Element <AnalysisXML>

Definition: The upper-most hierarchy level of PSI-PI containing data of Proteomics informatics, for example spectra search results or protein detection results.
Type: PSI-PI.Main.AnalysisXMLType
Attributes:
Attribute NameData TypeUseDefinition
BibliographicReference_refxsd:string-A literature reference for this analysisXML file, provided in the ReferenceCollection.
creationDatexsd:dateTime-The 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:string- The potentially ambiguous common identifier, such as a human-readable name for the instance.
Subelements:
Subelement NameminOccursmaxOccursDefinition
pf:DatabaseReference01 A reference to a record in a database.
cvList11 The list of CVs used within the file
AnalysisSoftwareList01 The software used to perform the analyses (specify at least name, manufacturer, version, URL).
pf:Provider01The Provider of the AnalysisXML record in terms of the contact and software.
pf:AuditCollection01The complete set of Contacts (people and organisations) for this file.
pf:ReferenceableCollection0unboundedThe collection of literature references and database entries associated with this record, referenced elsewhere in the file.
AnalysisSampleCollection01The samples analysed can optionally be recorded using CV terms for descriptions.
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.
Graphical Context:
Example Context: 
<AnalysisXML id="MPC_use_case" creationDate="2008-11-28T13:56:00" xmlns="http://psidev.info/psi/pi/analysis/1.0" xmlns:pf="http://psidev.info/fuge-light/1.0" xmlns:psi-pi="http://psidev.info/psi/pi/analysis/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/analysis/1.0 ../schema/AnalysisXML_working.xsd">
  <!-- 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! -->
  <!-- CAUTION: spectrumID/SpectrumElement changed to fulfill primary key constraint. It has to be checked, whether in this use case this
constraint is valid! -->
  <cvList>
    <pf:cv id="PSI-PI" fullName="Proteomics Standards Initiative - Proteome Informatics" URI="http://www.psidev.info/psi-pi" version="0.8"/>
    <pf:cv id="BTO" fullName="BRENDA tissue 7 enzyme source" URI="http://www.brenda-enzymes.info/" version="12/2007"/>
  ...
</AnalysisXML>
Notes and Constraints: Special notes may arbitrarily appear like this in the documentation even when not in the xsd.

Element <pf:DatabaseReference>

Definition: A reference to a record in a database.
Type: pf:FuGE.Common.References.DatabaseReferenceType
Attributes:
Attribute NameData TypeUseDefinition
Database_refxsd:stringrequired Reference to the database where the DatabaseEntry instance can be found.
accessionxsd:stringrequired The identifier used to look up the record.
accessionVersionxsd:string- The appropriate version of the accession (if applicable).
Subelements: none
Example Context: 









Element <cvList>






Definition:
 The list of CVs used within the file





Type:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cv1unboundedA source controlled vocabulary from which cvParams will be obtained.








Example Context:

  <cvList>
    <pf:cv id="PSI-PI" fullName="Proteomics Standards Initiative - Proteome Informatics" URI="http://www.psidev.info/psi-pi" version="0.8"/>
    <pf:cv id="BTO" fullName="BRENDA tissue 7 enzyme source" URI="http://www.brenda-enzymes.info/" version="12/2007"/>
    <pf:cv id="MPC-CV" fullName="MPC decoy databases" URI="http://www.medizinishces-proteom-center.de/MPC_ontology" version="to come"/>
    <pf:cv id="UNIMOD" fullName="UNIMOD CV for modifications" URI="http://www.unimod.org"/>
    <pf:cv id="NEWT" fullName="NEWT taxonomy database" URI="http://www.ebi.ac.uk/newt/display"/>
    <pf: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:






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">
      <pf:ContactRole Contact_ref="THERMO">
        <pf:role>
          <pf:cvParam accession="PI:00267" name="software vendor" cvRef="PSI-PI"/>
        </pf:role>
      </pf:ContactRole>
  ...
</AnalysisSoftwareList>










Element <pf:Provider>






Definition:
The Provider of the AnalysisXML record in terms of the contact and software.





Type:
pf:FuGE.Collection.ProviderType





Attributes:



Attribute NameData TypeUseDefinition


Software_refxsd:string- The Software that produced the document instance. 


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








Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:ContactRole01 The Contact that provided the document instance. 








Example Context:

<pf:Provider id="PROVIDER">
  <pf:ContactRole Contact_ref="PERSON_DOC_OWNER">
    <pf:role>
      <pf:cvParam accession="PI:00271" name="researcher" cvRef="PSI-PI" />
    </pf:role>
  </pf:ContactRole>
</pf:Provider>










Element <pf:AuditCollection>






Definition:
The complete set of Contacts (people and organisations) for this file.





Type:
pf:FuGE.Collection.AuditCollectionType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:Organization0unbounded The complete set of Contacts. 


pf:Person0unbounded The complete set of Contacts. 








Example Context:

  <pf:AuditCollection>
    <pf:Organization id="BRUKER" name="Bruker Daltonics GmbH" address="Bremen, Germany"/>
    <pf:Organization id="MATRIXSCIENCE" name="MatrixScience" address="UK"/>
    <pf:Organization id="THERMO" name="Thermo Corp." address="USA"/>
    <pf:Person id="MPCMEYER" name="Prof. Dr. Helmut E. Meyer" address="Universitaetsstr. 150, D-44795 Bochum, Germany" email="helmut.e.meyer@rub.de">
      <pf:affiliations Organization_ref="MPCINSTITUTE"/>
    </pf:Person>
  ...
</pf:AuditCollection>










Element <pf:ReferenceableCollection>






Definition:
The collection of literature references and database entries associated with this record, referenced elsewhere in the file.





Type:
pf:FuGE.Collection.ReferenceableCollectionType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:BibliographicReference0unbounded Reference to the complete set of BibliographicReference objects in the FuGE document. 


pf:Database0unbounded Reference to the complete set of Database objects in the FuGE document. 








Example Context:










Element <AnalysisSampleCollection>






Definition:
The samples analysed can optionally be recorded using CV terms for descriptions.





Type:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:GenericMaterial1unbounded A subclass of the abstract Material class, which should be used in conjunction with controlled vocabulary terms to describe Materials of any types used in an investigation. 








Example Context:

  <AnalysisSampleCollection>
    <pf:GenericMaterial id="sample1">
      <pf:cvParam accession="NEWT:9606" name="Homo sapiens" cvRef="NEWT"/>
      <pf:cvParam accession="BTO:0000255" name="brain cell line" cvRef="BTO"/>
    </pf:GenericMaterial>
  </AnalysisSampleCollection>










Element <SequenceCollection>






Definition:
The collection of sequences (DBSequence or Peptide) identified to be referenced in the results.





Type:






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). Specify sequence length, mass and pI (attributes), and sequence, modifications and taxa (elements). 








Graphical Context:






Example Context:

<SequenceCollection>
  <DBSequence id="DBSeq_PML_HUMAN" length="882" SearchDatabase_ref="SDB_SwissProt" accession="PML_HUMAN" >
    <seq>MEPAPARSPRPQQDPARPQEPTMPPPETPSEGRQPSPSPSPTERAPASEEEFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASGMQCPICQAPWPLGADTPALDNVFFESLQRRLSVYRQIVDAQAVCTRCKESADFWCFECEQLLCAKCFEAHQWFLKHEARPLAELRNQSVREFLDGTRKTNNIFCSNPNHRTPTLTSIYCRGCSKPLCCSCALLDSSHSELKCDISAEIQQRQEELDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAETEELIRERVRQVVAHVRAQERELLEAVDARYQRDYEEMASRLGRLDAVLQRIRTGSALVQRMKCYASDQEVLDMHGFLRQALCRLRQEEPQSLQAAVRTDGFDEFKVRLQDLSSCITQGKDAAVSKKASPEAASTPRDPIDVDLPEEAERVKAQVQALGLAEAQPMAVVQSVPGAHPVPVYAFSIKGPSYGEDVSNTTTAQKRKCSQTQCPRKVIKMESEEGKEARLARSSPEQPRPSTSKAVSPPHLDGPPSPRSPVIGSEVFLPNSNHVASGAGEAEERVVVISSSEDSDAENSSSRELDDSSSESSDLQLEGPSTLRVLDENLADPQAEDRPLVFFDLKIDNETQKISQLAAVNRESKFRVVIQPEALFSIYSKAVSLEVGLQHFLSFLSSMRRPILACYKLWGPGLPNFFRALEDINRLWEFQEAISGFLAALPLIRERVPGASSFKLKNLAQTYLARNMSERSAMAAVLAMRDLCRLLEVSPGPQLAQHVYPFSSLQCFASLQPLVQAAVLPRAEARLLALHNVSFMELLSAHRRDRQGGLKKYSRYLSLQTTTLPPAQPAFNLQALGTYFEGLLEGPALARAEGVSTPLAGRGLAERASQQS</seq>
    <pf:cvParam accession="PI:00088" name="protein description" cvRef="PSI-PI" value="Probable transcription factor PML (Tripartite motif-containing protein 19) (RING finger protein 71)" />
  </DBSequence>
  <DBSequence id="DBSeq_MURC_IDILO" length="490" SearchDatabase_ref="SDB_SwissProt" accession="MURC_IDILO" >
    <seq>MTSMTATNAQPFTIVNVPEMRRVQRIHFVGIGGAGMAGIAEVLLNQGYQISGSDIAENANTERLRCLGATVVLGHMANNIEGASVVVVSSAIKADNAELVAAHQLRVPVVRRAEMLAELMRFRHGIAVAGTHGKTTTTSLVASIFAEAGRDPTFVIGGLLNSAGSNARLGNSKYLIAEADESDASFLHLQPMVAIVTNIEADHMDTYEGDFNKLLDTYVEFLHNLPFYGLAVMCVDDPVVSDLIPRLGRQTMTYGFSEAADVRAIDYKQTASESCFTILRKGLKPLDVCLNLPGKHNVLNALAAVAVATDEGINDEAIKSALNKFEGIGRRFQHYGNFAISDKDSNKEPGEVMLVDDYGHHPSEVAATIQAAREGWPERRLVMAFQPHRYSRTRDLYEDFVNVLSQVDVLLMLEVYSAGETPVSGADSRSLCRSIRQRGQIDPVYVATVDDMPEVLESVLAPGDLLLTQGAGNIGALAKRIATEVLSHES</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:






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. Specify a DetectionProtocol, a result list DetectionList (attributes) and SpectrumIdentification lists as inputs (child elements). 








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:






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>
      <pf:cvParam accession="PI:00083" name="ms-ms search" cvRef="PSI-PI" value=""/>
    </SearchType>
    <AdditionalSearchParams>
      <pf:cvParam accession="PI:00002" name="user name"                cvRef="PSI-PI" value="David Creasy"/>
  ...
</AnalysisProtocolCollection>










Element <DataCollection>






Definition:
The collection of input and output data sets of the analyses.





Type:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


Inputs11The inputs to the analyses including the databases searched, the spectral data and the source file converted to AnalysisXML.


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">
        <!--pf:cvParam accession="PI:00275" name="ProteinScape SearchEvent" cvRef="PSI-PI"/-->
      </SourceFile>
      <SearchDatabase id="ipi.HUMAN_decoy" location="uri://www.medizinisches-proteom-center.de/ipi.HUMAN_decoy/3.15" name="ipi.HUMAN_decoy" version="3.15" releaseDate="22 February, 2006" numDatabaseSequences="58099">
        <DatabaseName>
  ...
</DataCollection>










Element <pf:cv>






Definition:
A source controlled vocabulary from which cvParams will be obtained.





Type:
pf:FuGE.Common.Ontology.cvType





Attributes:



Attribute NameData TypeUseDefinition


URIxsd:anyURIrequiredThe URI of the source CV.


fullNamexsd:stringrequiredThe full name of the CV.


idxsd:stringrequiredThe unique identifier of this cv within the document to be referenced by cvParam elements.


versionxsd:string-The version of the CV.








Subelements:
none






Example Context:

<pf:cv id="UO"            fullName="UNIT-ONTOLOGY" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"></pf:cv>










Element <AnalysisSoftware>






Definition:
 The software used for performing the analyses. 





Type:
PSI-PI.analysis.search.AnalysisSoftwareType





Attributes:



Attribute NameData TypeUseDefinition


URIxsd:anyURI-URI 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:string- The potentially ambiguous common identifier, such as a human-readable name for the instance. 


versionxsd:string- The version of Software used. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:ContactRole01 The Contact that provided the document instance. 


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">
      <pf:ContactRole Contact_ref="THERMO">
        <pf:role>
          <pf:cvParam accession="PI:00267" name="software vendor" cvRef="PSI-PI"/>
        </pf:role>
      </pf:ContactRole>
    </AnalysisSoftware>










Element <pf:ContactRole>






Definition:
 The Contact that provided the document instance. 





Type:
pf: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:

      <pf:ContactRole Contact_ref="MATRIXSCIENCE">
        <pf:role>
          <pf:cvParam accession="PI:00267" name="software vendor" cvRef="PSI-PI"/>
        </pf:role>
      </pf:ContactRole>










Element <pf:Organization>






Definition:
 Organizations are entities like companies, universities, government agencies for which the attributes are self describing. 





Type:
pf:FuGE.Common.Audit.OrganizationType





Attributes:



Attribute NameData TypeUseDefinition


addressxsd:string- The address of the Contact. 


emailxsd:string- The email address of the Contact. 


faxxsd:string- The fax number of the Contact. 


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


phonexsd:string- The telephone number of the Contact including the suitable area codes. 


tollFreePhonexsd:string- A toll free phone number for the Contact, including suitable area codes. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:parent01 The containing organization (the university or business which a lab belongs to, etc.) 








Example Context:

<pf:Organization id="ORG_MSL" name="Matrix Science Limited" address="64 Baker Street, London W1U 7GB, UK" email="support@matrixscience.com"  fax="+44 (0)20 7224 1344" phone="+44 (0)20 7486 1050" />










Element <pf:Person>






Definition:
 A person for which the attributes are self describing. 





Type:
pf:FuGE.Common.Audit.PersonType





Attributes:



Attribute NameData TypeUseDefinition


addressxsd:string- The address of the Contact. 


emailxsd:string- The email address of the Contact. 


faxxsd:string- The fax number of the Contact. 


firstNamexsd:string- The Person's first name. 


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. 


lastNamexsd:string- The Person's last/family name. 


midInitialsxsd:string- The Person's middle initial. 


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


phonexsd:string- The telephone number of the Contact including the suitable area codes. 


tollFreePhonexsd:string- A toll free phone number for the Contact, including suitable area codes. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:affiliations0unbounded The organization a person belongs to. 








Example Context:

    <pf:Person id="MPCMEYER" name="Prof. Dr. Helmut E. Meyer" address="Universitaetsstr. 150, D-44795 Bochum, Germany" email="helmut.e.meyer@rub.de">
      <pf:affiliations Organization_ref="MPCINSTITUTE"/>
    </pf:Person>










Element <pf:BibliographicReference>






Definition:
 Reference to the complete set of BibliographicReference objects in the FuGE document. 





Type:
pf:FuGE.Common.References.BibliographicReferenceType





Attributes:



Attribute NameData TypeUseDefinition


authorsxsd:string- The names of the authors of the reference. 


editorxsd:string- The editor(s) of the reference. 


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. 


issuexsd:string- The issue name or number. 


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


pagesxsd:string- The page numbers. 


publicationxsd:string- The name of the journal, book etc. 


publisherxsd:string- The publisher of the publication. 


titlexsd:string- The title of the BibliographicReference. 


volumexsd:string- The volume name or number. 


yearxsd:int- The year of publication. 








Subelements:
none






Example Context:










Element <pf:Database>






Definition:
 Reference to the complete set of Database objects in the FuGE document. 





Type:
pf:FuGE.Common.References.DatabaseType





Attributes:



Attribute NameData TypeUseDefinition


URIxsd:anyURI- The location of the Database. 


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


versionxsd:string- The version of the Database. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:ContactRole0unbounded The Contact that provided the document instance. 








Example Context:










Element <pf:GenericMaterial>






Definition:
 A subclass of the abstract Material class, which should be used in conjunction with controlled vocabulary terms to describe Materials of any types used in an investigation. 





Type:
pf:FuGE.Bio.Material.GenericMaterialType





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:string- 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. 


pf:cvParam0unbounded The default value for this parameter. 


pf:components0unbounded Association from a GenericMaterial to other GenericMaterials that are sub-components (such as wells within an array plate). If a subcomponent undergoes a ProtocolApplication, then the containing GenericMaterial MUST also be an input to the ProtocolApplication and be output as a new GenericMaterial or version of the GenericMaterial. 








Example Context:

    <pf:GenericMaterial id="sample1">
      <pf:cvParam accession="NEWT:9606" name="Homo sapiens" cvRef="NEWT"/>
      <pf:cvParam accession="BTO:0000255" name="brain cell line" cvRef="BTO"/>
    </pf:GenericMaterial>










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:int-The length of the sequence as an integers number of bases or residues.


namexsd:string- 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.


pf:cvParam0unbounded The default value for this parameter. 


pf:userParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.








Example Context:

    <DBSequence id="prot5_IPI" accession="IPI00398776.3" SearchDatabase_ref="ipi.HUMAN_decoy">
      <seq>
MKIVPDERDRVQKKTFTKWVNKHLIKAQRHISDLYEDLRDGHNLISLLEVLSGDSLPREKGRMRFHKLQNVQIALDYLRHRQVKLVNIRNDDIADGNPKLTLGLIWTIILHFQISDIQVSGQSEDMTAKEKLLLWSQRMVEGYQGLRCDNFTSSWRDGRLFNAIIHRHKPLLIDMNKVYRQTNLENLDQAFSVAERDLGVTRLLDPEDVDVPQPDEKSIITYVSSLYDAMPRVPDVQDGVRANELQLRWQEYRELVLLLLQWMRHHTAAFEERRFPSSFEEIEILWSQFLKFKEMELPAKEADKNRSKGIYQSLEGAVQAGQLKVPPGYHPLDVEKEWGKLHVAILEREKQLRSEFERLECLQRIVTKLQMEAGLCEEQLNQADALLQSDVRLLAAGKVPQRAGEVERDLDKADSMIRLLFNDVQTLKDGRHPQGEQMYRRVYRLHERLVAIRTEYNLRLKAGVAAPATQVAQVTLQSVQRRPELEDSTLRYLQDLLAWVEENQHRVDGAEWGVDLPSVEAQLGSHRGLHQSIEEFRAKIERARSDEGQLSPATRGAYRDCLGRLDLQYAKLLNSSKARLRSLESLHSFVAAATKELMWLNEKEEEEVGFDWSDRNTNMTAKKESYSALMRELELKEKKIKELQNAGDRLLREDHPARPTVESFQAALQTQWSWMLQLCCCIEAHLKENAAYFQFFSDVREAEGQLQKLQEALRRKYSCDRSATVTRLEDLLQDAQDEKEQLNEYKGHLSGLAKRAKAVVQLKPRHPAHPMRGRLPLLAVCDYKQVEVTVHKGDECQLVGPAQPSHWKVLSSSGSEAAVPSVCFLVPPPNQEAQEAVTRLEAQHQALVTLWHQLHVDMKSLLAWQSLRRDVQLIRSWSLATFRTLKPEEQRQALHSLELHYQAFLRDSQDAGGFGPEDRLMAEREYGSCSHHYQQLLQSLEQGAQEESRCQRCISELKDIRLQLEACETRTVHRLRLPLDKEPARECAQRIAEQQKAQAEVEGLGKGVARLSAEAEKVLALPEPSPAAPTLRSELELTLGKLEQVRSLSAIYLEKLKTISLVIRGTQGAEEVLRAHEEQLKEAQAVPATLPELEATKASLKKLRAQAEAQQPTFDALRDELRGAQEVGERLQQRHGERDVEVERWRERVAQLLERWQAVLAQTDVRQRELEQLGRQLRYYRESADPLGAWLQDARRRQEQIQAMPLADSQAVREQLRQEQALLEEIERHGEKVEECQRFAKQYINAIKDYELQLVTYKAQLEPVASPAKKPKVQSGSESVIQEYVDLRTHYSELTTLTSQYIKFISETLRRMEEEERLAEQQRAEERERLAEVEAALEKQRQLAEAHAQAKAQAEREAKELQQRMQEEVVRREEAAVDAQQQKRSIQEELQQLRQSSEAEIQAKARQAEAAERSRLRIEEEIRVVRLQLEATERQRGGAEGELQALRARAEEAEAQKRQAQEEAERLRRQVQDESQRKRQAEVELASRVKAEAEAAREKQRALQALEELRLQAEEAERRLRQAEVERARQVQVALETAQRSAEAELQSKRASFAEKTAQLERSLQEEHVAVAQLREEAERRAQQQAEAERAREEAERELERWQLKANEALRLRLQAEEVAQQKSLAQAEAEKQKEEAEREARRRGKAEEQAVRQRELAEQELEKQRQLAEGTAQQRLAAEQELIRLRAETEQGEQQRQLLEEELARLQREAAAATQKRQELEAELAKVRAEMEVLLASKARAEEESRSTSEKSKQRLEAEAGRFRELAEEAARLRALAEEAKRQRQLAEEDAARQRAEAERVLAEKLAAIGEATRLKTEAEIALKEKEAENERLRRLAEDEAFQRRRLEEQAAQHKADIEERLAQLRKASDSELERQKGLVEDTLRQRRQVEEEILALKASFEKAAAGKAELELELGRIRSNAEDTLRSKEQAELEAARQRQLAAEEERRRREAEERVQKSLAAEEEAARQRKAALEEVERLKAKVEEARRLRERAEQESARQLQLAQEAAQKRLQAEEKAHAFAVQQKEQELQQTLQQEQSVLDQLRGEAEAARRAAEEAEEARVQAEREAAQSRRQVEEAERLKQSAEEQAQARAQAQAAAEKLRKEAEQEAARRAQAEQAALRQKQAADAEMEKHKKFAEQTLRQKAQVEQELTTLRLQLEETDHQKNLLDEELQRLKAEATEAARQRSQVEEELFSVRVQMEELSKLKARIEAENRALILRDKDNTQRFLQEEAEKMKQVAEEAARLSVAAQEAARLRQLAEEDLAQQRALAEKMLKEKMQAVQEATRLKAEAELLQQQKELAQEQARRLQEDKEQMAQQLAEETQGFQRTLEAERQRQLEMSAEAERLKLRVAEMSRAQARAEEDAQRFRKQAEEIGEKLHRTELATQEKVTLVQTLEIQRQQSDHDAERLREAIAELEREKEKLQQEAKLLQLKSEEMQTVQQEQLLQETQALQQSFLSEKDSLLQRERFIEQEKAKLEQLFQDEVAKAQQLREEQQRQQQQMEQERQRLVASMEEARRRQHEAEEGVRRKQEELQQLEQQRRQQEELLAEENQRLREQLQLLEEQHRAALAHSEEVTASQVAATKTLPNGRDALDGPAAEAEPEHSFDGLRRKVSAQRLQEAGILSAEELQRLAQGHTTVDELARREDVRHYLQGRSSIAGLLLKATNEKLSVYAALQRQLLSPGTALILLEAQAASGFLLDPVRNRRLTVNEAVKEGVVGPELHHKLLSAERAVTGYKDPYTGQQISLFQAMQKGLIVREHGIRLLEAQIATGGVIDPVHSHRVPVDVAYRRGYFDEEMNRVLADPSDDTKGFFDPNTHENLTYLQLLERCVEDPETGLCLLPLTDKAAKGGELVYTDSEARDVFEKATVSAPFGKFQGKTVTIWEIINSEYFTAEQRRDLLRQFRTGRITVEKIIKIIITVVEEQEQKGRLCFEGLRSLVPAAELLESRVIDRELYQQLQRGERSVRDVAEVDTVRRALRGANVIAGVWLEEAGQKLSIYNALKKDLLPSDMAVALLEAQAGTGHIIDPATSARLTVDEAVRAGLVGPEFHEKLLSAEKAVTGYRDPYTGQSVSLFQALKKGLIPREQGLRLLDAQLSTGGIVDPSKSHRVPLDVACARGCLDEETSRALSAPRADAKAYSDPSTGEPATYGELQQRCRPDQLTGLSLLPLSEKAARARQEELYSELQARETFEKTPVEVPVGGFKGRTVTVWELISSEYFTAEQRQELLRQFRTGKVTVEKVIKILITIVEEVETLRQERLSFSGLRAPVPASELLASGVLSRAQFEQLKDGKTTVKDLSELGSVRTLLQGSGCLAGIYLEDTKEKVSIYEAMRRGLLRATTAALLLEAQAATGFLVDPVRNQRLYVHEAVKAGVVGPELHEQLLSAEKAVTGYRDPYSGSTISLFQAMQKGLVLRQHGIRLLEAQIATGGIIDPVHSHRVPVDVAYQRGYFSEEMNRVLADPSDDTKGFFDPNTHENLTYRQLLERCVEDPETGLRLLPLKGAEKAEVVETTQVYTEEETRRAFEETQIDIPGGGSHGGSTMSLWEVMQSDLIPEEQRAQLMADFQAGRVTKERMIIIIIEIIEKTEIIRQQGLASYDYVRRRLTAEDLFEARIISLETYNLLREGTRSLREALEAESAWCYLYGTGSVAGVYLPGSRQTLSIYQALKKGLLSAEVARLLLEAQAATGFLLDPVKGERLTVDEAVRKGLVGPELHDRLLSAERAVTGYRDPYTEQTISLFQAMKKELIPTEEALRLLDAQLATGGIVDPRLGFHLPLEVAYQRGYLNKDTHDQLSEPSEVRSYVDPSTDERLSYTQLLRRCRRDDGTGQLLLPLSDARKLTFRGLRKQITMEELVRSQVMDEATALQLREGLTSIEEVTKNLQKFLEGTSCIAGVFVDATKERLSVYQAMKKGIIRPGTAFELLEAQAATGYVIDPIKGLKLTVEEAVRMGIVGPEFKDKLLSAERAVTGYKDPYSGKLISLFQAMKKGLILKDHGIRLLEAQIATGGIIDPEESHRLPVEVAYKRGLFDEEMNEILTDPSDDTKGFFDPNTEENLTYLQLMERCITDPQTGLCLLPLKEKKRERKTSSKSSVRKRRVVIVDPETGKEMSVYEAYRKGLIDHQTYLELSEQECEWEEITISSSDGVVKSMIIDRRSGRQYDIDDAIAKNLIDRSALDQYRAGTLSITEFADMLSGNAGGFRSRSSSVGSSSSYPISPAVSRTQLASWSDPTEETGPVAGILDTETLEKVSITEAMHRNLVDNITGQRLLEAQACTGGIIDPSTGERFPVTDAVNKGLVDKIMVDRINLAQKAFCGFEDPRTKTKMSAAQALKKGWLYYEAGQRFLEVQYLTGGLIEPDTPGRVPLDEALQRGTVDARTAQKLRDVGAYSKYLTCPKTKLKISYKDALDRSMVEEGTGLRLLEAAAQSTKGYYSPYSVSGSGSTAGSRTGSRTGSRAGSRRGSFDATGSGFSMTFSSSSYSSSGYGRRYASGSSASLGGPESAVA
      </seq>
      <pf:cvParam accession="PI:00088" name="protein description" cvRef="PSI-PI" value=">IPI:IPI00398776.3|TREMBL:Q6S379;Q96IE3|REFSEQ:NP_958783 Tax_Id=9606 plectin 1 isoform 7"/>
    </DBSequence>







cvParam Mapping Rules:

Path /AnalysisXML/SequenceCollection/DBSequence
MAY supply a *child* term of PI:00342 (database sequence details) only once
  e.g.: PI:00088 (protein description)
  e.g.: PI:00343 (NA sequence)
  e.g.: PI:00344 (AA sequence)










Element <Peptide>






Definition:
 One (poly)peptide (a sequence with modifications). Specify sequence length, mass and pI (attributes), and sequence, modifications and taxa (elements). 





Type:
PSI-PI.polypeptide.PeptideType





Attributes:



Attribute NameData TypeUseDefinition


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


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


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


sequenceLengthxsd:int- The length of the (poly)peptide (number of amino acids). 


sequenceMassxsd:double- The sum of the masses of (poly)peptide sequence residues,including any modifications and the termini masses in Daltons. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


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.


pf:cvParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


peptideSequence01 The amino acid sequence of the (poly)peptide. 








Example Context:

<Peptide id="peptide_139_3" sequenceMass="1536.666336" sequenceLength="13" MassTable_ref="MT_heavy">
  <Modification location="1" residues="C" monoisotopicMassDelta="57.021469">
    <pf:cvParam accession="UNIMOD:4" name="Carbamidomethyl" cvRef="UNIMOD" />
  </Modification>
  <Modification location="9" residues="C" monoisotopicMassDelta="57.021469">
    <pf:cvParam accession="UNIMOD:4" name="Carbamidomethyl" cvRef="UNIMOD" />
  </Modification>
  ...
</Peptide>







cvParam Mapping Rules:

Path /AnalysisXML/SequenceCollection/Peptide
MAY supply a *child* term of PI:00355 (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:string- A reference to the SearchResultSet in the DataCollection section. 


SpectrumIdentificationProtocol_refxsd:stringrequired A reference to the search protocol used for this PolypeptideSearch. 


activityDatexsd:dateTime- 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:string- 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. 


InputSpectra1unbounded The attribute referencing an identifier within the SpectraData section. 


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. Specify a DetectionProtocol, a result list DetectionList (attributes) and SpectrumIdentification lists as inputs (child elements). 





Type:
PSI-PI.analysis.process.ProteinDetectionType





Attributes:



Attribute NameData TypeUseDefinition


ProteinDetectionList_refxsd:string- A reference to the ProteinDetectionList in the DataCollection section. 


ProteinDetectionProtocol_refxsd:stringrequired A reference to the detection protocol used for this ProteinDetection. 


activityDatexsd:dateTime- 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:string- 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. 


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:string- 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.


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>
    <pf:cvParam accession="PI:00083" name="ms-ms search" cvRef="PSI-PI" value=""/>
  </SearchType>
  <AdditionalSearchParams>
    <pf:cvParam accession="PI:00002" name="user name"                cvRef="PSI-PI" value="Some Person"/>
    <pf:cvParam accession="PI:00003" name="user email address"       cvRef="PSI-PI" value="someone@someuniversity.edu"/>
  ...
</SpectrumIdentificationProtocol>










Element <ProteinDetectionProtocol>






Definition:
 The parameters and settings of a ProteinDetection process. 





Type:
PSI-PI.analysis.process.ProteinDetectionProtocolType





Attributes:



Attribute NameData TypeUseDefinition


AnalysisSoftware_refxsd:string- 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:string- 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. 








Graphical Context:






Example Context:

<ProteinDetectionProtocol id="PDP_MascotParser_1"  AnalysisSoftware_ref="AS_mascot_parser">
  <AnalysisParams>
    <pf:cvParam accession="PI:00316" name="mascot:SigThreshold"                               cvRef="PSI-PI" value="0.05"/>
    <pf:cvParam accession="PI:00317" name="mascot:MaxProteinHits"                             cvRef="PSI-PI" value="Auto"/>
    <pf:cvParam accession="PI:00318" name="mascot:ProteinScoringMethod"                       cvRef="PSI-PI" value="Standard"/>
    <pf:cvParam accession="PI:00319" name="mascot:MinMSMSThreshold"                           cvRef="PSI-PI" value="0"/>
    <pf:cvParam accession="PI:00320" name="mascot:ShowHomologousProteinsWithSamePeptides"     cvRef="PSI-PI" value="1"/>
  ...
</ProteinDetectionProtocol>










Element <Inputs>






Definition:
The inputs to the analyses including the databases searched, the spectral data and the source file converted to AnalysisXML.





Type:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


SourceFile0unbounded A file from which this AnalysisXML 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">
        <!--pf:cvParam accession="PI:00275" name="ProteinScape SearchEvent" cvRef="PSI-PI"/-->
      </SourceFile>
      <SearchDatabase id="ipi.HUMAN_decoy" location="uri://www.medizinisches-proteom-center.de/ipi.HUMAN_decoy/3.15" name="ipi.HUMAN_decoy" version="3.15" releaseDate="22 February, 2006" numDatabaseSequences="58099">
        <DatabaseName>
          <pf:userParam name="ipi.HUMAN_decoy"/>
  ...
</Inputs>










Element <AnalysisData>






Definition:
Data sets generated by the analyses, including peptide and protein lists.





Type:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


SpectrumIdentificationList1unbounded Represents the set of all search results from SpectrumIdentification and ProteinDetection. 


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="813.47084" chargeState="1" experimentalMassToCharge="814.43" Peptide_ref="peptide_1_1" rank="0" passThreshold="true">
        <PeptideEvidence id="PE_1_1_PML_HUMAN" start="319" end="325" pre="R" post="I" frame="0" isDecoy="false" DBSequence_Ref="DBSeq_PML_HUMAN" />
      </SpectrumIdentificationItem>
      <SpectrumIdentificationItem id="SII_1_5"  calculatedMassToCharge="813.398071" chargeState="1" experimentalMassToCharge="814.43" Peptide_ref="peptide_1_5" rank="0" passThreshold="true">
  ...
</AnalysisData>










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 <pf:role>






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





Type:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam11 The default value for this parameter. 








Example Context:

        <pf:role>
          <pf:cvParam accession="PI:00267" name="software vendor" cvRef="PSI-PI"/>
        </pf:role>







cvParam Mapping Rules:

Path /AnalysisXML/pf:Provider/pf:ContactRole/pf:role
MUST supply a *child* term of PI:00266 (role type) one or more times
  e.g.: PI:00267 (software vendor)
  e.g.: PI:00268 (programmer)
  e.g.: PI:00269 (instrument vendor)
  e.g.: PI:00270 (lab personnell)
  e.g.: PI:00271 (researcher)



Path /AnalysisXML/pf:ReferenceableCollection/pf:Database/pf:ContactRole/pf:role
MUST supply a *child* term of PI:00266 (role type) one or more times
  e.g.: PI:00267 (software vendor)
  e.g.: PI:00268 (programmer)
  e.g.: PI:00269 (instrument vendor)
  e.g.: PI:00270 (lab personnell)
  e.g.: PI:00271 (researcher)
MUST supply a *child* term of BTO:0000000 (brenda source tissue ontology) one or more times



Path /AnalysisXML/AnalysisCollection/SpectrumIdentification/pf:ContactRole/pf:role
MUST supply a *child* term of PI:00266 (role type) one or more times
  e.g.: PI:00267 (software vendor)
  e.g.: PI:00268 (programmer)
  e.g.: PI:00269 (instrument vendor)
  e.g.: PI:00270 (lab personnell)
  e.g.: PI:00271 (researcher)



Path /AnalysisXML/AnalysisSoftwareList/AnalysisSoftware/pf:ContactRole/pf:role
MUST supply a *child* term of PI:00266 (role type) one or more times
  e.g.: PI:00267 (software vendor)
  e.g.: PI:00268 (programmer)
  e.g.: PI:00269 (instrument vendor)
  e.g.: PI:00270 (lab personnell)
  e.g.: PI:00271 (researcher)










Element <pf:parent>






Definition:
 The containing organization (the university or business which a lab belongs to, etc.) 





Type:






Attributes:



Attribute NameData TypeUseDefinition


Organization_refxsd:stringrequired








Subelements:
none






Example Context:

      <pf:parent Organization_ref="RUB"/>










Element <pf:affiliations>






Definition:
 The organization a person belongs to. 





Type:






Attributes:



Attribute NameData TypeUseDefinition


Organization_refxsd:stringrequired








Subelements:
none






Example Context:

      <pf:affiliations Organization_ref="MPCINSTITUTE"/>










Element <pf:cvParam>






Definition:
 The default value for this parameter. 





Type:
pf: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:string-An 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:string-The name of the unit.


valuexsd:stringoptionalThe user-entered value of the parameter.








Subelements:
none






Example Context:

      <pf:cvParam accession="PI:00088" name="protein description" cvRef="PSI-PI" 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"/>







Example cvParams:

<pf:cvParam cvRef="PSI-PI" accession="PI:00225" name="product ion m/z"/>
<pf:cvParam cvRef="PSI-PI" accession="PI:00226" name="product ion intensity"/>
<pf:cvParam cvRef="PSI-PI" accession="PI:00227" name="product ion m/z error"/>










Element <pf:components>






Definition:
 Association from a GenericMaterial to other GenericMaterials that are sub-components (such as wells within an array plate). If a subcomponent undergoes a ProtocolApplication, then the containing GenericMaterial MUST also be an input to the ProtocolApplication and be output as a new GenericMaterial or version of the GenericMaterial. 





Type:






Attributes:



Attribute NameData TypeUseDefinition


GenericMaterial_refxsd:stringrequired








Subelements:
none






Example Context:










Element <seq>






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





Type:
xsd:string





Attributes:
none






Subelements:
none






Example Context:

      <seq>
MKIVPDERDRVQKKTFTKWVNKHLIKAQRHISDLYEDLRDGHNLISLLEVLSGDSLPREKGRMRFHKLQNVQIALDYLRHRQVKLVNIRNDDIADGNPKLTLGLIWTIILHFQISDIQVSGQSEDMTAKEKLLLWSQRMVEGYQGLRCDNFTSSWRDGRLFNAIIHRHKPLLIDMNKVYRQTNLENLDQAFSVAERDLGVTRLLDPEDVDVPQPDEKSIITYVSSLYDAMPRVPDVQDGVRANELQLRWQEYRELVLLLLQWMRHHTAAFEERRFPSSFEEIEILWSQFLKFKEMELPAKEADKNRSKGIYQSLEGAVQAGQLKVPPGYHPLDVEKEWGKLHVAILEREKQLRSEFERLECLQRIVTKLQMEAGLCEEQLNQADALLQSDVRLLAAGKVPQRAGEVERDLDKADSMIRLLFNDVQTLKDGRHPQGEQMYRRVYRLHERLVAIRTEYNLRLKAGVAAPATQVAQVTLQSVQRRPELEDSTLRYLQDLLAWVEENQHRVDGAEWGVDLPSVEAQLGSHRGLHQSIEEFRAKIERARSDEGQLSPATRGAYRDCLGRLDLQYAKLLNSSKARLRSLESLHSFVAAATKELMWLNEKEEEEVGFDWSDRNTNMTAKKESYSALMRELELKEKKIKELQNAGDRLLREDHPARPTVESFQAALQTQWSWMLQLCCCIEAHLKENAAYFQFFSDVREAEGQLQKLQEALRRKYSCDRSATVTRLEDLLQDAQDEKEQLNEYKGHLSGLAKRAKAVVQLKPRHPAHPMRGRLPLLAVCDYKQVEVTVHKGDECQLVGPAQPSHWKVLSSSGSEAAVPSVCFLVPPPNQEAQEAVTRLEAQHQALVTLWHQLHVDMKSLLAWQSLRRDVQLIRSWSLATFRTLKPEEQRQALHSLELHYQAFLRDSQDAGGFGPEDRLMAEREYGSCSHHYQQLLQSLEQGAQEESRCQRCISELKDIRLQLEACETRTVHRLRLPLDKEPARECAQRIAEQQKAQAEVEGLGKGVARLSAEAEKVLALPEPSPAAPTLRSELELTLGKLEQVRSLSAIYLEKLKTISLVIRGTQGAEEVLRAHEEQLKEAQAVPATLPELEATKASLKKLRAQAEAQQPTFDALRDELRGAQEVGERLQQRHGERDVEVERWRERVAQLLERWQAVLAQTDVRQRELEQLGRQLRYYRESADPLGAWLQDARRRQEQIQAMPLADSQAVREQLRQEQALLEEIERHGEKVEECQRFAKQYINAIKDYELQLVTYKAQLEPVASPAKKPKVQSGSESVIQEYVDLRTHYSELTTLTSQYIKFISETLRRMEEEERLAEQQRAEERERLAEVEAALEKQRQLAEAHAQAKAQAEREAKELQQRMQEEVVRREEAAVDAQQQKRSIQEELQQLRQSSEAEIQAKARQAEAAERSRLRIEEEIRVVRLQLEATERQRGGAEGELQALRARAEEAEAQKRQAQEEAERLRRQVQDESQRKRQAEVELASRVKAEAEAAREKQRALQALEELRLQAEEAERRLRQAEVERARQVQVALETAQRSAEAELQSKRASFAEKTAQLERSLQEEHVAVAQLREEAERRAQQQAEAERAREEAERELERWQLKANEALRLRLQAEEVAQQKSLAQAEAEKQKEEAEREARRRGKAEEQAVRQRELAEQELEKQRQLAEGTAQQRLAAEQELIRLRAETEQGEQQRQLLEEELARLQREAAAATQKRQELEAELAKVRAEMEVLLASKARAEEESRSTSEKSKQRLEAEAGRFRELAEEAARLRALAEEAKRQRQLAEEDAARQRAEAERVLAEKLAAIGEATRLKTEAEIALKEKEAENERLRRLAEDEAFQRRRLEEQAAQHKADIEERLAQLRKASDSELERQKGLVEDTLRQRRQVEEEILALKASFEKAAAGKAELELELGRIRSNAEDTLRSKEQAELEAARQRQLAAEEERRRREAEERVQKSLAAEEEAARQRKAALEEVERLKAKVEEARRLRERAEQESARQLQLAQEAAQKRLQAEEKAHAFAVQQKEQELQQTLQQEQSVLDQLRGEAEAARRAAEEAEEARVQAEREAAQSRRQVEEAERLKQSAEEQAQARAQAQAAAEKLRKEAEQEAARRAQAEQAALRQKQAADAEMEKHKKFAEQTLRQKAQVEQELTTLRLQLEETDHQKNLLDEELQRLKAEATEAARQRSQVEEELFSVRVQMEELSKLKARIEAENRALILRDKDNTQRFLQEEAEKMKQVAEEAARLSVAAQEAARLRQLAEEDLAQQRALAEKMLKEKMQAVQEATRLKAEAELLQQQKELAQEQARRLQEDKEQMAQQLAEETQGFQRTLEAERQRQLEMSAEAERLKLRVAEMSRAQARAEEDAQRFRKQAEEIGEKLHRTELATQEKVTLVQTLEIQRQQSDHDAERLREAIAELEREKEKLQQEAKLLQLKSEEMQTVQQEQLLQETQALQQSFLSEKDSLLQRERFIEQEKAKLEQLFQDEVAKAQQLREEQQRQQQQMEQERQRLVASMEEARRRQHEAEEGVRRKQEELQQLEQQRRQQEELLAEENQRLREQLQLLEEQHRAALAHSEEVTASQVAATKTLPNGRDALDGPAAEAEPEHSFDGLRRKVSAQRLQEAGILSAEELQRLAQGHTTVDELARREDVRHYLQGRSSIAGLLLKATNEKLSVYAALQRQLLSPGTALILLEAQAASGFLLDPVRNRRLTVNEAVKEGVVGPELHHKLLSAERAVTGYKDPYTGQQISLFQAMQKGLIVREHGIRLLEAQIATGGVIDPVHSHRVPVDVAYRRGYFDEEMNRVLADPSDDTKGFFDPNTHENLTYLQLLERCVEDPETGLCLLPLTDKAAKGGELVYTDSEARDVFEKATVSAPFGKFQGKTVTIWEIINSEYFTAEQRRDLLRQFRTGRITVEKIIKIIITVVEEQEQKGRLCFEGLRSLVPAAELLESRVIDRELYQQLQRGERSVRDVAEVDTVRRALRGANVIAGVWLEEAGQKLSIYNALKKDLLPSDMAVALLEAQAGTGHIIDPATSARLTVDEAVRAGLVGPEFHEKLLSAEKAVTGYRDPYTGQSVSLFQALKKGLIPREQGLRLLDAQLSTGGIVDPSKSHRVPLDVACARGCLDEETSRALSAPRADAKAYSDPSTGEPATYGELQQRCRPDQLTGLSLLPLSEKAARARQEELYSELQARETFEKTPVEVPVGGFKGRTVTVWELISSEYFTAEQRQELLRQFRTGKVTVEKVIKILITIVEEVETLRQERLSFSGLRAPVPASELLASGVLSRAQFEQLKDGKTTVKDLSELGSVRTLLQGSGCLAGIYLEDTKEKVSIYEAMRRGLLRATTAALLLEAQAATGFLVDPVRNQRLYVHEAVKAGVVGPELHEQLLSAEKAVTGYRDPYSGSTISLFQAMQKGLVLRQHGIRLLEAQIATGGIIDPVHSHRVPVDVAYQRGYFSEEMNRVLADPSDDTKGFFDPNTHENLTYRQLLERCVEDPETGLRLLPLKGAEKAEVVETTQVYTEEETRRAFEETQIDIPGGGSHGGSTMSLWEVMQSDLIPEEQRAQLMADFQAGRVTKERMIIIIIEIIEKTEIIRQQGLASYDYVRRRLTAEDLFEARIISLETYNLLREGTRSLREALEAESAWCYLYGTGSVAGVYLPGSRQTLSIYQALKKGLLSAEVARLLLEAQAATGFLLDPVKGERLTVDEAVRKGLVGPELHDRLLSAERAVTGYRDPYTEQTISLFQAMKKELIPTEEALRLLDAQLATGGIVDPRLGFHLPLEVAYQRGYLNKDTHDQLSEPSEVRSYVDPSTDERLSYTQLLRRCRRDDGTGQLLLPLSDARKLTFRGLRKQITMEELVRSQVMDEATALQLREGLTSIEEVTKNLQKFLEGTSCIAGVFVDATKERLSVYQAMKKGIIRPGTAFELLEAQAATGYVIDPIKGLKLTVEEAVRMGIVGPEFKDKLLSAERAVTGYKDPYSGKLISLFQAMKKGLILKDHGIRLLEAQIATGGIIDPEESHRLPVEVAYKRGLFDEEMNEILTDPSDDTKGFFDPNTEENLTYLQLMERCITDPQTGLCLLPLKEKKRERKTSSKSSVRKRRVVIVDPETGKEMSVYEAYRKGLIDHQTYLELSEQECEWEEITISSSDGVVKSMIIDRRSGRQYDIDDAIAKNLIDRSALDQYRAGTLSITEFADMLSGNAGGFRSRSSSVGSSSSYPISPAVSRTQLASWSDPTEETGPVAGILDTETLEKVSITEAMHRNLVDNITGQRLLEAQACTGGIIDPSTGERFPVTDAVNKGLVDKIMVDRINLAQKAFCGFEDPRTKTKMSAAQALKKGWLYYEAGQRFLEVQYLTGGLIEPDTPGRVPLDEALQRGTVDARTAQKLRDVGAYSKYLTCPKTKLKISYKDALDRSMVEEGTGLRLLEAAAQSTKGYYSPYSVSGSGSTAGSRTGSRTGSRAGSRRGSFDATGSGFSMTFSSSSYSSSGYGRRYASGSSASLGGPESAVA
      </seq>










Element <pf:userParam>






Definition:
A single user-defined parameter.





Type:
pf:FuGE.Common.Ontology.userParamType





Attributes:



Attribute NameData TypeUseDefinition


namexsd:stringrequiredThe name of the parameter.


unitAccessionxsd:string-An 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:string-The name of the unit.


valuexsd:stringoptionalThe user-entered value of the parameter.








Subelements:
none






Example Context:

        <pf:userParam name="ProteinExtractor ProteinSolverPeptideScoreThreshold" value="0.0"/>










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.





Type:
PSI-PI.polypeptide.ModificationType





Attributes:



Attribute NameData TypeUseDefinition


avgMassDeltaxsd:double- Atomic mass considering the natural distribution of isotopes in Daltons. 


locationxsd:int-Location 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:double- Atomic mass when assuming only the most common isotope of elements in Daltons. 


residuespsi-pi:listOfChars-Specification 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:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.








Example Context:

<Modification location="10" residues="C" monoisotopicMassDelta="57.021469">
  <pf:cvParam accession="UNIMOD:4" name="Carbamidomethyl" cvRef="UNIMOD" />
</Modification>







cvParam Mapping Rules:

Path /AnalysisXML/SequenceCollection/Peptide/Modification
MUST supply a *child* term of UNIMOD:0 (UNIMOD root) one or more times










Element <peptideSequence>






Definition:
 The amino acid sequence of the (poly)peptide. 





Type:
xsd:string





Attributes:
none






Subelements:
none






Example Context:

<peptideSequence>GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG</peptideSequence>










Element <InputSpectra>






Definition:
 The attribute referencing an identifier within the SpectraData section. 





Type:






Attributes:



Attribute NameData TypeUseDefinition


SpectraData_refxsd:string-A 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:
PSI-PI.analysis.search.SearchDatabaseType





Attributes:



Attribute NameData TypeUseDefinition


SearchDatabase_refxsd:string-A reference to the database searched.


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


numDatabaseSequencesxsd:int-The total number of sequences in the database.


numResiduesxsd:int-The number of residues in the database.


releaseDatexsd:string-The release date of the database.


versionxsd:string-The version of the database.








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. 
          


DatabaseName11-


pf:cvParam0unbounded The default value for this parameter. 








Example Context:

<SearchDatabase location="file:////usr/local/mascot_2_1_99_1/sequence/SwissProt/current/SwissProt_51.6.fasta" id="SDB_SwissProt" name="SwissProt" numDatabaseSequences="257964" numResidues="93947433" releaseDate="SwissProt_51.6.fasta" version="SwissProt_51.6.fasta">
  <pf:fileFormat>
    <pf:cvParam accession="PI:00348" name="FASTA format" cvRef="PSI-PI" />
  </pf:fileFormat>
  <DatabaseName>
    <pf:userParam name="SwissProt_51.6.fasta" />
  </DatabaseName>
  ...
</SearchDatabase>







cvParam Mapping Rules:

Path /AnalysisXML/DataCollection/Inputs/SearchDatabase
MAY supply a *child* term of PI:00011 (search database details) one or more times
  e.g.: PI:00014 (database local file path)
  e.g.: PI:00015 (database original uri)
  e.g.: PI:00016 (database version)
  e.g.: PI:00017 (database release date)
  e.g.: PI:00020 (DB filter taxonomy)
  e.g.: PI:00021 (DB filter on accession numbers)
  e.g.: PI:00024 (translation frame)
  e.g.: PI:00025 (translation table)
  e.g.: PI:00027 (DB filter on sequences)
  e.g.: PI:00029 (number of sequences searched)
  et al.










Element <InputSpectrumIdentifications>






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





Type:






Attributes:



Attribute NameData TypeUseDefinition


SpectrumIdentificationList_refxsd:string-A 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:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam11Abstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam11Abstract entity allowing either cvParam or userParam to be referenced in other schemas.








Example Context:

<SearchType>
  <pf:cvParam accession="PI:00083" name="ms-ms search" cvRef="PSI-PI" value=""/>
</SearchType>







cvParam Mapping Rules:

Path /AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/SearchType
MUST supply a *child* term of PI:00080 (search type) one or more times
  e.g.: PI:00010 (de novo search)
  e.g.: PI:00031 (spectral library search)
  e.g.: PI:00081 (pmf search)
  e.g.: PI:00082 (tag search)
  e.g.: PI:00083 (ms-ms search)










Element <AdditionalSearchParams>






Definition:
The search parameters other than the modifications searched.





Type:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.








Example Context:

<AdditionalSearchParams>
  <pf:cvParam accession="PI:00002" name="user name"                cvRef="PSI-PI" value="Some Person"/>
  <pf:cvParam accession="PI:00003" name="user email address"       cvRef="PSI-PI" value="someone@someuniversity.edu"/>
  <pf:cvParam accession="PI:00004" name="user comments"            cvRef="PSI-PI" value="Example Mascot MS-MS search for PSI AnalysisXML"/>
  <pf:cvParam accession="PI:00279" name="ESI-TRAP"                 cvRef="PSI-PI" />
  <pf:cvParam accession="PI:00211" name="parent mass type mono"    cvRef="PSI-PI"/>
  <pf:cvParam accession="PI:00259" name="param: immonium ion" cvRef="PSI-PI"/>
  ...
</AdditionalSearchParams>







cvParam Mapping Rules:

Path /AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/AdditionalSearchParams
MAY supply a *child* term of PI:00001 (user details) one or more times
  e.g.: PI:00002 (user name)
  e.g.: PI:00003 (user email address)
  e.g.: PI:00004 (user comments)
MAY supply a *child* term of PI:00210 (mass type settings) one or more times
  e.g.: PI:00211 (parent mass type mono)
  e.g.: PI:00212 (parent mass type average)
  e.g.: PI:00255 (fragment mass type average)
  e.g.: PI:00256 (fragment mass type mono)
MAY supply a *child* term of PI:00063 (instrument details) one or more times
  e.g.: PI:00065 (TODOscoring model)
  e.g.: PI:00108 (param: a ion)
  e.g.: PI:00118 (param: b ion)
  e.g.: PI:00119 (param: c ion)
  e.g.: PI:00146 (param: a ion-NH3)
  e.g.: PI:00148 (param: a ion-H2O)
  e.g.: PI:00149 (param: b ion-NH3)
  e.g.: PI:00150 (param: b ion-H2O)
  e.g.: PI:00151 (param: y ion-NH3)
  e.g.: PI:00152 (param: y ion-H2O)
  et al.
MAY supply a *child* term of PI:00066 (ions series considered in search) one or more times
  e.g.: PI:00108 (param: a ion)
  e.g.: PI:00118 (param: b ion)
  e.g.: PI:00119 (param: c ion)
  e.g.: PI:00146 (param: a ion-NH3)
  e.g.: PI:00148 (param: a ion-H2O)
  e.g.: PI:00149 (param: b ion-NH3)
  e.g.: PI:00150 (param: b ion-H2O)
  e.g.: PI:00151 (param: y ion-NH3)
  e.g.: PI:00152 (param: y ion-H2O)
  e.g.: PI:00257 (param: v ion)
  et al.
MAY supply a *child* term of PI:00302 (search engine specific input parameter) one or more times
  e.g.: PI:00005 (sequest:CleavesAt)
  e.g.: PI:00007 (sequest:OutputLines)
  e.g.: PI:00009 (sequest:DescriptionLines)
  e.g.: PI:00026 (sequest:NormalizeXCorrValues)
  e.g.: PI:00028 (sequest:SequenceHeaderFilter)
  e.g.: PI:00032 (sequest:SequencePartialFilter)
  e.g.: PI:00037 (sequest:ShowFragmentIons)
  e.g.: PI:00038 (sequest:Consensus)
  e.g.: PI:00042 (sequest:LimitTo)
  e.g.: PI:00046 (sequest:sort_by_dCn)
  et al.










Element <ModificationParams>






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





Type:






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 accession="UNIMOD:4" name="Carbamidomethyl" cvRef="UNIMOD" massDelta="57.021469" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton" residues="C"/>
  </SearchModification>
  <SearchModification fixedMod="false" >
    <ModParam accession="UNIMOD:35" name="Oxidation" cvRef="UNIMOD" massDelta="15.994919" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton" residues="M"/>
  </SearchModification>
  ...
</ModificationParams>










Element <Enzymes>






Definition:
The list of enzymes used in experiment





Type:
PSI-PI.analysis.search.EnzymesType





Attributes:



Attribute NameData TypeUseDefinition


independentxsd:boolean-If 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>
      <pf:cvParam accession="PI:00307" name="CNBr" cvRef="PSI-PI" />
    </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. 


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








Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


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">
  <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 /AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/MassTable
MAY supply a *child* term of PI:00354 (mass table options) one or more times
  e.g.: PI:00346 (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


pf:cvParam1unbounded The default value for this parameter. 








Example Context:

      <FragmentTolerance>
        <pf:cvParam accession="PI:00412" name="search tolerance plus value" cvRef="PSI-PI" value="0.9" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"/>
        <pf:cvParam accession="PI:00413" name="search tolerance minus value" cvRef="PSI-PI" value="0.9" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"/>
      </FragmentTolerance>







cvParam Mapping Rules:

Path /AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance
MUST supply term PI:00412 (search tolerance plus value)
MUST supply term PI:00413 (search tolerance minus value)










Element <ParentTolerance>






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





Type:
ToleranceType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam1unbounded The default value for this parameter. 








Example Context:

      <ParentTolerance>
        <pf:cvParam accession="PI:00412" name="search tolerance plus value" cvRef="PSI-PI" value="75.0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO"/>
        <pf:cvParam accession="PI:00413" name="search tolerance minus value" cvRef="PSI-PI" value="75.0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO"/>
      </ParentTolerance>







cvParam Mapping Rules:

Path /AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance
MUST supply term PI:00412 (search tolerance plus value)
MUST supply term PI:00413 (search tolerance minus value)










Element <DatabaseFilters>






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





Type:






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>
      <pf:cvParam accession="PI:00020" name="DB filter taxonomy" cvRef="PSI-PI" />
    </FilterType>
    <Include>
      <pf:cvParam accession="NCBI:3702" name="Arabidopsis thaliana" cvRef="NCBI-TAXONOMY" />
  ...
</DatabaseFilters>










Element <DatabaseTranslation>






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





Type:






Attributes:



Attribute NameData TypeUseDefinition


framespsi-pi:listOfIntegers-The 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 4 5 6">
  <TranslationTable id="TT_1" name="Standard">
    <pf:cvParam accession="PI:00025" name="translation table" cvRef="PSI-PI" value="FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG" />
    <pf:cvParam accession="PI:00410" name="translation start codons" cvRef="PSI-PI" value="---M---------------M---------------M----------------------------" />
    <pf:cvParam accession="PI:00423" name="translation table description" cvRef="PSI-PI" 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:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam1unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam1unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.








Example Context:

<AnalysisParams>
  <pf:cvParam accession="PI:00316" name="mascot:SigThreshold"                               cvRef="PSI-PI" value="0.05"/>
  <pf:cvParam accession="PI:00317" name="mascot:MaxProteinHits"                             cvRef="PSI-PI" value="Auto"/>
  <pf:cvParam accession="PI:00318" name="mascot:ProteinScoringMethod"                       cvRef="PSI-PI" value="Standard"/>
  <pf:cvParam accession="PI:00319" name="mascot:MinMSMSThreshold"                           cvRef="PSI-PI" value="0"/>
  <pf:cvParam accession="PI:00320" name="mascot:ShowHomologousProteinsWithSamePeptides"     cvRef="PSI-PI" value="1"/>
  <pf:cvParam accession="PI:00321" name="mascot:ShowHomologousProteinsWithSubsetOfPeptides" cvRef="PSI-PI" value="1"/>
  ...
</AnalysisParams>







cvParam Mapping Rules:

Path /AnalysisXML/AnalysisProtocolCollection/ProteinDetectionProtocol/AnalysisParams
MAY supply a *child* term of PI:00194 (quality estimation with decoy database) one or more times
  e.g.: PI:00195 (reverse decoy DB)
  e.g.: PI:00196 (randomized decoy DB)
  e.g.: PI:00197 (forward+reverse decoy DB)
  e.g.: PI:00283 (decoy DB accession regexp)
  e.g.: PI:00291 (decoy DB from nr)
  e.g.: PI:00292 (decoy DB from IPI_rat)
  e.g.: PI:00293 (decoy DB from IPI_mouse)
  e.g.: PI:00294 (decoy DB from IPI_arabidopsis)
  e.g.: PI:00295 (decoy DB from EST)
  e.g.: PI:00296 (decoy DB from IPI_zebrafish)
  et al.
MAY supply a *child* term of PI:00302 (search engine specific input parameter) one or more times
  e.g.: PI:00005 (sequest:CleavesAt)
  e.g.: PI:00007 (sequest:OutputLines)
  e.g.: PI:00009 (sequest:DescriptionLines)
  e.g.: PI:00026 (sequest:NormalizeXCorrValues)
  e.g.: PI:00028 (sequest:SequenceHeaderFilter)
  e.g.: PI:00032 (sequest:SequencePartialFilter)
  e.g.: PI:00037 (sequest:ShowFragmentIons)
  e.g.: PI:00038 (sequest:Consensus)
  e.g.: PI:00042 (sequest:LimitTo)
  e.g.: PI:00046 (sequest:sort_by_dCn)
  et al.










Element <SourceFile>






Definition:
 A file from which this AnalysisXML 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:string- 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. 
          


pf:cvParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.








Example Context:

      <SourceFile id="SF1" location="proteinscape://www.medizinisches-proteom-center.de/PSServer/Project/Sample/Separation_1D_LC/Fraction_X/SpectraData/Results1">
        <!--pf:cvParam accession="PI:00275" name="ProteinScape SearchEvent" cvRef="PSI-PI"/-->
      </SourceFile>







cvParam Mapping Rules:

Path /AnalysisXML/DataCollection/Inputs/SourceFile
MAY supply a *child* term of PI:00008 (source file name) one or more times










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:string- 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="" id="SD_1">
  <pf:fileFormat>
    <pf:cvParam accession="PI:00062" name="Mascot MGF file" cvRef="PSI-PI" />
  </pf:fileFormat>
</SpectraData>










Element <SpectrumIdentificationList>






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





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


numSequencesSearchedxsd:int-This 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.


pf:cvParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.








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="813.47084" chargeState="1" experimentalMassToCharge="814.43" Peptide_ref="peptide_1_1" rank="0" passThreshold="true">
      <PeptideEvidence id="PE_1_1_PML_HUMAN" start="319" end="325" pre="R" post="I" frame="0" isDecoy="false" DBSequence_Ref="DBSeq_PML_HUMAN" />
    </SpectrumIdentificationItem>
    <SpectrumIdentificationItem id="SII_1_5"  calculatedMassToCharge="813.398071" chargeState="1" experimentalMassToCharge="814.43" Peptide_ref="peptide_1_5" rank="0" passThreshold="true">
      <PeptideEvidence id="PE_1_5_PTXR_PSEAE" start="159" end="166" pre="R" post="L" frame="0" isDecoy="false" DBSequence_Ref="DBSeq_PTXR_PSEAE" />
  ...
</SpectrumIdentificationList>







cvParam Mapping Rules:

Path /AnalysisXML/DataCollection/AnalysisData/SpectrumIdentificationList
MAY supply a *child* term of PI:00184 (search statistics) one or more times
  e.g.: PI:00035 (date / time search performed)
  e.g.: PI:00036 (search time taken)
  e.g.: PI:00177 (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:string- The potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


ProteinAmbiguityGroup1unboundedRepresents 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" />
      <pf:cvParam accession="PI:00171" name="mascot:score" cvRef="PSI-PI" value="405.72" />
      <pf:cvParam accession="PI:00093" name="coverage" cvRef="PSI-PI" value="99" />
      <pf:cvParam accession="PI:00097" name="distinct peptide sequences" cvRef="PSI-PI" value="1" />
  ...
</ProteinDetectionList>







cvParam Mapping Rules:

Path /AnalysisXML/DataCollection/AnalysisData/ProteinDetectionList
MAY supply a *child* term of PI:00184 (search statistics) one or more times
  e.g.: PI:00035 (date / time search performed)
  e.g.: PI:00036 (search time taken)
  e.g.: PI:00177 (number of molecular hypothesis considered)










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:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:URI11 A URI is short for Uniform Resource Identifier.   A URI is a compact sequence of characters that identifies an abstract or physical resource. 








Example Context:










Element <pf:fileFormat>






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





Type:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam11 The default value for this parameter. 








Example Context:

<pf:fileFormat>
  <pf:cvParam accession="PI:00199" name="Mascot DAT file" cvRef="PSI-PI" />
</pf:fileFormat>







cvParam Mapping Rules:

Path /AnalysisXML/DataCollection/Inputs/SourceFile/pf:fileFormat
MUST supply a *child* term of PI:00040 (source file format) only once
  e.g.: PI:00199 (Mascot DAT file)
  e.g.: PI:00200 (Sequest out file)
  e.g.: PI:00242 (Sequest out folder)
  e.g.: PI:00243 (Sequest summary)
  e.g.: PI:00275 (ProteinScape SearchEvent)
  e.g.: PI:00276 (ProteinScape Gel)
  e.g.: PI:00399 (OMSSA csv file)
  e.g.: PI:00400 (OMSSA xml file)
  e.g.: PI:00401 (tandem xml file)
  e.g.: PI:00421 (pepXML file)
  et al.



Path /AnalysisXML/DataCollection/Inputs/SpectraData/pf:fileFormat
MUST supply a *child* term of PI:00043 (input data type) one or more times
  e.g.: PI:00054 (mzML file)
  e.g.: PI:00062 (Mascot MGF file)
  e.g.: PI:00067 (Sequest DTA files)
  e.g.: PI:00244 (Micromass PKL file)
  e.g.: PI:00245 (PerSeptive PKS file)
  e.g.: PI:00246 (Sciex API III file)
  e.g.: PI:00247 (Bruker XML file)
  e.g.: PI:00248 (mzData XML file)
  e.g.: PI:00369 (text file)



Path /AnalysisXML/DataCollection/Inputs/SearchDatabase/pf:fileFormat
MUST supply a *child* term of PI:00347 (database file formats) one or more times
  e.g.: PI:00348 (FASTA format)
  e.g.: PI:00349 (ASN.1)
  e.g.: PI:00350 (NCBI *.p*)
  e.g.: PI:00351 (clustal aln)
  e.g.: PI:00352 (embl em)
  e.g.: PI:00353 (NBRF PIR)










Element <DatabaseName>






Definition:
-





Type:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam11Abstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam11Abstract entity allowing either cvParam or userParam to be referenced in other schemas.








Example Context:

        <DatabaseName>
          <pf:userParam name="ipi.HUMAN_decoy"/>
        </DatabaseName>







cvParam Mapping Rules:

Path /AnalysisXML/DataCollection/Inputs/SearchDatabase/DatabaseName
MAY supply a *child* term of PI:00013 (database name) one or more times
  e.g.: PI:00084 (database nr)
  e.g.: PI:00104 (database SwissProt)
  e.g.: PI:00142 (database IPI_human)
  e.g.: PI:00178 (database EST)
  e.g.: PI:00285 (database IPI_mouse)
  e.g.: PI:00286 (database IPI_rat)
  e.g.: PI:00287 (database IPI_zebrafish)
  e.g.: PI:00288 (database IPI_chicken)
  e.g.: PI:00289 (database IPI_cow)
  e.g.: PI:00290 (database IPI_arabidopsis)










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


SpecificityRule0unboundedThe specificity rule 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 accession="UNIMOD:29" name="SMA" cvRef="UNIMOD" massDelta="127.063324" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton" residues=""/>
  <SpecificityRule accession="PI:00189" cvRef="PSI-PI" name="modification specificity N-term"/>
</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.


semiSpecificxsd:booleanoptional1: enzyme cleaves semispecific (i.e. one terminus MUST cleave according to the rules, the other can cleave at any residue), 0: else.








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>
    <pf:cvParam accession="PI:00251" name="Trypsin" cvRef="PSI-PI" />
  </EnzymeName>
</Enzyme>










Element <Residue>






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





Type:






Attributes:



Attribute NameData TypeUseDefinition


Codepsi-pi:charsrequiredThe 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:






Attributes:



Attribute NameData TypeUseDefinition


Codepsi-pi:charsrequired








Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam1unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam1unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.








Example Context:

<AmbiguousResidue Code="X">
  <pf:cvParam accession="PI:00360" name="alternate single letter codes" cvRef="PSI-PI" value="A C D E F G H I K L M N O P Q R S T U V W W"/>
</AmbiguousResidue>







cvParam Mapping Rules:

Path /AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/MassTable/AmbiguousResidue
MAY supply a *child* term of PI:00359 (ambiguous residues) one or more times
  e.g.: PI:00360 (alternate single letter codes)
  e.g.: PI:00361 (alternate mass)










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:






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>
    <pf:cvParam accession="PI:00020" name="DB filter taxonomy" cvRef="PSI-PI" />
  </FilterType>
  <Include>
    <pf:cvParam accession="NCBI:3702" name="Arabidopsis thaliana" cvRef="NCBI-TAXONOMY" />
  </Include>
  ...
</Filter>










Element <TranslationTable>






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





Type:






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








Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam0unbounded The default value for this parameter. 








Example Context:

<TranslationTable id="TT_4" name="Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma">
  <pf:cvParam accession="PI:00025" name="translation table" cvRef="PSI-PI" value="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG" />
  <pf:cvParam accession="PI:00410" name="translation start codons" cvRef="PSI-PI" value="--MM---------------M------------MMMM---------------M------------" />
  <pf:cvParam accession="PI:00423" name="translation table description" cvRef="PSI-PI" value="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG4" />
</TranslationTable>







cvParam Mapping Rules:

Path /AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/DatabaseTranslation/TranslationTable
MUST supply term PI:00410 (translation start codons)
MUST supply term PI:00025 (translation table)
MUST supply term PI:00423 (translation table description)










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:






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">
            <pf:cvParam cvRef="PSI-PI" accession="PI:00225" name="product ion m/z"/>
          </Measure>
          <Measure id="m_intensity">
            <pf:cvParam cvRef="PSI-PI" accession="PI:00226" 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:string- 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. 


pf:cvParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.








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" frame="0" isDecoy="false" DBSequence_Ref="DBSeq_HSP70_ECHGR" />
    <PeptideEvidence id="PE_1_1_HSP70_ONCMY" start="160" end="171" pre="K" post="L" frame="0" isDecoy="false" DBSequence_Ref="DBSeq_HSP70_ONCMY" />
    <PeptideEvidence id="PE_1_1_HSP7C_ICTPU" start="160" end="171" pre="K" post="I" frame="0" isDecoy="false" DBSequence_Ref="DBSeq_HSP7C_ICTPU" />
    <PeptideEvidence id="PE_1_1_HSP7C_ORYLA" start="160" end="171" pre="K" post="I" frame="0" isDecoy="false" DBSequence_Ref="DBSeq_HSP7C_ORYLA" />
    <PeptideEvidence id="PE_1_1_HSP7D_MANSE" start="160" end="171" pre="K" post="I" frame="0" isDecoy="false" DBSequence_Ref="DBSeq_HSP7D_MANSE" />
  ...
</SpectrumIdentificationResult>







cvParam Mapping Rules:

Path /AnalysisXML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult
MAY supply a *child* term of PI:00405 (spectrum identification result details) one or more times
  e.g.: PI:00030 (number of peptide seqs compared to each spectrum)
  e.g.: PI:00370 (mascot:homology threshold)
  e.g.: PI:00371 (mascot:identity threshold)
  e.g.: PI:00414 (MGF scans)
  e.g.: PI:00415 (MGF raw scans)
  e.g.: PI:00416 (spectrum title)










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:string- 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).


pf:cvParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.








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" />
    <pf:cvParam accession="PI:00171" name="mascot:score" cvRef="PSI-PI" value="104.854382332144" />
    <pf:cvParam accession="PI:00093" name="coverage" cvRef="PSI-PI" value="4" />
    <pf:cvParam accession="PI:00097" name="distinct peptide sequences" cvRef="PSI-PI" value="2" />
  ...
</ProteinAmbiguityGroup>










Element <pf:URI>






Definition:
 A URI is short for Uniform Resource Identifier.   A URI is a compact sequence of characters that identifies an abstract or physical resource. 





Type:
pf:FuGE.Common.Description.URIType





Attributes:



Attribute NameData TypeUseDefinition


locationxsd:anyURIrequired The Uniform Resource Indicator for this object. 








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


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.


massDeltaxsd:floatrequiredThe mass delta of the searched modification in Daltons


namexsd:stringrequiredThe name of the parameter.


residuespsi-pi:listOfCharsrequiredThe residue(s) searched with the specified modification


unitAccessionxsd:string-An 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:string-The name of the unit.


valuexsd:stringoptionalThe user-entered value of the parameter.








Subelements:
none






Example Context:

<ModParam accession="UNIMOD:4" name="Carbamidomethyl" cvRef="UNIMOD" massDelta="57.021469" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton" residues="C"/>










Element <SpecificityRule>






Definition:
The specificity rule 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:
pf: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:string-An 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:string-The name of the unit.


valuexsd:stringoptionalThe user-entered value of the parameter.








Subelements:
none






Example Context:

<SpecificityRule accession="PI:00189" cvRef="PSI-PI" name="modification specificity N-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:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam1unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam1unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.








Example Context:

          <EnzymeName>
            <pf:cvParam accession="PI:00251" name="Trypsin" cvRef="PSI-PI"/>
          </EnzymeName>







cvParam Mapping Rules:

Path /AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/Enzymes/Enzyme/EnzymeName
MAY supply a *child* term of PI:00045 (cleavage agent name) only once
  e.g.: PI:00091 (NoEnzyme)
  e.g.: PI:00251 (Trypsin)
  e.g.: PI:00303 (Arg-C)
  e.g.: PI:00304 (Asp-N)
  e.g.: PI:00305 (Asp-N_ambic)
  e.g.: PI:00306 (Chymotrypsin)
  e.g.: PI:00307 (CNBr)
  e.g.: PI:00308 (Formic_acid)
  e.g.: PI:00309 (Lys-C)
  e.g.: PI:00310 (Lys-C/P)
  et al.










Element <FilterType>






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





Type:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam11Abstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam11Abstract entity allowing either cvParam or userParam to be referenced in other schemas.








Example Context:

<FilterType>
  <pf:cvParam accession="PI:00020" name="DB filter taxonomy" cvRef="PSI-PI" />
</FilterType>







cvParam Mapping Rules:

Path /AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/DatabaseFilters/Filter/FilterType
MUST supply a *child* term of PI:00019 (database filtering) one or more times
  e.g.: PI:00020 (DB filter taxonomy)
  e.g.: PI:00021 (DB filter on accession numbers)
  e.g.: PI:00027 (DB filter on sequences)
  e.g.: PI:00201 (DB MW filter maximum)
  e.g.: PI:00202 (DB MW filter minimum)
  e.g.: PI:00203 (DB PI filter maximum)
  e.g.: PI:00204 (DB PI filter minimum)










Element <Include>






Definition:
All sequences fulfilling the specifed criteria are included.





Type:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam1unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam1unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.








Example Context:

<Include>
  <pf:cvParam accession="NCBI:3702" name="Arabidopsis thaliana" cvRef="NCBI-TAXONOMY" />
</Include>







cvParam Mapping Rules:

Path /AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/DatabaseFilters/Filter/Include
MAY supply a *child* term of PI:00019 (database filtering) one or more times
  e.g.: PI:00020 (DB filter taxonomy)
  e.g.: PI:00021 (DB filter on accession numbers)
  e.g.: PI:00027 (DB filter on sequences)
  e.g.: PI:00201 (DB MW filter maximum)
  e.g.: PI:00202 (DB MW filter minimum)
  e.g.: PI:00203 (DB PI filter maximum)
  e.g.: PI:00204 (DB PI filter minimum)










Element <Exclude>






Definition:
All sequences fulfilling the specifed criteria are excluded.





Type:






Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam1unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam1unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.








Example Context:







cvParam Mapping Rules:

Path /AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/DatabaseFilters/Filter/Exclude
MAY supply a *child* term of PI:00019 (database filtering) one or more times
  e.g.: PI:00020 (DB filter taxonomy)
  e.g.: PI:00021 (DB filter on accession numbers)
  e.g.: PI:00027 (DB filter on sequences)
  e.g.: PI:00201 (DB MW filter maximum)
  e.g.: PI:00202 (DB MW filter minimum)
  e.g.: PI:00203 (DB PI filter maximum)
  e.g.: PI:00204 (DB PI filter minimum)










Element <Measure>






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





Type:






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








Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam1unbounded The default value for this parameter. 








Example Context:

<Measure id="m_intensity">
  <pf:cvParam cvRef="PSI-PI" accession="PI:00226" name="product ion intensity"/>
</Measure>







cvParam Mapping Rules:

Path /AnalysisXML/DataCollection/AnalysisData/SpectrumIdentificationList/FragmentationTable/Measure
MUST supply a *child* term of  ([to complete]) one or more times
MUST supply term PI:00227 (product ion m/z error)
MUST supply term PI:00225 (product ion m/z)
MUST supply term PI:00226 (product ion intensity)










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. 





Type:
PSI-PI.analysis.search.SpectrumIdentificationItemType





Attributes:



Attribute NameData TypeUseDefinition


Peptide_refxsd:string- A reference to the identified polypeptide of this SearchResultItem. 


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


chargeStatexsd:int- The charge state of the identified peptide. 


experimentalMassToChargexsd:double- 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:string- 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. 


pf:cvParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


Fragmentation01The product ions identified in this result.








Graphical Context:






Example Context:

<SpectrumIdentificationItem id="SII_2_1"  calculatedMassToCharge="806.878662" chargeState="2" experimentalMassToCharge="808.3" Peptide_ref="peptide_2_1" rank="1" passThreshold="false">
  <PeptideEvidence id="PE_2_1_HS70A_BOVIN" start="37" end="49" pre="R" post="L" frame="0" isDecoy="false" DBSequence_Ref="DBSeq_HS70A_BOVIN" />
  <PeptideEvidence id="PE_2_1_HS70A_MOUSE" start="37" end="49" pre="R" post="L" frame="0" isDecoy="false" DBSequence_Ref="DBSeq_HS70A_MOUSE" />
  <PeptideEvidence id="PE_2_1_HS70B_BOSMU" start="37" end="49" pre="R" post="L" frame="0" isDecoy="false" DBSequence_Ref="DBSeq_HS70B_BOSMU" />
  <PeptideEvidence id="PE_2_1_HS70B_BOVIN" start="37" end="49" pre="R" post="L" frame="0" isDecoy="false" DBSequence_Ref="DBSeq_HS70B_BOVIN" />
  <PeptideEvidence id="PE_2_1_HS70B_MOUSE" start="37" end="49" pre="R" post="L" frame="0" isDecoy="false" DBSequence_Ref="DBSeq_HS70B_MOUSE" />
  <PeptideEvidence id="PE_2_1_HS70B_PIG" start="37" end="49" pre="R" post="L" frame="0" isDecoy="false" DBSequence_Ref="DBSeq_HS70B_PIG" />
  ...
</SpectrumIdentificationItem>







cvParam Mapping Rules:

Path /AnalysisXML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem
MAY supply a *child* term of PI:00213 (search result details) one or more times
  e.g.: PI:00035 (date / time search performed)
  e.g.: PI:00036 (search time taken)
  e.g.: PI:00088 (protein description)
  e.g.: PI:00090 (taxonomy nomenclature)
  e.g.: PI:00093 (coverage)
  e.g.: PI:00097 (distinct peptide sequences)
  e.g.: PI:00098 (confident distinct peptide sequences)
  e.g.: PI:00099 (confident peptide qualification)
  e.g.: PI:00100 (confident peptide)
  e.g.: PI:00101 (protein group/subset relationship)
  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:string-A reference to the corresponding DBSequence entry. This is optional and redundant, because once again stated in the PeptideEvidence elements referenced from here.


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:string- 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. 


pf:cvParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.








Example Context:

          <ProteinDetectionHypothesis passThreshold = "true"  id="id_prot3">
            <PeptideHypothesis PeptideEvidence_Ref="PE1_SEQ_spec15_pep1"/>
            <PeptideHypothesis PeptideEvidence_Ref="PE1_SEQ_spec20_pep1"/>
            <pf:cvParam accession="PI:00093" name="coverage" cvRef="PSI-PI" value="0.59"/>
            <pf:cvParam accession="PI:00301" name="protein rank" cvRef="PSI-PI" value="3"/>
            <pf:cvParam accession="PI:00097" name="distinct peptide sequences" cvRef="PSI-PI" value="2"/>
            <pf:cvParam accession="PI:00250" name="local FDR" cvRef="PSI-PI" value="33.33" unitAccession="UO:0000187" unitName="percent" unitCvRef="UO"/>
  ...
</ProteinDetectionHypothesis>







cvParam Mapping Rules:

Path /AnalysisXML/DataCollection/AnalysisData/ProteinDetectionList/ProteinAmbiguityGroup/ProteinDetectionHypothesis
MAY supply a *child* term of  ([to complete]) one or more times
MAY supply a *child* term of PI:00060 (quality estimation method) one or more times
  e.g.: PI:00058 (quality estimation by manual validation)
  e.g.: PI:00195 (reverse decoy DB)
  e.g.: PI:00196 (randomized decoy DB)
  e.g.: PI:00197 (forward+reverse decoy DB)
  e.g.: PI:00283 (decoy DB accession regexp)
  e.g.: PI:00291 (decoy DB from nr)
  e.g.: PI:00292 (decoy DB from IPI_rat)
  e.g.: PI:00293 (decoy DB from IPI_mouse)
  e.g.: PI:00294 (decoy DB from IPI_arabidopsis)
  e.g.: PI:00295 (decoy DB from EST)
  et al.
MAY supply a *child* term of PI:00085 (protein result details) one or more times
  e.g.: PI:00088 (protein description)
  e.g.: PI:00090 (taxonomy nomenclature)
  e.g.: PI:00093 (coverage)
  e.g.: PI:00097 (distinct peptide sequences)
  e.g.: PI:00098 (confident distinct peptide sequences)
  e.g.: PI:00099 (confident peptide qualification)
  e.g.: PI:00100 (confident peptide)
  e.g.: PI:00101 (protein group/subset relationship)
  e.g.: PI:00125 (manual validation)
  e.g.: PI:00157 (sequest:sp)
  et al.
MAY supply a *child* term of PI:00153 (search engine specific score) one or more times
  e.g.: PI:00154 (sequest:probability)
  e.g.: PI:00155 (sequest:xcorr)
  e.g.: PI:00156 (sequest:deltacn)
  e.g.: PI:00157 (sequest:sp)
  e.g.: PI:00158 (sequest:Uniq)
  e.g.: PI:00159 (sequest:expectation value)
  e.g.: PI:00160 (sequest:sf)
  e.g.: PI:00161 (sequest:matched ions)
  e.g.: PI:00162 (sequest:total ions)
  e.g.: PI:00163 (sequest:consensus score)
  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:int- End position of the peptide inside the protein sequence, where the first amino acid of the protein sequence is position 1. 


framexsd:intoptionalThe 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:boolean-Set 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:string- The potentially ambiguous common identifier, such as a human-readable name for the instance. 


post- 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.  


pre- 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:int- Start position of the peptide inside the protein sequence, where the first amino acid of the protein sequence is position 1.  








Subelements:



Subelement NameminOccursmaxOccursDefinition


pf:cvParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.


pf:userParam0unboundedAbstract entity allowing either cvParam or userParam to be referenced in other schemas.








Example Context:

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










Element <Fragmentation>






Definition:
The product ions identified in this result.





Type:






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 cvRef="PSI-PI" accession="PI:00231" name="frag: c ion" 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">
    <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>
  <IonType cvRef="PSI-PI" accession="PI:00220" name="frag: y ion" index="51 21 5" charge="1">
  ...
</Fragmentation>










Element <PeptideHypothesis>






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





Type:






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:






Attributes:



Attribute NameData TypeUseDefinition


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


chargexsd:intrequiredThe charge of the identified fragmentation ions.


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


indexpsi-pi:listOfIntegers-The 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. 


namexsd:stringrequiredThe name of the parameter.


unitAccessionxsd:string-An 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:string-The name of the unit.


valuexsd:stringoptionalThe user-entered value of the parameter.








Subelements:



Subelement NameminOccursmaxOccursDefinition


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 cvRef="PSI-PI" accession="PI:00231" name="frag: c ion" 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">
  <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>










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:






Attributes:



Attribute NameData TypeUseDefinition


Measure_refxsd:stringrequiredA reference to the Measure defined in the FragmentationTable


valuespsi-pi:listOfFloatsrequiredThe 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"/>