranslationTable1unboundedThe table used to translate codons into nucleic acids e.g. by reference to the NCBI translation table.








Example Context:

<DatabaseTranslation frames="1 2 3 -1 -2 -3">
  <TranslationTable id="TT_1" name="Standard">
    <cvParam accession="MS:1001025" name="translation table" cvRef="PSI-MS" value="FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG" />
    <cvParam accession="MS:1001410" name="translation start codons" cvRef="PSI-MS" value="---M---------------M---------------M----------------------------" />
    <cvParam accession="MS:1001423" name="translation table description" cvRef="PSI-MS" value="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG1" />
  </TranslationTable>
  <TranslationTable id="TT_2" name="Vertebrate Mitochondrial">
  ...
</DatabaseTranslation>










Element <AnalysisParams>






Definition:
The parameters and settings for the protein detection given as CV terms. 





Type:
ParamListType





Attributes:
none






Subelements:
none






Example Context:

<AnalysisParams>
  <cvParam accession="MS:1001316" name="mascot:SigThreshold"                               cvRef="PSI-MS" value="0.05"/>
  <cvParam accession="MS:1001317" name="mascot:MaxProteinHits"                             cvRef="PSI-MS" value="Auto"/>
  <cvParam accession="MS:1001318" name="mascot:ProteinScoringMethod"                       cvRef="PSI-MS" value="Standard"/>
  <cvParam accession="MS:1001319" name="mascot:MinMSMSThreshold"                           cvRef="PSI-MS" value="0"/>
  <cvParam accession="MS:1001320" name="mascot:ShowHomologousProteinsWithSamePeptides"     cvRef="PSI-MS" value="1"/>
  <cvParam accession="MS:1001321" name="mascot:ShowHomologousProteinsWithSubsetOfPeptides" cvRef="PSI-MS" value="1"/>
  ...
</AnalysisParams>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/ProteinDetectionProtocol/AnalysisParams
MAY supply a *child* term of MS:1001302 (search engine specific input parameter) one or more times
  e.g.: MS:1001005 (sequest:CleavesAt)
  e.g.: MS:1001007 (sequest:OutputLines)
  e.g.: MS:1001009 (sequest:DescriptionLines)
  e.g.: MS:1001026 (sequest:NormalizeXCorrValues)
  e.g.: MS:1001028 (sequest:SequenceHeaderFilter)
  e.g.: MS:1001032 (sequest:SequencePartialFilter)
  e.g.: MS:1001037 (sequest:ShowFragmentIons)
  e.g.: MS:1001038 (sequest:Consensus)
  e.g.: MS:1001042 (sequest:LimitTo)
  e.g.: MS:1001046 (sequest:sort_by_dCn)
  et al.
MAY supply a *child* term of MS:1001194 (quality estimation with decoy database) one or more times










Element <SourceFile>






Definition:
 A file from which this mzIdentML instance was created. 





Type:
PSI-PI.analysis.search.SourceFileType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use. 


locationxsd:anyURIrequired The location of the data file. 


namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:externalFormatDocumentation01 A URI to access documentation and tools to interpret the external format of the ExternalData instance. For example, XML Schema or static libraries (APIs) to access binary formats. 
         					 


pf:fileFormat01 The format of the ExternalData file, for example "tiff" for image files.








Example Context:

      <SourceFile id="SF1" location="proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X/SpectraData/Results1">
        <fileFormat>
          <cvParam accession="MS:1001275" name="ProteinScape SearchEvent" cvRef="PSI-MS"/>
        </fileFormat>
      </SourceFile>







cvParam Mapping Rules:

Path /mzIdentML/DataCollection/Inputs/SourceFile
MAY supply a *child* term of MS:1000561 (data file checksum type) one or more times
  e.g.: MS:1000568 (MD5)
  e.g.: MS:1000569 (SHA-1)










Element <SpectraData>






Definition:
 A data set containing spectra data (consisting of one or more spectra). 





Type:
PSI-PI.spectra.SpectraDataType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use. 


locationxsd:anyURIrequired The location of the data file. 


namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:externalFormatDocumentation01 A URI to access documentation and tools to interpret the external format of the ExternalData instance. For example, XML Schema or static libraries (APIs) to access binary formats. 
         					 


pf:fileFormat01 The format of the ExternalData file, for example "tiff" for image files.








Example Context:

<SpectraData location="file:///C:/DOCUME~1/DAVIDC~1.MAT/LOCALS~1/Temp/Dis83.tmp" id="SD_1">
  <fileFormat>
    <cvParam accession="MS:1001062" name="Mascot MGF file" cvRef="PSI-MS" />
  </fileFormat>
</SpectraData>










Element <SpectrumIdentificationList>






Definition:
 Represents the set of all search results from SpectrumIdentification. 





Type:
PSI-PI.analysis.search.SpectrumIdentificationListType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use. 


namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance. 


numSequencesSearchedxsd:intoptionalThis value should be provided unless a de novo search has been performed.








Subelements:



Subelement NameminOccursmaxOccursDefinition


FragmentationTable01Contains the types of measures that will be reported in generic arrays for each SpectrumIdentificationItem e.g. product ion m/z, product ion intensity, product ion m/z error


SpectrumIdentificationResult1unbounded All identifications made from searching one spectrum. For PMF data, all peptide identifications will be listed underneath as SpectrumIdentificationItems. For MS/MS data, there will be ranked SpectrumIdentificationItems corresponding to possible different peptide IDs.








Graphical Context:






Example Context:

<SpectrumIdentificationList id="SIL_1" numSequencesSearched="257964">
  <SpectrumIdentificationResult id="SIR_1" spectrumID="1" SpectraData_ref="SD_1">
    <SpectrumIdentificationItem id="SII_1_1"  calculatedMassToCharge="1107.534897" chargeState="1" experimentalMassToCharge="1108.53" Peptide_ref="peptide_1_1" rank="0" passThreshold="true">
      <PeptideEvidence id="PE_1_1_UVRB_THET8" start="542" end="550" pre="R" post="V" missedCleavages="0" isDecoy="false" DBSequence_Ref="DBSeq_UVRB_THET8" />
    </SpectrumIdentificationItem>
    <SpectrumIdentificationItem id="SII_1_8"  calculatedMassToCharge="1107.617584" chargeState="1" experimentalMassToCharge="1108.53" Peptide_ref="peptide_1_8" rank="0" passThreshold="true">
    </SpectrumIdentificationItem>
  ...
</SpectrumIdentificationList>







cvParam Mapping Rules:

Path /mzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList
MAY supply a *child* term of MS:1001184 (search statistics) one or more times
  e.g.: MS:1001035 (date / time search performed)
  e.g.: MS:1001036 (search time taken)
  e.g.: MS:1001177 (number of molecular hypothesis considered)










Element <ProteinDetectionList>






Definition:
 The protein list resulting from a protein detection process. 





Type:
PSI-PI.analysis.process.ProteinDetectionListType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use. 


namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


ProteinAmbiguityGroup0unboundedRepresents a set of logically related results from a protein detection, for example to represent conflicting assignments of peptides to proteins.








Example Context:

<ProteinDetectionList id="PDL_1">
  <ProteinAmbiguityGroup id="PAG_hit_1" >
    <ProteinDetectionHypothesis id="PDH_MYG_EQUBU" DBSequence_ref="DBSeq_MYG_EQUBU"  passThreshold="true">
      <PeptideHypothesis  PeptideEvidence_Ref="PE_1_1_MYG_EQUBU" />
      <cvParam accession="MS:1001171" name="mascot:score" cvRef="PSI-MS" value="405.72" />
      <cvParam accession="MS:1001093" name="sequence coverage" cvRef="PSI-MS" value="99" />
      <cvParam accession="MS:1001097" name="distinct peptide sequences" cvRef="PSI-MS" value="1" />
  ...
</ProteinDetectionList>







cvParam Mapping Rules:

Path /mzIdentML/DataCollection/AnalysisData/ProteinDetectionList
MAY supply a *child* term of MS:1001184 (search statistics) one or more times
  e.g.: MS:1001035 (date / time search performed)
  e.g.: MS:1001036 (search time taken)
  e.g.: MS:1001177 (number of molecular hypothesis considered)










Element <pf:role>






Definition:
 The roles (lab equipment sales, contractor, etc.) the Contact fills. 





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam11 A single entry from an ontology or a controlled vocabulary.








Example Context:










Element <SearchModification>






Definition:
 Specification of a search modification as parameter for a spectra search. Contains the name of the modification, the mass, the specificity and whether it is a static modification. 





Type:
PSI-PI.analysis.search.SearchModificationType





Attributes:



Attribute NameData TypeUseDefinition


fixedModxsd:booleanrequired True, if the modification is static (i.e. occurs always). 








Subelements:



Subelement NameminOccursmaxOccursDefinition


ModParam11The modification searched for, sourced from e.g. UniMod and the mass delta


SpecificityRules01The specificity rules of the searched modification including for example the probability of a modification's presence or peptide or protein termini. Standard fixed or variable status should be provided by the attribute fixedMod.








Example Context:

<SearchModification fixedMod="false" >
  <ModParam massDelta="127.063324" residues="">
    <cvParam accession="UNIMOD:29" name="SMA" cvRef="UNIMOD"/>
  </ModParam>
  <SpecificityRules>
    <cvParam accession="MS:1001189" cvRef="PSI-MS" name="modification specificity N-term"/>
  </SpecificityRules>
  ...
</SearchModification>










Element <Enzyme>






Definition:
The details of an individual cleavage enzyme should be provided by giving a regular expression or a CV term if a "standard" enzyme cleavage has been performed.





Type:
PSI-PI.analysis.search.EnzymeType





Attributes:



Attribute NameData TypeUseDefinition


CTermGainoptionalElement formula gained at CTerm.


NTermGainoptionalElement formula gained at NTerm.


idxsd:stringrequired


minDistanceoptionalMinimal distance for another cleavage (minimum: 1).


missedCleavagesxsd:intoptionalThe number of missed cleavage sites allowed by the search. The attribute MUST be provided if an enzyme has been used.


semiSpecificxsd:booleanoptionalSet to true if the enzyme cleaves semi-specifically (i.e. one terminus MUST cleave according to the rules, the other can cleave at any residue), false if the enzyme cleavage is assumed to be specific to both termini (accepting for any missed cleavages).








Subelements:



Subelement NameminOccursmaxOccursDefinition


SiteRegexp01Regular expression for specifying the enzyme cleavage site.


EnzymeName01The name of the enzyme from a CV.








Example Context:

<Enzyme id="ENZ_1" CTermGain="OH" NTermGain="H" missedCleavages="1" semiSpecific="0">
  <SiteRegexp><![CDATA[(?<=[KR])(?!P)]]></SiteRegexp>
  <EnzymeName>
    <cvParam accession="MS:1001251" name="Trypsin" cvRef="PSI-MS" />
  </EnzymeName>
</Enzyme>










Element <Residue>






Definition:
The specification of a single residue within the mass table.





Type:
ResidueType





Attributes:



Attribute NameData TypeUseDefinition


CodecharsrequiredThe single letter code for the residue.


Massxsd:floatrequiredThe residue mass in Daltons. 








Subelements:
none






Example Context:

<Residue Code="C" Mass="103.009184505"/>










Element <AmbiguousResidue>






Definition:
Ambiguous residues e.g. X can be specified by the Code attribute and a set of parameters for example giving the different masses that will be used in the search.





Type:
AmbiguousResidueType





Attributes:



Attribute NameData TypeUseDefinition


Codecharsrequired








Subelements:
none






Example Context:

<AmbiguousResidue Code="X">
  <cvParam accession="MS:1001360" name="alternate single letter codes" cvRef="PSI-MS" value="A C D E F G H I K L M N O P Q R S T U V W Y"/>
</AmbiguousResidue>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/MassTable/AmbiguousResidue
MAY supply a *child* term of MS:1001359 (ambiguous residues) one or more times
  e.g.: MS:1001360 (alternate single letter codes)
  e.g.: MS:1001361 (alternate mass)










Element <cvParam>






Definition:
-





Attributes:
none






Subelements:
none






Example Context:

      <cvParam accession="MS:1001088" name="protein description" cvRef="PSI-MS" value=">IPI:IPI00414676.5|SWISS-PROT:P08238|TREMBL:Q5T9W7;Q6PK50;Q9H6X9|ENSEMBL:ENSP00000325875|REFSEQ:NP_031381|H-INV:HIT000008644;HIT000032091;HIT000034201;HIT000035963;HIT000036733;HIT000049765;HIT000057726|VEGA:OTTHUMP00000016517;OTTHUMP00000016518;OTTHUMP00000016519 Tax_Id=9606 Heat shock protein HSP 90-beta"/>










Element <Filter>






Definition:
The filter MUST include at least one of Include and Exclude. If both are used, it is assumed that inclusion is performed first.





Type:
FilterType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


FilterType11The type of filter e.g. database taxonomy filter, pi filter, mw filter 


Include01All sequences fulfilling the specifed criteria are included.


Exclude01All sequences fulfilling the specifed criteria are excluded.








Example Context:

<Filter>
  <FilterType>
    <cvParam accession="MS:1001020" name="DB filter taxonomy" cvRef="PSI-MS" />
  </FilterType>
  <Include>
    <cvParam accession="MS:1001467" name="taxonomy: NCBI TaxID" cvRef="PSI-MS" value="33208"/>
  </Include>
  ...
</Filter>










Element <TranslationTable>






Definition:
The table used to translate codons into nucleic acids e.g. by reference to the NCBI translation table.





Type:
TranslationTableType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use. 


namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam0unbounded-








Example Context:

<TranslationTable id="TT_4" name="Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma">
  <cvParam accession="MS:1001025" name="translation table" cvRef="PSI-MS" value="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG" />
  <cvParam accession="MS:1001410" name="translation start codons" cvRef="PSI-MS" value="--MM---------------M------------MMMM---------------M------------" />
  <cvParam accession="MS:1001423" name="translation table description" cvRef="PSI-MS" value="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG4" />
</TranslationTable>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/DatabaseTranslation/TranslationTable
MUST supply term MS:1001410 (translation start codons) only once
MUST supply term MS:1001025 (translation table) only once
MUST supply term MS:1001423 (translation table description) only once










Element <pf:externalFormatDocumentation>






Definition:
 A URI to access documentation and tools to interpret the external format of the ExternalData instance. For example, XML Schema or static libraries (APIs) to access binary formats. 
         					 





Type:
xsd:anyURI





Attributes:
none






Subelements:
none






Example Context:










Element <pf:fileFormat>






Definition:
 The format of the ExternalData file, for example "tiff" for image files.





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam11 A single entry from an ontology or a controlled vocabulary.








Example Context:










Element <FragmentationTable>






Definition:
Contains the types of measures that will be reported in generic arrays for each SpectrumIdentificationItem e.g. product ion m/z, product ion intensity, product ion m/z error





Type:
FragmentationTableType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


Measure1unboundedReferences to CV terms defining the measures about product ions to be reported in SpectrumIdentificationItem








Example Context:

      <FragmentationTable>
          <Measure id="m_mz">
            <cvParam cvRef="PSI-MS" accession="MS:1001225" name="product ion m/z"/>
          </Measure>
          <Measure id="m_intensity">
            <cvParam cvRef="PSI-MS" accession="MS:1001226" name="product ion intensity"/>
          </Measure>
  ...
</FragmentationTable>










Element <SpectrumIdentificationResult>






Definition:
 All identifications made from searching one spectrum. For PMF data, all peptide identifications will be listed underneath as SpectrumIdentificationItems. For MS/MS data, there will be ranked SpectrumIdentificationItems corresponding to possible different peptide IDs.





Type:
PSI-PI.analysis.search.SpectrumIdentificationResultType





Attributes:



Attribute NameData TypeUseDefinition


SpectraData_refxsd:stringrequired A reference to a spectra data set (e.g. a spectra file). 


idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use. 


namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance. 


spectrumIDxsd:stringrequired The locally unique id for the spectrum in the spectra data set specified by SpectraData_ref. External guidelines are provided on the use of consistent identifiers for spectra in different external formats.








Subelements:



Subelement NameminOccursmaxOccursDefinition


SpectrumIdentificationItem1unbounded An identification of a single (poly)peptide, resulting from querying an input spectra, along with the set of confidence values for that identification. PeptideEvidence elements should be given for all mappings of the corresponding Peptide sequence within protein sequences.








Example Context:

<SpectrumIdentificationResult id="SIR_1" spectrumID="query_1" SpectraData_ref="SD_1">
  <SpectrumIdentificationItem id="SII_1_1"  calculatedMassToCharge="670.86261" chargeState="2" experimentalMassToCharge="671.9" Peptide_ref="peptide_1_1" rank="1" passThreshold="true">
    <PeptideEvidence id="PE_1_1_HSP70_ECHGR" start="161" end="172" pre="K" post="I" missedCleavages="0" isDecoy="false" DBSequence_Ref="DBSeq_HSP70_ECHGR" />
    <PeptideEvidence id="PE_1_1_HSP70_ONCMY" start="160" end="171" pre="K" post="L" missedCleavages="0" isDecoy="false" DBSequence_Ref="DBSeq_HSP70_ONCMY" />
    <PeptideEvidence id="PE_1_1_HSP7C_ICTPU" start="160" end="171" pre="K" post="I" missedCleavages="0" isDecoy="false" DBSequence_Ref="DBSeq_HSP7C_ICTPU" />
    <PeptideEvidence id="PE_1_1_HSP7C_ORYLA" start="160" end="171" pre="K" post="I" missedCleavages="0" isDecoy="false" DBSequence_Ref="DBSeq_HSP7C_ORYLA" />
    <PeptideEvidence id="PE_1_1_HSP7D_MANSE" start="160" end="171" pre="K" post="I" missedCleavages="0" isDecoy="false" DBSequence_Ref="DBSeq_HSP7D_MANSE" />
  ...
</SpectrumIdentificationResult>







cvParam Mapping Rules:

Path /mzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult
MAY supply a *child* term of MS:1001405 (spectrum identification result details) one or more times
  e.g.: MS:1000796 (spectrum title)
  e.g.: MS:1000797 (peak list scans)
  e.g.: MS:1000798 (peak list raw scans)
  e.g.: MS:1001030 (number of peptide seqs compared to each spectrum)
  e.g.: MS:1001035 (date / time search performed)
  e.g.: MS:1001036 (search time taken)
  e.g.: MS:1001088 (protein description)
  e.g.: MS:1001090 (taxonomy nomenclature)
  e.g.: MS:1001093 (sequence coverage)
  e.g.: MS:1001097 (distinct peptide sequences)
  et al.










Element <ProteinAmbiguityGroup>






Definition:
Represents a set of logically related results from a protein detection, for example to represent conflicting assignments of peptides to proteins.





Type:
PSI-PI.analysis.process.ProteinAmbiguityGroupType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use. 


namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


ProteinDetectionHypothesis1unbounded A single result of the ProteinDetection analysis (i.e. a protein).








Example Context:

<ProteinAmbiguityGroup id="PAG_hit_1" >
  <ProteinDetectionHypothesis id="PDH_HSP7D_MANSE" DBSequence_ref="DBSeq_HSP7D_MANSE"  passThreshold="true">
    <PeptideHypothesis  PeptideEvidence_Ref="PE_1_1_HSP7D_MANSE" />
    <PeptideHypothesis  PeptideEvidence_Ref="PE_3_1_HSP7D_MANSE" />
    <cvParam accession="MS:1001171" name="mascot:score" cvRef="PSI-MS" value="104.854382332144" />
    <cvParam accession="MS:1001093" name="sequence coverage" cvRef="PSI-MS" value="4" />
    <cvParam accession="MS:1001097" name="distinct peptide sequences" cvRef="PSI-MS" value="2" />
  ...
</ProteinAmbiguityGroup>










Element <pf:cvParam>






Definition:
 A single entry from an ontology or a controlled vocabulary.





Type:
FuGE.Common.Ontology.cvParamType





Attributes:



Attribute NameData TypeUseDefinition


accessionxsd:stringrequiredThe accession or ID number of this CV term in the source CV.


cvRefxsd:stringrequiredA reference to the cv element from which this term originates.


namexsd:stringrequiredThe name of the parameter.


unitAccessionxsd:stringoptionalAn accession number identifying the unit within the OBO foundry Unit CV.


unitCvRefxsd:stringoptionalIf a unit term is referenced, this attribute MUST refer to the CV 'id' attribute defined in the cvList in this file.


unitNamexsd:stringoptionalThe name of the unit.


valuexsd:stringoptionalThe user-entered value of the parameter.








Subelements:
none






Example Context:










Element <ModParam>






Definition:
The modification searched for, sourced from e.g. UniMod and the mass delta





Type:
PSI-PI.polypeptide.ModParamType





Attributes:



Attribute NameData TypeUseDefinition


massDeltaxsd:floatrequiredThe mass delta of the searched modification in Daltons


residueslistOfCharsrequiredThe residue(s) searched with the specified modification








Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam11-








Example Context:

          <ModParam residues="M" massDelta="15.994914622">
            <cvParam accession="UNIMOD:35" name="Oxidation" cvRef="UNIMOD"/>
          </ModParam>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ModificationParams/SearchModification/ModParam
MUST supply a *child* term of UNIMOD:0 (UNIMOD root) one or more times
MUST supply a *child* term of MS:1001471 (peptide modification details) one or more times
  e.g.: MS:1001460 (unknown modification)
  e.g.: MS:1001524 (fragment neutral loss)
  e.g.: MS:1001525 (precursor neutral loss )
MUST supply a *child* term of MOD:00000 (protein modification) one or more times










Element <SpecificityRules>






Definition:
The specificity rules of the searched modification including for example the probability of a modification's presence or peptide or protein termini. Standard fixed or variable status should be provided by the attribute fixedMod.





Type:
SpecificityRulesType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam1unbounded-








Example Context:

<SpecificityRules>
  <cvParam accession="MS:1001189" cvRef="PSI-MS" name="modification specificity N-term"/>
</SpecificityRules>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ModificationParams/SearchModification/SpecificityRules
MUST supply a *child* term of MS:1001056 (modification specificity rule) one or more times
  e.g.: MS:1001189 (modification specificity N-term)
  e.g.: MS:1001190 (modification specificity C-term)










Element <SiteRegexp>






Definition:
Regular expression for specifying the enzyme cleavage site.





Type:
PSI-PI.analysis.search.SiteRegexpType





Attributes:
none






Subelements:
none






Example Context:

<SiteRegexp><![CDATA[(?<=[KR])(?!P)]]></SiteRegexp>










Element <EnzymeName>






Definition:
The name of the enzyme from a CV.





Type:
ParamListType





Attributes:
none






Subelements:
none






Example Context:

          <EnzymeName>
            <cvParam accession="MS:1001251" name="Trypsin" cvRef="PSI-MS"/>
          </EnzymeName>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/Enzymes/Enzyme/EnzymeName
MAY supply a *child* term of MS:1001045 (cleavage agent name) only once
  e.g.: MS:1001091 (NoEnzyme)
  e.g.: MS:1001251 (Trypsin)
  e.g.: MS:1001303 (Arg-C)
  e.g.: MS:1001304 (Asp-N)
  e.g.: MS:1001305 (Asp-N_ambic)
  e.g.: MS:1001306 (Chymotrypsin)
  e.g.: MS:1001307 (CNBr)
  e.g.: MS:1001308 (Formic_acid)
  e.g.: MS:1001309 (Lys-C)
  e.g.: MS:1001310 (Lys-C/P)
  et al.










Element <FilterType>






Definition:
The type of filter e.g. database taxonomy filter, pi filter, mw filter 





Type:
ParamType





Attributes:
none






Subelements:
none






Example Context:

<FilterType>
  <cvParam accession="MS:1001020" name="DB filter taxonomy" cvRef="PSI-MS" />
</FilterType>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/DatabaseFilters/Filter/FilterType
MUST supply a *child* term of MS:1001511 (Sequence database filter types) one or more times
  e.g.: MS:1001020 (DB filter taxonomy)
  e.g.: MS:1001021 (DB filter on accession numbers)
  e.g.: MS:1001022 (DB MW filter)
  e.g.: MS:1001023 (DB PI filter)
  e.g.: MS:1001027 (DB filter on sequence pattern)










Element <Include>






Definition:
All sequences fulfilling the specifed criteria are included.





Type:
ParamListType





Attributes:
none






Subelements:
none






Example Context:

<Include>
  <cvParam accession="MS:1001467" name="taxonomy: NCBI TaxID" cvRef="PSI-MS" value="33208"/>
</Include>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/DatabaseFilters/Filter/Include
MAY supply a *child* term of MS:1001512 (Sequence database filters) one or more times
  e.g.: MS:1001090 (taxonomy nomenclature)
  e.g.: MS:1001201 (DB MW filter maximum)
  e.g.: MS:1001202 (DB MW filter minimum)
  e.g.: MS:1001203 (DB PI filter maximum)
  e.g.: MS:1001204 (DB PI filter minimum)
  e.g.: MS:1001467 (taxonomy: NCBI TaxID)
  e.g.: MS:1001468 (taxonomy: common name)
  e.g.: MS:1001469 (taxonomy: scientific name)
  e.g.: MS:1001470 (taxonomy: Swiss-Prot ID)
  e.g.: MS:1001513 (DB sequence filter pattern)
  et al.










Element <Exclude>






Definition:
All sequences fulfilling the specifed criteria are excluded.





Type:
ParamListType





Attributes:
none






Subelements:
none






Example Context:

<Exclude>
  <cvParam accession="MS:1001467" name="taxonomy: NCBI TaxID" cvRef="PSI-MS" value="45251"/>
</Exclude>







cvParam Mapping Rules:

Path /mzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/DatabaseFilters/Filter/Exclude
MAY supply a *child* term of MS:1001512 (Sequence database filters) one or more times
  e.g.: MS:1001090 (taxonomy nomenclature)
  e.g.: MS:1001201 (DB MW filter maximum)
  e.g.: MS:1001202 (DB MW filter minimum)
  e.g.: MS:1001203 (DB PI filter maximum)
  e.g.: MS:1001204 (DB PI filter minimum)
  e.g.: MS:1001467 (taxonomy: NCBI TaxID)
  e.g.: MS:1001468 (taxonomy: common name)
  e.g.: MS:1001469 (taxonomy: scientific name)
  e.g.: MS:1001470 (taxonomy: Swiss-Prot ID)
  e.g.: MS:1001513 (DB sequence filter pattern)
  et al.










Element <Measure>






Definition:
References to CV terms defining the measures about product ions to be reported in SpectrumIdentificationItem





Type:
MeasureType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use. 


namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam1unbounded-








Example Context:

<Measure id="m_error">
  <cvParam cvRef="PSI-MS" accession="MS:1001227" name="product ion m/z error" unitAccession="MS:1000040" unitName="m/z" unitCvRef="PSI-MS"/>
</Measure>







cvParam Mapping Rules:

Path /mzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/FragmentationTable/Measure
MUST supply a *child* term of  (???) one or more times
MUST supply term MS:1001226 (product ion intensity) only once
MUST supply term MS:1001225 (product ion m/z) only once
MUST supply term MS:1001227 (product ion m/z error) only once










Element <SpectrumIdentificationItem>






Definition:
 An identification of a single (poly)peptide, resulting from querying an input spectra, along with the set of confidence values for that identification. PeptideEvidence elements should be given for all mappings of the corresponding Peptide sequence within protein sequences.





Type:
PSI-PI.analysis.search.SpectrumIdentificationItemType





Attributes:



Attribute NameData TypeUseDefinition


MassTable_refxsd:stringoptionalA reference should be given to the MassTable used to calculate the sequenceMass only if more than one MassTable has been given


Peptide_refxsd:stringoptional A reference to the identified (poly)peptide sequence in the Peptide element. 


Sample_refxsd:stringoptionalA reference should be provided to link the SpectrumIdentificationItem to a Sample if more than one sample has been described in the AnalysisSampleCollection. 


calculatedMassToChargexsd:doubleoptional The theoretical mass-to-charge value calculated for the peptide in Daltons / charge. 


calculatedPIxsd:floatoptional The calculated isoelectric point of the (poly)peptide, with relevant modifications included. Do not supply this value if the PI cannot be calcuated properly. 


chargeStatexsd:intrequired The charge state of the identified peptide. 


experimentalMassToChargexsd:doublerequired The mass-to-charge value measured in the experiment in Daltons / charge. 


idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use. 


namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance. 


passThresholdxsd:booleanrequiredSet to true if the producers of the file has deemed that the identification has passed a given threshold or been validated as correct. If no such threshold has been set, value of true should be given for all results. 


rankxsd:intrequiredFor an MS/MS result set, this is the rank of the identification quality as scored by the search engine. 1 is the top rank. If multiple identifications have the same top score, they should all be assigned rank =1. For PMF data, the rank attribute may be meaningless and values of rank = 0 should be given. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


PeptideEvidence0unboundedPeptideEvidence maps a spectrum identification to DBSequence in which such a peptide is located. 


Fragmentation01The product ions identified in this result.








Graphical Context:






Example Context:

<SpectrumIdentificationItem id="SII_10_18"  calculatedMassToCharge="2040.993866" chargeState="1" experimentalMassToCharge="2041.99" Peptide_ref="peptide_10_18" rank="0" passThreshold="true">
  <PeptideEvidence id="PE_10_18_VP3_BTV10" start="152" end="169" pre="R" post="N" missedCleavages="1" isDecoy="false" DBSequence_Ref="DBSeq_VP3_BTV10" />
  <PeptideEvidence id="PE_10_18_VP3_BTV11" start="152" end="169" pre="R" post="N" missedCleavages="1" isDecoy="false" DBSequence_Ref="DBSeq_VP3_BTV11" />
  <PeptideEvidence id="PE_10_18_VP3_BTV17" start="152" end="169" pre="R" post="N" missedCleavages="1" isDecoy="false" DBSequence_Ref="DBSeq_VP3_BTV17" />
  <PeptideEvidence id="PE_10_18_VP3_BTV1S" start="152" end="169" pre="R" post="N" missedCleavages="1" isDecoy="false" DBSequence_Ref="DBSeq_VP3_BTV1S" />
  <PeptideEvidence id="PE_10_18_VP3_BTV1A" start="152" end="169" pre="R" post="N" missedCleavages="1" isDecoy="false" DBSequence_Ref="DBSeq_VP3_BTV1A" />
  <PeptideEvidence id="PE_10_18_VP3_BTV13" start="152" end="169" pre="R" post="N" missedCleavages="1" isDecoy="false" DBSequence_Ref="DBSeq_VP3_BTV13" />
  ...
</SpectrumIdentificationItem>







cvParam Mapping Rules:

Path /mzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem
MAY supply a *child* term of MS:1001405 (spectrum identification result details) one or more times
  e.g.: MS:1000796 (spectrum title)
  e.g.: MS:1000797 (peak list scans)
  e.g.: MS:1000798 (peak list raw scans)
  e.g.: MS:1001030 (number of peptide seqs compared to each spectrum)
  e.g.: MS:1001035 (date / time search performed)
  e.g.: MS:1001036 (search time taken)
  e.g.: MS:1001088 (protein description)
  e.g.: MS:1001090 (taxonomy nomenclature)
  e.g.: MS:1001093 (sequence coverage)
  e.g.: MS:1001097 (distinct peptide sequences)
  et al.










Element <ProteinDetectionHypothesis>






Definition:
 A single result of the ProteinDetection analysis (i.e. a protein).





Type:
PSI-PI.analysis.process.ProteinDetectionHypothesisType





Attributes:



Attribute NameData TypeUseDefinition


DBSequence_refxsd:stringoptionalA reference to the corresponding DBSequence entry. This is optional and redundant, because the PeptideEvidence elements referenced from here also map to the DBSequence.


idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use. 


namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance. 


passThresholdxsd:booleanrequiredSet to true if the producers of the file has deemed that the ProteinDetectionHypothesis has passed a given threshold or been validated as correct. If no such threshold has been set, value of true should be given for all results. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


PeptideHypothesis1unboundedPeptide evidence on which this ProteinHypothesis is based by reference to a PeptideEvidence element in a SpectrumIdentificationItem. 








Example Context:

          <ProteinDetectionHypothesis id="id_prot3" passThreshold="false">
            <PeptideHypothesis PeptideEvidence_Ref="PE1_SEQ_spec15_pep1"/>
            <PeptideHypothesis PeptideEvidence_Ref="PE1_SEQ_spec20_pep1"/>
            <cvParam accession="MS:1001093" name="sequence coverage" cvRef="PSI-MS" value="0.59"/>
            <cvParam accession="MS:1001301" name="protein rank" cvRef="PSI-MS" value="3"/>
            <cvParam accession="MS:1001097" name="distinct peptide sequences" cvRef="PSI-MS" value="2"/>
            <cvParam accession="MS:1001250" name="local FDR" cvRef="PSI-MS" value="33.33" unitAccession="UO:0000187" unitName="percent" unitCvRef="UO"/>
  ...
</ProteinDetectionHypothesis>







cvParam Mapping Rules:

Path /mzIdentML/DataCollection/AnalysisData/ProteinDetectionList/ProteinAmbiguityGroup/ProteinDetectionHypothesis
MAY supply a *child* term of  (???) one or more times
MAY supply a *child* term of MS:1001153 (search engine specific score) one or more times
  e.g.: MS:1001154 (sequest:probability)
  e.g.: MS:1001155 (sequest:xcorr)
  e.g.: MS:1001156 (sequest:deltacn)
  e.g.: MS:1001157 (sequest:sp)
  e.g.: MS:1001158 (sequest:Uniq)
  e.g.: MS:1001159 (sequest:expectation value)
  e.g.: MS:1001160 (sequest:sf)
  e.g.: MS:1001161 (sequest:matched ions)
  e.g.: MS:1001162 (sequest:total ions)
  e.g.: MS:1001163 (sequest:consensus score)
  et al.
MAY supply a *child* term of MS:1001060 (quality estimation method details) one or more times
  e.g.: MS:1001058 (quality estimation by manual validation)
  e.g.: MS:1001194 (quality estimation with decoy database)
  e.g.: MS:1001447 (prot:FDR threshold)
  e.g.: MS:1001448 (pep:FDR threshold)
  e.g.: MS:1001454 (quality estimation with implicite decoy sequences)
  e.g.: MS:1001494 (no threshold)
MAY supply a *child* term of MS:1001085 (protein result details) one or more times
  e.g.: MS:1001088 (protein description)
  e.g.: MS:1001090 (taxonomy nomenclature)
  e.g.: MS:1001093 (sequence coverage)
  e.g.: MS:1001097 (distinct peptide sequences)
  e.g.: MS:1001098 (confident distinct peptide sequences)
  e.g.: MS:1001099 (confident peptide qualification)
  e.g.: MS:1001100 (confident peptide)
  e.g.: MS:1001101 (protein group/subset relationship)
  e.g.: MS:1001125 (manual validation)
  e.g.: MS:1001157 (sequest:sp)
  et al.










Element <PeptideEvidence>






Definition:
PeptideEvidence maps a spectrum identification to DBSequence in which such a peptide is located. 





Type:
PSI-PI.analysis.process.PeptideEvidenceType





Attributes:



Attribute NameData TypeUseDefinition


DBSequence_Refxsd:stringrequiredA reference to the sequence from which this identification has been made.


TranslationTable_refxsd:stringoptionalA reference to the translation table used if this is PeptideEvidence derived from nucleic acid sequence


endxsd:intoptional The index position of the last amino acid of the peptide inside the protein sequence, where the first amino acid of the protein sequence is position 1. 


framepsi-pi:allowed_framesoptionalThe translation frame of this sequence if this is PeptideEvidence derived from nucleic acid sequence


idxsd:stringrequired An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use. 


isDecoyxsd:booleanoptionalSet to true if the peptide is matched to a decoy sequence.


missedCleavagesxsd:intoptionalNumber of missed cleavage sites (not required if no enzyme has been used).


namexsd:stringoptional The potentially ambiguous common identifier, such as a human-readable name for the instance. 


postoptional Post flanking residue.  If the peptide is C-terminal, post="-" and not post="". If for any reason it is unknown (e.g. denovo), post="?" should be used.  


preoptional Previous flanking residue. If the peptide is N-terminal, pre="-" and not pre="". If for any reason it is unknown (e.g. denovo), pre="?" should be used. 


startxsd:intoptional Start position of the peptide inside the protein sequence, where the first amino acid of the protein sequence is position 1.  








Subelements:
none






Example Context:

<PeptideEvidence id="PE_4_1_gi|152812279" start="130" end="139" pre="R" post="V" missedCleavages="0" TranslationTable_ref="TT_1" frame="2" isDecoy="false" DBSequence_Ref="DBSeq_gi|152812279" />










Element <Fragmentation>






Definition:
The product ions identified in this result.





Type:
FragmentationType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


IonType1unboundedIonType defines the index of fragmentation ions being reported, importing a CV term for the type of ion e.g. b ion. Example: if b3 b7 b8 and b10 have been identified, the index attribute will contain 3 7 8 10, and the corresponding values will be reported in parallel arrays below








Example Context:

<Fragmentation>
  <IonType index="5 6 7 11 12 15 17 21 22 23 24 26 27 30 31 33 34 35 38 39 40 41 42 43 44 45 46 47 48 50 51 52 53 54 55 56 59 61 62 65 69 73 76 78 83 86 96" charge="1">
    <cvParam cvRef="PSI-MS" accession="MS:1001231" name="frag: c ion"/>
    <FragmentArray values="447.216737 576.26154 762.38947 1230.608358 1344.651696 1686.8204 1913.9818 2342.1727 2413.208 2470.2302 2607.2849 2792.370851 2921.413169 3246.646488 3402.747973 3662.8968 3763.9465 3820.9689 4184.122757 4285.1695 4398.254701 4527.295803 4655.3939 4802.459719 4917.4869 5045.580864 5192.648576 5320.7443 5457.7927 5698.9794 5800.027 5929.0677 6000.106688 6129.151636 6260.190033 6388.2896 6675.395079 6903.506231 7031.607787 7353.773068 7766.0424 8108.2303 8391.422 8647.6118 9235.887 9549.050832 10610.644 " Measure_ref="m_mz"/>
    <FragmentArray values="4380000 854900 7506000 30210000 12170000 11670000 9618000 10810000 8991000 15620000 5489000 13310000 21520000 31540000 19790000 5384000 9486000 12940000 28610000 8175000 24870000 46070000 10500000 46930000 19710000 22930000 31270000 10140000 5954000 7813000 17080000 9987000 16830000 35420000 14530000 5249000 56680000 13460000 14780000 17410000 5084000 8978000 8186000 7804000 7299000 22380000 6606000" Measure_ref="m_intensity"/>
    <FragmentArray values="-0.0031 -0.0008 0.0478 -0.0030 -0.0026 -0.0030 -0.0050 -0.0048 -0.0067 -0.0059 -0.0101 -0.0042 -0.0045 -0.0077 -0.0073 -0.0110 -0.0090 -0.0080 -0.0084 -0.0094 -0.0082 -0.0097 -0.0066 -0.0092 -0.0090 -0.0100 -0.0107 -0.0099 -0.0204 -0.0127 -0.0128 -0.0147 -0.0128 -0.0105 -0.0126 -0.0080 -0.0142 -0.0141 -0.0075 -0.0175 -0.0168 -0.0192 -0.0171 -0.0172 -0.0189 -0.0188 -0.0238" Measure_ref="m_error"/>
  </IonType>
  ...
</Fragmentation>










Element <PeptideHypothesis>






Definition:
Peptide evidence on which this ProteinHypothesis is based by reference to a PeptideEvidence element in a SpectrumIdentificationItem. 





Type:
PeptideHypothesisType





Attributes:



Attribute NameData TypeUseDefinition


PeptideEvidence_Refxsd:stringrequiredA reference to the PeptideEvidence element on which this hypothesis is based.








Subelements:
none






Example Context:

            <PeptideHypothesis PeptideEvidence_Ref="PE1_SEQ_spec10_pep1"/>










Element <IonType>






Definition:
IonType defines the index of fragmentation ions being reported, importing a CV term for the type of ion e.g. b ion. Example: if b3 b7 b8 and b10 have been identified, the index attribute will contain 3 7 8 10, and the corresponding values will be reported in parallel arrays below





Type:
IonTypeType





Attributes:



Attribute NameData TypeUseDefinition


chargexsd:intrequiredThe charge of the identified fragmentation ions.


indexlistOfIntegersoptionalThe index of ions identified as integers, following standard notation for a-c, x-z e.g. if b3 b5 and b6 have been identified, the index would store "3 5 6". For internal ions, the index contains pairs defining the start and end point - see specification document for examples. For immonium ions, the index is the position of the identified ion within the peptide sequence - if the peptide contains the same amino acid in multiple positions that cannot be distinguished, all positions should be given. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam11-


FragmentArray0unboundedAn array of values for a given type of measure and for a particular ion type, in parallel to the index of ions identified.








Example Context:

<IonType index="5 6 7 11 12 15 17 21 22 23 24 26 27 30 31 33 34 35 38 39 40 41 42 43 44 45 46 47 48 50 51 52 53 54 55 56 59 61 62 65 69 73 76 78 83 86 96" charge="1">
  <cvParam cvRef="PSI-MS" accession="MS:1001231" name="frag: c ion"/>
  <FragmentArray values="447.216737 576.26154 762.38947 1230.608358 1344.651696 1686.8204 1913.9818 2342.1727 2413.208 2470.2302 2607.2849 2792.370851 2921.413169 3246.646488 3402.747973 3662.8968 3763.9465 3820.9689 4184.122757 4285.1695 4398.254701 4527.295803 4655.3939 4802.459719 4917.4869 5045.580864 5192.648576 5320.7443 5457.7927 5698.9794 5800.027 5929.0677 6000.106688 6129.151636 6260.190033 6388.2896 6675.395079 6903.506231 7031.607787 7353.773068 7766.0424 8108.2303 8391.422 8647.6118 9235.887 9549.050832 10610.644 " Measure_ref="m_mz"/>
  <FragmentArray values="4380000 854900 7506000 30210000 12170000 11670000 9618000 10810000 8991000 15620000 5489000 13310000 21520000 31540000 19790000 5384000 9486000 12940000 28610000 8175000 24870000 46070000 10500000 46930000 19710000 22930000 31270000 10140000 5954000 7813000 17080000 9987000 16830000 35420000 14530000 5249000 56680000 13460000 14780000 17410000 5084000 8978000 8186000 7804000 7299000 22380000 6606000" Measure_ref="m_intensity"/>
  <FragmentArray values="-0.0031 -0.0008 0.0478 -0.0030 -0.0026 -0.0030 -0.0050 -0.0048 -0.0067 -0.0059 -0.0101 -0.0042 -0.0045 -0.0077 -0.0073 -0.0110 -0.0090 -0.0080 -0.0084 -0.0094 -0.0082 -0.0097 -0.0066 -0.0092 -0.0090 -0.0100 -0.0107 -0.0099 -0.0204 -0.0127 -0.0128 -0.0147 -0.0128 -0.0105 -0.0126 -0.0080 -0.0142 -0.0141 -0.0075 -0.0175 -0.0168 -0.0192 -0.0171 -0.0172 -0.0189 -0.0188 -0.0238" Measure_ref="m_error"/>
</IonType>







cvParam Mapping Rules:

Path /mzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem/Fragmentation/IonType
MAY supply a *child* term of MS:1001221 (fragmentation information) one or more times
  e.g.: MS:1001220 (frag: y ion)
  e.g.: MS:1001222 (frag: b ion - H2O)
  e.g.: MS:1001223 (frag: y ion - H2O)
  e.g.: MS:1001224 (frag: b ion)
  e.g.: MS:1001225 (product ion m/z)
  e.g.: MS:1001226 (product ion intensity)
  e.g.: MS:1001227 (product ion m/z error)
  e.g.: MS:1001228 (frag: x ion)
  e.g.: MS:1001229 (frag: a ion)
  e.g.: MS:1001230 (frag: z ion)
  et al.










Element <FragmentArray>






Definition:
An array of values for a given type of measure and for a particular ion type, in parallel to the index of ions identified.





Type:
FragmentArrayType





Attributes:



Attribute NameData TypeUseDefinition


Measure_refxsd:stringrequiredA reference to the Measure defined in the FragmentationTable


valueslistOfFloatsrequiredThe values of this particular measure, corresponding to the index defined in ion type








Subelements:
none






Example Context:

<FragmentArray values="447.216737 576.26154 762.38947 1230.608358 1344.651696 1686.8204 1913.9818 2342.1727 2413.208 2470.2302 2607.2849 2792.370851 2921.413169 3246.646488 3402.747973 3662.8968 3763.9465 3820.9689 4184.122757 4285.1695 4398.254701 4527.295803 4655.3939 4802.459719 4917.4869 5045.580864 5192.648576 5320.7443 5457.7927 5698.9794 5800.027 5929.0677 6000.106688 6129.151636 6260.190033 6388.2896 6675.395079 6903.506231 7031.607787 7353.773068 7766.0424 8108.2303 8391.422 8647.6118 9235.887 9549.050832 10610.644 " Measure_ref="m_mz"/>