Element <MzIdentML>

Definition: The upper-most hierarchy level of mzIdentML with sub-containers for example describing software, protocols and search results (spectrum identifications or protein detection results).
Type: MzIdentMLType
Attributes:
Attribute NameData TypeUseDefinition
creationDatexsd:dateTimeoptionalThe date on which the file was produced.
idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance.
versionversionRegexrequiredThe version of the schema this instance document refers to, in the format x.y.z. Changes to z should not affect prevent instance documents from validating.
Subelements:
Subelement NameminOccursmaxOccursDefinition
cvList11The list of controlled vocabularies used in the file.
AnalysisSoftwareList01The software packages used to perform the analyses.
Provider01The Provider of the mzIdentML record in terms of the contact and software.
AuditCollection01The complete set of Contacts (people and organisations) for this file.
AnalysisSampleCollection01The samples analysed can optionally be recorded using CV terms for descriptions. If a composite sample has been analysed, the subsample association can be used to build a hierarchical description.
SequenceCollection01The collection of sequences (DBSequence or Peptide) identified and their relationship between each other (PeptideEvidence) to be referenced elsewhere in the results.
AnalysisCollection11The 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).
AnalysisProtocolCollection11The collection of protocols which include the parameters and settings of the performed analyses.
DataCollection11The collection of input and output data sets of the analyses.
BibliographicReference0unboundedAny bibliographic references associated with the file
Graphical Context:
Example Context: 
<MzIdentML id="PeptideShaker v1.11.1-beta" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.2 mzIdentML1.2.0.xsd" xmlns="http://psidev.info/psi/pi/mzIdentML/1.2" version="1.2.0" creationDate="2016-06-22T19:35:50">
  <cvList>
    <cv id="PSI-MS" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" fullName="PSI-MS"/>
    <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/>
    <cv id="UO" uri="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" fullName="UNIT-ONTOLOGY"/>
    <cv id="PRIDE" uri="https://github.com/PRIDE-Utilities/pride-ontology/blob/master/pride_cv.obo" fullName="PRIDE"/>
  </cvList>
  ...
</MzIdentML>

Element <AdditionalSearchParams>

Definition: The search parameters other than the modifications searched.
Type: ParamListType
Attributes: none
Subelements:
Subelement NameminOccursmaxOccursDefinition
cvParam1unboundedA single entry from an ontology or a controlled vocabulary.
userParam1unboundedA single user-defined parameter.
Example Context: 
      <AdditionalSearchParams>
        <cvParam cvRef="PSI-MS" accession="MS:1001211" name="parent mass type mono"/>
        <cvParam cvRef="PSI-MS" accession="MS:1001256" name="fragment mass type mono"/>
        <cvParam cvRef="PSI-MS" accession="MS:1002492" name="consensus scoring"/>
        <cvParam cvRef="PSI-MS" accession="MS:1002490" name="peptide-level scoring"/>
        <cvParam cvRef="PSI-MS" accession="MS:1002497" name="group PSMs by sequence with modifications"/>
        <cvParam cvRef="PSI-MS" accession="MS:1002491" name="modification localization scoring"/>
  ...
</AdditionalSearchParams>
cvParam Mapping Rules: 
Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/AdditionalSearchParams
MAY supply a *child* term of MS:1001302 (search engine specific input parameter) one or more times
  e.g.: MS:1001005 (SEQUEST:CleavesAt) WARNING: Term has no definition!
  e.g.: MS:1001007 (SEQUEST:OutputLines) 
  e.g.: MS:1001009 (SEQUEST:DescriptionLines) 
  e.g.: MS:1001026 (SEQUEST:NormalizeXCorrValues) WARNING: Term has no definition!
  e.g.: MS:1001028 (SEQUEST:SequenceHeaderFilter) 
  e.g.: MS:1001032 (SEQUEST:SequencePartialFilter) WARNING: Term has no definition!
  e.g.: MS:1001037 (SEQUEST:ShowFragmentIons) 
  e.g.: MS:1001038 (SEQUEST:Consensus) 
  e.g.: MS:1001042 (SEQUEST:LimitTo) 
  e.g.: MS:1001046 (SEQUEST:sort by dCn) 
  et al.
MAY supply term MS:1002635 (proteogenomics search) only once
MAY supply a *child* term of MS:1000044 (dissociation method) one or more times
  e.g.: MS:1000134 (plasma desorption) 
  e.g.: MS:1000135 (post-source decay) 
  e.g.: MS:1000136 (surface-induced dissociation) 
  e.g.: MS:1000242 (blackbody infrared radiative dissociation) 
  e.g.: MS:1000250 (electron capture dissociation) 
  e.g.: MS:1000262 (infrared multiphoton dissociation) 
  e.g.: MS:1000282 (sustained off-resonance irradiation) 
  e.g.: MS:1000433 (low-energy collision-induced dissociation) 
  e.g.: MS:1000435 (photodissociation) 
  e.g.: MS:1000598 (electron transfer dissociation) 
  et al.
MAY supply a *child* term of MS:1002473 (ion series considered in search) one or more times
  e.g.: MS:1001108 (param: a ion) 
  e.g.: MS:1001118 (param: b ion) 
  e.g.: MS:1001119 (param: c ion) 
  e.g.: MS:1001257 (param: v ion) 
  e.g.: MS:1001258 (param: d ion) 
  e.g.: MS:1001259 (param: immonium ion) 
  e.g.: MS:1001260 (param: w ion) 
  e.g.: MS:1001261 (param: x ion) 
  e.g.: MS:1001262 (param: y ion) 
  e.g.: MS:1001263 (param: z ion) 
  et al.
MAY supply a *child* term of MS:1002489 (special processing) one or more times
  e.g.: MS:1002490 (peptide-level scoring) 
  e.g.: MS:1002491 (modification localization scoring) 
  e.g.: MS:1002492 (consensus scoring) 
  e.g.: MS:1002493 (sample pre-fractionation) 
  e.g.: MS:1002494 (cross-linking search) 
  e.g.: MS:1002495 (no special processing) 
  e.g.: MS:1002635 (proteogenomics search) 
MAY supply term MS:1002490 (peptide-level scoring) only once
MAY supply a *child* term of MS:1001066 (ions series considered in search) one or more times
MAY supply term MS:1002494 (cross-linking search) only once
MAY supply term MS:1002491 (modification localization scoring) only once
MAY supply a *child* term of MS:1002658 (identification parameter) only once
  e.g.: MS:1002496 (group PSMs by sequence) 
  e.g.: MS:1002497 (group PSMs by sequence with modifications) 
  e.g.: MS:1002498 (group PSMs by sequence with modifications and charge) 
MAY supply a *child* term of MS:1001210 (mass type settings) one or more times
  e.g.: MS:1001211 (parent mass type mono) 
  e.g.: MS:1001212 (parent mass type average) 
  e.g.: MS:1001255 (fragment mass type average) 
  e.g.: MS:1001256 (fragment mass type mono)
Example cvParams: 
<cvParam cvRef="PSI-MS" accession="MS:1001211" name="parent mass type mono"/>
<cvParam cvRef="PSI-MS" accession="MS:1001256" name="fragment mass type mono"/>
<cvParam cvRef="PSI-MS" accession="MS:1002492" name="consensus scoring"/>
<cvParam cvRef="PSI-MS" accession="MS:1002490" name="peptide-level scoring"/>
<cvParam cvRef="PSI-MS" accession="MS:1002497" name="group PSMs by sequence with modifications"/>
<cvParam cvRef="PSI-MS" accession="MS:1002491" name="modification localization scoring"/>

Element <Affiliation>

Definition: The organization a person belongs to.
Type: AffiliationType
Attributes:
Attribute NameData TypeUseDefinition
organization_refxsd:stringrequiredA reference to the organization this contact belongs to.
Subelements: none
Example Context: 
      <Affiliation organization_ref="ORG_DOC_OWNER"/>

Element <AmbiguousResidue>

Definition: Ambiguous residues e.g. X can be specified by the Code attribute and a set of parameters for example giving the different masses that will be used in the search.
Type: AmbiguousResidueType
Attributes:
Attribute NameData TypeUseDefinition
codecharsrequiredThe single letter code of the ambiguous residue e.g. X.
Subelements:
Subelement NameminOccursmaxOccursDefinition
cvParam1unboundedA single entry from an ontology or a controlled vocabulary.
userParam1unboundedA single user-defined parameter.
Example Context: 






cvParam Mapping Rules:

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










Element <AnalysisCollection>






Definition:
The analyses performed to get the results, which map the input and output data sets. Analyses are for example: SpectrumIdentification (resulting in peptides) or ProteinDetection (assemble proteins from peptides).





Type:
AnalysisCollectionType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


SpectrumIdentification1unboundedAn 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. 


ProteinDetection01An Analysis which assembles a set of peptides (e.g. from a spectra search analysis) to proteins. 








Example Context:

  <AnalysisCollection>
    <SpectrumIdentification spectrumIdentificationList_ref="SIL_1" spectrumIdentificationProtocol_ref="SearchProtocol_1" id="SpecIdent_1">
      <InputSpectra spectraData_ref="qExactive01819.mgf"/>
      <SearchDatabaseRef searchDatabase_ref="SearchDB_1"/>
    </SpectrumIdentification>
    <ProteinDetection proteinDetectionProtocol_ref="PeptideShaker_1" proteinDetectionList_ref="Protein_groups" id="PD_1">
      <InputSpectrumIdentifications spectrumIdentificationList_ref="SIL_1"/>
  ...
</AnalysisCollection>










Element <AnalysisData>






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





Type:
AnalysisDataType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


SpectrumIdentificationList1unboundedRepresents the set of all search results from SpectrumIdentification.


ProteinDetectionList01The protein list resulting from a protein detection process.








Example Context:

    <AnalysisData>
      <SpectrumIdentificationList id="SIL_1">
        <FragmentationTable>
          <Measure id="Measure_MZ">
            <cvParam cvRef="PSI-MS" accession="MS:1001225" name="product ion m/z" unitCvRef="PSI-MS" unitAccession="MS:1000040" unitName="m/z" />
          </Measure>
          <Measure id="Measure_Int">
  ...
</AnalysisData>










Element <AnalysisParams>






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





Type:
ParamListType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam1unboundedA single entry from an ontology or a controlled vocabulary.


userParam1unboundedA single user-defined parameter.








Example Context:







cvParam Mapping Rules:

Path /MzIdentML/AnalysisProtocolCollection/ProteinDetectionProtocol/AnalysisParams
MAY supply a *child* term of MS:1001302 (search engine specific input parameter) one or more times
  e.g.: MS:1001005 (SEQUEST:CleavesAt) WARNING: Term has no definition!
  e.g.: MS:1001007 (SEQUEST:OutputLines) 
  e.g.: MS:1001009 (SEQUEST:DescriptionLines) 
  e.g.: MS:1001026 (SEQUEST:NormalizeXCorrValues) WARNING: Term has no definition!
  e.g.: MS:1001028 (SEQUEST:SequenceHeaderFilter) 
  e.g.: MS:1001032 (SEQUEST:SequencePartialFilter) WARNING: Term has no definition!
  e.g.: MS:1001037 (SEQUEST:ShowFragmentIons) 
  e.g.: MS:1001038 (SEQUEST:Consensus) 
  e.g.: MS:1001042 (SEQUEST:LimitTo) 
  e.g.: MS:1001046 (SEQUEST:sort by dCn) 
  et al.










Element <AnalysisProtocolCollection>






Definition:
The collection of protocols which include the parameters and settings of the performed analyses. 





Type:
AnalysisProtocolCollectionType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


SpectrumIdentificationProtocol1unboundedThe parameters and settings of a SpectrumIdentification analysis.


ProteinDetectionProtocol01The parameters and settings of a ProteinDetection process.








Example Context:

  <AnalysisProtocolCollection>
    <SpectrumIdentificationProtocol analysisSoftware_ref="ID_software" id="SearchProtocol_1">
      <SearchType>
        <cvParam cvRef="PSI-MS" accession="MS:1001083" name="ms-ms search"/>
      </SearchType>
      <AdditionalSearchParams>
        <cvParam cvRef="PSI-MS" accession="MS:1001211" name="parent mass type mono"/>
  ...
</AnalysisProtocolCollection>










Element <AnalysisSampleCollection>






Definition:
The samples analysed can optionally be recorded using CV terms for descriptions. If a composite sample has been analysed, the subsample association can be used to build a hierarchical description. 





Type:
AnalysisSampleCollectionType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


Sample1unbounded A description of the sample analysed by mass spectrometry using CVParams or UserParams. If a composite sample has been analysed, a parent sample should be defined, which references subsamples. This represents any kind of substance used in an experimental workflow, such as whole organisms, cells, DNA, solutions, compounds and experimental substances (gels, arrays etc.).	








Example Context:










Element <AnalysisSoftware>






Definition:
The software used for performing the analyses.





Type:
AnalysisSoftwareType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance. 


urixsd:anyURIoptionalURI of the analysis software e.g. manufacturer's website


versionxsd:stringoptionalThe version of Software used.








Subelements:



Subelement NameminOccursmaxOccursDefinition


ContactRole01The Contact that provided the document instance.


SoftwareName11The name of the analysis software package, sourced from a CV if available. 


Customizations01Any customizations to the software, such as alternative scoring mechanisms implemented, should be documented here as free text. 








Example Context:

    <AnalysisSoftware name="PeptideShaker" version="1.11.1-beta" id="ID_software" uri="http://compomics.github.io/projects/peptide-shaker.html">
      <ContactRole contact_ref="PS_DEV">
        <Role>
          <cvParam cvRef="PSI-MS" accession="MS:1001267" name="software vendor"/>
        </Role>
      </ContactRole>
      <SoftwareName>
  ...
</AnalysisSoftware>










Element <AnalysisSoftwareList>






Definition:
The software packages used to perform the analyses.
			





Type:
AnalysisSoftwareListType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


AnalysisSoftware1unboundedThe software used for performing the analyses.








Example Context:

  <AnalysisSoftwareList>
    <AnalysisSoftware name="PeptideShaker" version="1.11.1-beta" id="ID_software" uri="http://compomics.github.io/projects/peptide-shaker.html">
      <ContactRole contact_ref="PS_DEV">
        <Role>
          <cvParam cvRef="PSI-MS" accession="MS:1001267" name="software vendor"/>
        </Role>
      </ContactRole>
  ...
</AnalysisSoftwareList>










Element <AuditCollection>






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





Type:
AuditCollectionType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


Person11A person's name and contact details. Any additional information such as the address, contact email etc. should be supplied using CV parameters or user parameters.


Organization11Organizations are entities like companies, universities, government agencies. Any additional information such as the address, email etc. should be supplied either as CV parameters or as user parameters. 








Example Context:

  <AuditCollection>
    <Person firstName="test" lastName="test" id="PROVIDER">
      <cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="test"/>
      <cvParam cvRef="PSI-MS" accession="MS:1000588" name="contact URL" value="test"/>
      <cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="test"/>
      <Affiliation organization_ref="ORG_DOC_OWNER"/>
    </Person>
  ...
</AuditCollection>










Element <BibliographicReference>






Definition:
Any bibliographic references associated with the file





Type:
BibliographicReferenceType





Attributes:



Attribute NameData TypeUseDefinition


authorsxsd:stringoptionalThe names of the authors of the reference.


doixsd:stringoptionalThe DOI of the referenced publication.


editorxsd:stringoptionalThe editor(s) of the reference.


idxsd:stringrequiredAn 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:stringoptionalThe issue name or number.


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


pagesxsd:stringoptionalThe page numbers.


publicationxsd:stringoptionalThe name of the journal, book etc.


publisherxsd:stringoptionalThe publisher of the publication.


titlexsd:stringoptionalThe title of the BibliographicReference.


volumexsd:stringoptionalThe volume name or number.


yearxsd:intoptionalThe year of publication.








Subelements:
none






Example Context:










Element <ContactRole>






Definition:
Depending on context:

1: The contact details of the organisation or person that produced the software

2: Contact details for the Material. The association to ContactRole could specify, for example, the creator or provider of the Material. 

3: The Contact that provided the document instance.






Type:
ContactRoleType





Attributes:



Attribute NameData TypeUseDefinition


contact_refxsd:stringrequiredWhen a ContactRole is used, it specifies which Contact the role is associated with. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


Role11The roles (lab equipment sales, contractor, etc.) the Contact fills.
			








Example Context:

      <ContactRole contact_ref="PS_DEV">
        <Role>
          <cvParam cvRef="PSI-MS" accession="MS:1001267" name="software vendor"/>
        </Role>
      </ContactRole>










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 <cv>






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





Type:
cvType





Attributes:



Attribute NameData TypeUseDefinition


fullNamexsd:stringrequiredThe full name of the CV.


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


urixsd:anyURIrequiredThe URI of the source CV.


versionxsd:stringoptionalThe version of the CV.








Subelements:
none






Example Context:

    <cv id="UO" uri="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" fullName="UNIT-ONTOLOGY"/>










Element <cvList>






Definition:
The list of controlled vocabularies used in the file.





Type:
CVListType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cv1unboundedA source controlled vocabulary from which cvParams will be obtained.








Example Context:

  <cvList>
    <cv id="PSI-MS" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" fullName="PSI-MS"/>
    <cv id="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" fullName="UNIMOD"/>
    <cv id="UO" uri="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" fullName="UNIT-ONTOLOGY"/>
    <cv id="PRIDE" uri="https://github.com/PRIDE-Utilities/pride-ontology/blob/master/pride_cv.obo" fullName="PRIDE"/>
  </cvList>










Element <cvParam>






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





Type:
CVParamType





Attributes:



Attribute NameData TypeUseDefinition


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


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


namexsd:stringrequiredThe name of the parameter.


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


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


unitNamexsd:stringoptionalThe name of the unit.


valuexsd:stringoptionalThe user-entered value of the parameter.








Subelements:
none






Example Context:

      <cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="SMRCD_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 OS=Homo sapiens GN=SMARCAD1 PE=1 SV=2-REVERSED"/>










Element <DatabaseFilters>






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





Type:
DatabaseFiltersType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


Filter1unboundedFilters applied to the search database. The filter MUST include at least one of Include and Exclude. If both are used, it is assumed that inclusion is performed first. 








Example Context:










Element <DatabaseName>






Definition:
The database name may be given as a cvParam if it maps exactly to one of the release databases listed in the CV, otherwise a userParam should be used. 





Type:
ParamType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam11A single entry from an ontology or a controlled vocabulary.


userParam11A single user-defined parameter.








Example Context:

        <DatabaseName>
          <userParam name="uniprot-human-reviewed-trypsin-april-2016_concatenated_target_decoy.fasta"/>
        </DatabaseName>







cvParam Mapping Rules:

Path /MzIdentML/DataCollection/Inputs/SearchDatabase/DatabaseName
MAY supply a *child* term of MS:1001013 (database name) one or more times
  e.g.: MS:1001084 (database nr) 
  e.g.: MS:1001104 (database UniProtKB/Swiss-Prot) 
  e.g.: MS:1001142 (database IPI_human) 
  e.g.: MS:1001285 (database IPI_mouse) 
  e.g.: MS:1001286 (database IPI_rat) 
  e.g.: MS:1001287 (database IPI_zebrafish) 
  e.g.: MS:1001288 (database IPI_chicken) 
  e.g.: MS:1001289 (database IPI_cow) 
  e.g.: MS:1001290 (database IPI_arabidopsis) 
  e.g.: MS:1002060 (database UniProtKB/TrEMBL) 







Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1001073" name="database type amino acid"/>







Example userParams:

<userParam name="uniprot-human-reviewed-trypsin-april-2016_concatenated_target_decoy.fasta"/>










Element <DatabaseTranslation>






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





Type:
DatabaseTranslationType





Attributes:



Attribute NameData TypeUseDefinition


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








Subelements:



Subelement NameminOccursmaxOccursDefinition


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








Example Context:










Element <DataCollection>






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





Type:
DataCollectionType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


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


AnalysisData11Data sets generated by the analyses, including peptide and protein lists. 








Graphical Context:






Example Context:

  <DataCollection>
    <Inputs>
      <SourceFile location="C:\Users\hba041\My_Git_Applications\peptide-shaker.wiki\data\2016_04_05\.PeptideShaker_unzip_temp\searchgui_out_PeptideShaker_temp\qExactive01819.omx" id="SourceFile_1">
        <FileFormat>
          <cvParam cvRef="PSI-MS" accession="MS:1001400" name="OMSSA xml format"/>
        </FileFormat>
      </SourceFile>
  ...
</DataCollection>










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:
DBSequenceType





Attributes:



Attribute NameData TypeUseDefinition


accessionxsd:stringrequiredThe unique accession of this sequence.


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


lengthxsd:intoptionalThe length of the sequence as a number of bases or residues. 


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


searchDatabase_refxsd:stringrequiredThe source database of this sequence.








Subelements:



Subelement NameminOccursmaxOccursDefinition


Seq01The actual sequence of amino acids or nucleic acid.


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.


userParam0unboundedA single user-defined parameter.








Example Context:

    <DBSequence id="Q9H4L7_REVERSED" accession="Q9H4L7_REVERSED" searchDatabase_ref="SearchDB_1" >
      <cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="SMRCD_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 OS=Homo sapiens GN=SMARCAD1 PE=1 SV=2-REVERSED"/>
    </DBSequence>







cvParam Mapping Rules:

Path /MzIdentML/SequenceCollection/DBSequence
MUST supply term MS:1002638 (chromosome strand) only once
MAY supply a *child* term of MS:1001342 (database sequence details) one or more times
  e.g.: MS:1001088 (protein description) 
  e.g.: MS:1001090 (taxonomy nomenclature) 
  e.g.: MS:1001343 (NA sequence) 
  e.g.: MS:1001344 (AA sequence) 
  e.g.: MS:1001467 (taxonomy: NCBI TaxID) 
  e.g.: MS:1001468 (taxonomy: common name) 
  e.g.: MS:1001469 (taxonomy: scientific name) 
  e.g.: MS:1001470 (taxonomy: Swiss-Prot ID) 
MAY supply a *child* term of MS:1002636 (proteogenomics attribute) one or more times
  e.g.: MS:1002637 (chromosome name) 
  e.g.: MS:1002638 (chromosome strand) 
  e.g.: MS:1002639 (peptide start on chromosome) 
  e.g.: MS:1002640 (peptide end on chromosome) 
  e.g.: MS:1002641 (peptide exon count) 
  e.g.: MS:1002642 (peptide exon nucleotide sizes) 
  e.g.: MS:1002643 (peptide start positions on chromosome) 
  e.g.: MS:1002644 (genome reference version) 
MAY supply a *child* term of MS:1001089 (molecule taxonomy) one or more times
  e.g.: MS:1001090 (taxonomy nomenclature) 
  e.g.: MS:1001467 (taxonomy: NCBI TaxID) 
  e.g.: MS:1001468 (taxonomy: common name) 
  e.g.: MS:1001469 (taxonomy: scientific name) 
  e.g.: MS:1001470 (taxonomy: Swiss-Prot ID) 
MUST supply term MS:1002637 (chromosome name) only once
MAY supply term MS:1001088 (protein description) only once
MUST supply term MS:1002644 (genome reference version) only once







Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="1433T_HUMAN 14-3-3 protein theta OS=Homo sapiens GN=YWHAQ PE=1 SV=1"/>










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:
EnzymeType





Attributes:



Attribute NameData TypeUseDefinition


cTermGainxsd:string with restriction
[A-Za-z0-9 ]+
optionalElement formula gained at CTerm.


idxsd:stringrequiredAn 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.		


minDistancexsd:intoptionalMinimal distance for another cleavage (minimum: 1).


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


nTermGainxsd:string with restriction
[A-Za-z0-9 ]+
optionalElement formula gained at NTerm.


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


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








Subelements:



Subelement NameminOccursmaxOccursDefinition


SiteRegexp01Regular expression for specifying the enzyme cleavage site.


EnzymeName01The name of the enzyme from a CV.








Example Context:

        <Enzyme missedCleavages="2" semiSpecific="false" id="Enz1" name="Trypsin">
          <EnzymeName>
            <cvParam cvRef="PSI-MS" accession="MS:1001251" name="Trypsin"/>
          </EnzymeName>
        </Enzyme>










Element <EnzymeName>






Definition:
The name of the enzyme from a CV.





Type:
ParamListType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam1unboundedA single entry from an ontology or a controlled vocabulary.


userParam1unboundedA single user-defined parameter.








Example Context:

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







cvParam Mapping Rules:

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/Enzymes/Enzyme/EnzymeName
MAY supply a *child* term of MS:1001045 (cleavage agent name) only once
  e.g.: MS:1001091 (NoEnzyme) WARNING: Term has no definition!
  e.g.: MS:1001251 (Trypsin) 
  e.g.: MS:1001303 (Arg-C) 
  e.g.: MS:1001304 (Asp-N) 
  e.g.: MS:1001305 (Asp-N_ambic) 
  e.g.: MS:1001306 (Chymotrypsin) 
  e.g.: MS:1001307 (CNBr) 
  e.g.: MS:1001308 (Formic_acid) 
  e.g.: MS:1001309 (Lys-C) 
  e.g.: MS:1001310 (Lys-C/P) 
  et al.







Example cvParams:

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










Element <Enzymes>






Definition:
The list of enzymes used in experiment





Type:
EnzymesType





Attributes:



Attribute NameData TypeUseDefinition


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








Subelements:



Subelement NameminOccursmaxOccursDefinition


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








Example Context:

      <Enzymes independent="false">
        <Enzyme missedCleavages="2" semiSpecific="false" id="Enz1" name="Trypsin">
          <EnzymeName>
            <cvParam cvRef="PSI-MS" accession="MS:1001251" name="Trypsin"/>
          </EnzymeName>
        </Enzyme>
      </Enzymes>










Element <Exclude>






Definition:
All sequences fulfilling the specifed criteria are excluded.





Type:
ParamListType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam1unboundedA single entry from an ontology or a controlled vocabulary.


userParam1unboundedA single user-defined parameter.








Example Context:







cvParam Mapping Rules:

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










Element <ExternalFormatDocumentation>






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





Type:
xsd:anyURI





Attributes:
none






Subelements:
none






Example Context:










Element <FileFormat>






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





Type:
FileFormatType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam11A single entry from an ontology or a controlled vocabulary.








Example Context:

        <FileFormat>
          <cvParam cvRef="PSI-MS" accession="MS:1001401" name="X!Tandem xml format"/>
        </FileFormat>







cvParam Mapping Rules:

Path /MzIdentML/DataCollection/Inputs/SearchDatabase/FileFormat
MUST supply a *child* term of MS:1001347 (database file formats) one or more times
  e.g.: MS:1001348 (FASTA format) 
  e.g.: MS:1001349 (ASN.1) 
  e.g.: MS:1001350 (NCBI *.p*) 
  e.g.: MS:1001351 (clustal aln) 
  e.g.: MS:1001352 (embl em) 
  e.g.: MS:1001353 (NBRF PIR) 
  e.g.: MS:1001462 (PEFF format) 
  e.g.: MS:1002659 (UniProtKB text sequence format) 
  e.g.: MS:1002660 (UniProtKB XML sequence format) 



Path /MzIdentML/DataCollection/Inputs/SourceFile/FileFormat
MUST supply a *child* term of MS:1001040 (intermediate analysis format) only once
  e.g.: MS:1000742 (Bioworks SRF format) 
  e.g.: MS:1001107 (data stored in database) 
  e.g.: MS:1001199 (Mascot DAT format) 
  e.g.: MS:1001200 (SEQUEST out file format) 
  e.g.: MS:1001242 (SEQUEST out folder) 
  e.g.: MS:1001243 (SEQUEST summary) 
  e.g.: MS:1001275 (ProteinScape SearchEvent) 
  e.g.: MS:1001276 (ProteinScape Gel) 
  e.g.: MS:1001399 (OMSSA csv format) 
  e.g.: MS:1001400 (OMSSA xml format) 
  et al.



Path /MzIdentML/DataCollection/Inputs/SpectraData/FileFormat
MUST supply a *child* term of MS:1000560 (mass spectrometer file format) one or more times
  e.g.: MS:1000526 (Waters raw format) 
  e.g.: MS:1000562 (ABI WIFF format) 
  e.g.: MS:1000563 (Thermo RAW format) 
  e.g.: MS:1000564 (PSI mzData format) 
  e.g.: MS:1000565 (Micromass PKL format) 
  e.g.: MS:1000566 (ISB mzXML format) 
  e.g.: MS:1000567 (Bruker/Agilent YEP format) 
  e.g.: MS:1000584 (mzML format) 
  e.g.: MS:1000613 (DTA format) 
  e.g.: MS:1000614 (ProteinLynx Global Server mass spectrum XML format) 
  et al.







Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1001400" name="OMSSA xml format"/>
<cvParam cvRef="PSI-MS" accession="MS:1001401" name="X!Tandem xml format"/>
<cvParam cvRef="PSI-MS" accession="MS:1001348" name="FASTA format"/>
<cvParam cvRef="PSI-MS" accession="MS:1001062" name="Mascot MGF format"/>










Element <Filter>






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





Type:
FilterType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


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


Include01All sequences fulfilling the specifed criteria are included.


Exclude01All sequences fulfilling the specifed criteria are excluded.








Example Context:










Element <FilterType>






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





Type:
ParamType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam11A single entry from an ontology or a controlled vocabulary.


userParam11A single user-defined parameter.








Example Context:







cvParam Mapping Rules:

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










Element <FragmentArray>






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





Type:
FragmentArrayType





Attributes:



Attribute NameData TypeUseDefinition


measure_refxsd:stringrequiredA reference to the Measure defined in the FragmentationTable


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








Subelements:
none






Example Context:

                <FragmentArray measure_ref="Measure_Error" values="4.173258879802688E-4 -1.9794682032170385E-5 1.618474794895519E-5 0.001690052197886871 -0.0037214683721344954 0.0020060110579152024 -2.3719321211501665E-4 2.7168621795681247E-4 -0.0019049343519554895 0.0019553613780090018 2.6704080801209784E-4 0.007734020238103767 0.0013568713879976713 1.571508180404635E-4 -0.0017703817320580129 0.013774177127970688 0.0056154565579618065 0.004415735988004599 0.006145015418042021 -0.005059517131940083 0.01419863401793009 0.007626913448120831 0.007892192877989146"/>










Element <Fragmentation>






Definition:
The product ions identified in this result.





Type:
FragmentationType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


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








Example Context:

            <Fragmentation>
              <IonType charge="1" index="2 3 4 5 6 7 8 9 10 11 12 13">
                <FragmentArray measure_ref="Measure_MZ" values="141.06604 198.0867767 255.1083832 354.1768799 469.2016602 570.2514038 641.2855835 712.3236084 811.3933105 868.4135742 925.4346924 1024.512817"/>
                <FragmentArray measure_ref="Measure_Int" values="866.6297607422 1683.646484375 1591.5914306641 8459.6787109375 5963.1489257813 3577.7331542969 8420.6201171875 13378.169921875 8245.138671875 1536.9614257813 1653.0715332031 1660.8117675781"/>
                <FragmentArray measure_ref="Measure_Error" values="1.8602790797217494E-4 -5.409926620245642E-4 -3.9821323204591863E-4 -3.154262220732562E-4 -0.0024781500521271482 -4.130184621544686E-4 -0.0033471031722456246 -0.0024359878823361214 -0.0011478008724452593 -0.0023478214424130783 -0.002693342012321409 0.007017344997620967"/>
                <cvParam cvRef="PSI-MS" accession="MS:1001224" name="frag: b ion"/>
                <cvParam cvRef="PSI-MS" accession="MS:1000336" name="neutral loss" value="H2O"/>
  ...
</Fragmentation>










Element <FragmentationTable>






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





Type:
FragmentationTableType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


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








Example Context:

        <FragmentationTable>
          <Measure id="Measure_MZ">
            <cvParam cvRef="PSI-MS" accession="MS:1001225" name="product ion m/z" unitCvRef="PSI-MS" unitAccession="MS:1000040" unitName="m/z" />
          </Measure>
          <Measure id="Measure_Int">
            <cvParam cvRef="PSI-MS" accession="MS:1001226" name="product ion intensity" unitCvRef="PSI-MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
          </Measure>
  ...
</FragmentationTable>










Element <FragmentTolerance>






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





Type:
ToleranceType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam1unboundedA single entry from an ontology or a controlled vocabulary.








Example Context:

      <FragmentTolerance>
        <cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="dalton" unitAccession="UO:0000221" value="0.02" name="search tolerance plus value" />
        <cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="dalton" unitAccession="UO:0000221" value="0.02" name="search tolerance minus value" />
      </FragmentTolerance>







cvParam Mapping Rules:

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







Example cvParams:

<cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="dalton" unitAccession="UO:0000221" value="0.02" name="search tolerance plus value" />
<cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="dalton" unitAccession="UO:0000221" value="0.02" name="search tolerance minus value" />










Element <Include>






Definition:
All sequences fulfilling the specifed criteria are included.





Type:
ParamListType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam1unboundedA single entry from an ontology or a controlled vocabulary.


userParam1unboundedA single user-defined parameter.








Example Context:







cvParam Mapping Rules:

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










Element <Inputs>






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





Type:
InputsType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


SourceFile0unboundedA file from which this mzIdentML instance was created.


SearchDatabase0unboundedA database for searching mass spectra. Examples include a set of amino acid sequence entries, nucleotide databases (e.g. 6 frame translated) or annotated spectra libraries. 


SpectraData1unboundedA data set containing spectra data (consisting of one or more spectra). 








Example Context:

    <Inputs>
      <SourceFile location="C:\Users\hba041\My_Git_Applications\peptide-shaker.wiki\data\2016_04_05\.PeptideShaker_unzip_temp\searchgui_out_PeptideShaker_temp\qExactive01819.omx" id="SourceFile_1">
        <FileFormat>
          <cvParam cvRef="PSI-MS" accession="MS:1001400" name="OMSSA xml format"/>
        </FileFormat>
      </SourceFile>
      <SourceFile location="C:\Users\hba041\My_Git_Applications\peptide-shaker.wiki\data\2016_04_05\.PeptideShaker_unzip_temp\searchgui_out_PeptideShaker_temp\qExactive01819.t.xml" id="SourceFile_2">
  ...
</Inputs>










Element <InputSpectra>






Definition:
One of the spectra data sets used.





Type:
InputSpectraType





Attributes:



Attribute NameData TypeUseDefinition


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








Subelements:
none






Example Context:

      <InputSpectra spectraData_ref="qExactive01819.mgf"/>










Element <InputSpectrumIdentifications>






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





Type:
InputSpectrumIdentificationsType





Attributes:



Attribute NameData TypeUseDefinition


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








Subelements:
none






Example Context:

      <InputSpectrumIdentifications spectrumIdentificationList_ref="SIL_1"/>










Element <IonType>






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





Type:
IonTypeType





Attributes:



Attribute NameData TypeUseDefinition


chargexsd:intrequiredThe charge of the identified fragmentation ions.


indexlistOfIntegersoptionalThe index of ions identified as integers, following standard notation for a-c, x-z e.g. if b3 b5 and b6 have been identified, the index would store "3 5 6". For internal ions, the index contains pairs defining the start and end point - see specification document for examples. For immonium ions, the index is the position of the identified ion within the peptide sequence - if the peptide contains the same amino acid in multiple positions that cannot be distinguished, all positions should be given. For precursor ions, including neutral losses, the index value MUST be 0. For any other ions not related to the position within the peptide sequence e.g. quantification reporter ions, the index value MUST be 0. 








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. 


userParam0unboundedA single user-defined parameter.


cvParam1unboundedA single entry from an ontology or a controlled vocabulary.








Example Context:

              <IonType charge="1" index="1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23">
                <FragmentArray measure_ref="Measure_MZ" values="175.1193695 232.1403961 289.1618958 452.2268982 509.2429504 566.2701416 653.2999268 710.3218994 767.3411865 854.3770752 911.3968506 968.4257813 1065.472168 1122.492432 1285.553833 1399.612305 1456.62561 1513.645874 1570.669067 1733.721191 1830.793213 1887.808105 1944.829834"/>
                <FragmentArray measure_ref="Measure_Int" values="5939.5844726563 4933.5014648438 13310.7265625 5077.6694335938 5685.9287109375 13253.552734375 7620.0947265625 7724.3696289063 16868.541015625 10552.126953125 11589.0576171875 7839.9741210938 47821.64453125 60335.71484375 21759.3984375 8742.5595703125 11512.0908203125 18130.890625 30577.375 3801.3923339844 8051.07421875 1954.5501708984 4844.9125976563"/>
                <FragmentArray measure_ref="Measure_Error" values="4.173258879802688E-4 -1.9794682032170385E-5 1.618474794895519E-5 0.001690052197886871 -0.0037214683721344954 0.0020060110579152024 -2.3719321211501665E-4 2.7168621795681247E-4 -0.0019049343519554895 0.0019553613780090018 2.6704080801209784E-4 0.007734020238103767 0.0013568713879976713 1.571508180404635E-4 -0.0017703817320580129 0.013774177127970688 0.0056154565579618065 0.004415735988004599 0.006145015418042021 -0.005059517131940083 0.01419863401793009 0.007626913448120831 0.007892192877989146"/>
                <cvParam cvRef="PSI-MS" accession="MS:1001220" name="frag: y ion"/>
              </IonType>







cvParam Mapping Rules:

Path /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem/Fragmentation/IonType
MAY supply a *child* term of MS:1001221 (product ion attribute) one or more times
  e.g.: MS:1000903 (product ion series ordinal) 
  e.g.: MS:1000904 (product ion m/z delta) 
  e.g.: MS:1000926 (product interpretation rank) 
  e.g.: MS:1001220 (frag: y ion) 
  e.g.: MS:1001222 (frag: b ion - H2O) 
  e.g.: MS:1001223 (frag: y ion - H2O) 
  e.g.: MS:1001224 (frag: b ion) 
  e.g.: MS:1001225 (product ion m/z) 
  e.g.: MS:1001227 (product ion m/z error) 
  e.g.: MS:1001228 (frag: x ion) 
  et al.
MAY supply term MS:1000336 (neutral loss) one or more times







Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1001224" name="frag: b ion"/>
<cvParam cvRef="PSI-MS" accession="MS:1001220" name="frag: y ion"/>
<cvParam cvRef="PSI-MS" accession="MS:1002466" name="PeptideShaker PSM score" value="0.0"/>
<cvParam cvRef="PSI-MS" accession="MS:1002467" name="PeptideShaker PSM confidence" value="0.0"/>
<cvParam cvRef="PSI-MS" accession="MS:1002469" name="PeptideShaker peptide confidence" value="4.0000000000000036"/>
<cvParam cvRef="PSI-MS" accession="MS:1002468" name="PeptideShaker peptide score" value="-0.0"/>
<cvParam cvRef="PSI-MS" accession="MS:1002500" name="peptide passes threshold" value="false"/>
<cvParam cvRef="PSI-MS" accession="MS:1002520" name="peptide group ID" value="QKAQAAATVVK"/>
<cvParam cvRef="PSI-MS" accession="MS:1001328" name="OMSSA:evalue" value="68.145917448381"/>
<cvParam cvRef="PSI-MS" accession="MS:1001117" name="theoretical mass" value="1113.6506071554904" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton"/>
<cvParam cvRef="PSI-MS" accession="MS:1002540" name="PeptideShaker PSM confidence type" value="Not Validated"/>
<cvParam cvRef="PSI-MS" accession="MS:1000796" name="spectrum title" value="qExactive01819.13825.13825. File:"qExactive01819.raw", NativeID:"controllerType=0 controllerNumber=1 scan=13825""/>
<cvParam cvRef="PSI-MS" accession="MS:1000894" name="retention time" value="3266.09664" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
<cvParam cvRef="PSI-MS" accession="MS:1000336" name="neutral loss" value="H2O"/>
<cvParam cvRef="PSI-MS" accession="MS:1001239" name="frag: immonium ion"/>
<cvParam cvRef="PSI-MS" accession="MS:1002536" name="D-Score" value="2:99.6124031007752:1:true"/>
<cvParam cvRef="PSI-MS" accession="MS:1001330" name="X!Tandem:expect" value="0.0067"/>
<cvParam cvRef="PSI-MS" accession="MS:1001969" name="phosphoRS score" value="1:50.0:4:false"/>
<cvParam cvRef="PSI-MS" accession="MS:1002550" name="peptide:phosphoRS score" value="1:50.0:4:false"/>
<cvParam cvRef="PSI-MS" accession="MS:1002553" name="peptide:D-Score" value="1:1.4263074484944571:4:false"/>










Element <MassTable>






Definition:
The masses of residues used in the search.





Type:
MassTableType





Attributes:



Attribute NameData TypeUseDefinition


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


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


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








Subelements:



Subelement NameminOccursmaxOccursDefinition


Residue0unboundedThe specification of a single residue within the mass table. 


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


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.


userParam0unboundedA single user-defined parameter.








Example Context:







cvParam Mapping Rules:

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










Element <Measure>






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





Type:
MeasureType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam1unboundedA single entry from an ontology or a controlled vocabulary.








Example Context:

          <Measure id="Measure_Int">
            <cvParam cvRef="PSI-MS" accession="MS:1001226" name="product ion intensity" unitCvRef="PSI-MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
          </Measure>







cvParam Mapping Rules:

Path /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/FragmentationTable/Measure
MUST supply term MS:1001226 (product ion intensity) only once
MUST supply term MS:1001225 (product ion m/z) only once
MUST supply term MS:1001227 (product ion m/z error) only once







Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1001225" name="product ion m/z" unitCvRef="PSI-MS" unitAccession="MS:1000040" unitName="m/z" />
<cvParam cvRef="PSI-MS" accession="MS:1001226" name="product ion intensity" unitCvRef="PSI-MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
<cvParam cvRef="PSI-MS" accession="MS:1001227" name="product ion m/z error" unitCvRef="PSI-MS" unitAccession="MS:1000040" unitName="m/z"/>










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. A cvParam MUST be provided with the identification of the modification sourced from a suitable CV e.g. UNIMOD. If the modification is not present in the CV (and this will be checked by the semantic validator within a given tolerance window), there is a “unknown modification” CV term that MUST be used instead. A neutral loss should be defined as an additional CVParam within Modification. If more complex information should be given about neutral losses (such as presence/absence on particular product ions), this can additionally be encoded within the FragmentationArray. 





Type:
ModificationType





Attributes:



Attribute NameData TypeUseDefinition


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


locationxsd:intoptionalLocation of the modification within the peptide - position in peptide sequence, counted from the N-terminus residue, starting at position 1. Specific modifications to the N-terminus should be given the location 0. Modification to the C-terminus should be given as peptide length + 1. If the modification location is unknown e.g. for PMF data, this attribute should be omitted.	


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


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








Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam1unboundedA single entry from an ontology or a controlled vocabulary.








Example Context:

      <Modification monoisotopicMassDelta="-17.026549" residues="Q" location="0" >
        <cvParam cvRef="UNIMOD" accession="UNIMOD:28" name="Gln->pyro-Glu"/>
      </Modification>







cvParam Mapping Rules:

Path /MzIdentML/SequenceCollection/Peptide/Modification
MAY supply term MS:1002509 (cross-link donor) only once
MAY supply term MS:1002510 (cross-link acceptor) only once
MAY supply a *child* term of UNIMOD:0 (unimod root node) only once
MAY supply a *child* term of XLMOD:00004 (cross-linker) only once
MAY supply a *child* term of MS:1001471 (peptide modification details) only once
  e.g.: MS:1001460 (unknown modification) 
  e.g.: MS:1001524 (fragment neutral loss) 
  e.g.: MS:1001525 (precursor neutral loss) 
  e.g.: MS:1001972 (PTM scoring algorithm version) 
  e.g.: MS:1002028 (nucleic acid base modification) 
  e.g.: MS:1002029 (original nucleic acid sequence) 
  e.g.: MS:1002030 (modified nucleic acid sequence) 
MAY supply a *child* term of XLMOD:00002 (cross-linker related PTM) only once
MAY supply a *child* term of MOD:00000 (protein modification) only once







Example cvParams:

<cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"/>
<cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/>
<cvParam cvRef="UNIMOD" accession="UNIMOD:28" name="Gln->pyro-Glu"/>
<cvParam cvRef="UNIMOD" accession="UNIMOD:27" name="Glu->pyro-Glu"/>
<cvParam cvRef="UNIMOD" accession="UNIMOD:1" name="Acetyl"/>
<cvParam cvRef="UNIMOD" accession="UNIMOD:385" name="Ammonia-loss"/>










Element <ModificationParams>






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





Type:
ModificationParamsType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


SearchModification1unboundedSpecification 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 residues="C" massDelta="57.021464" fixedMod= "true" >
          <cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"/>
          <cvParam cvRef="PSI-MS" accession="MS:1002504" name="modification index" value="0"/>
        </SearchModification>
        <SearchModification residues="M" massDelta="15.994915" fixedMod= "false" >
          <cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/>
  ...
</ModificationParams>










Element <Organization>






Definition:
Organizations are entities like companies, universities, government agencies. Any additional information such as the address, email etc. should be supplied either as CV parameters or as user parameters. 





Type:
OrganizationType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.


userParam0unboundedA single user-defined parameter.


Parent01The containing organization (the university or business which a lab belongs to, etc.) 








Example Context:

    <Organization name="PeptideShaker developers" id="PS_DEV">
      <cvParam cvRef="PSI-MS" accession="MS:1000586" name="contact name" value="PeptideShaker developers"/>
      <cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="Proteomics Unit, Building for Basic Biology, University of Bergen, Jonas Liesvei 91, N-5009 Bergen, Norway"/>
      <cvParam cvRef="PSI-MS" accession="MS:1000588" name="contact URL" value="http://compomics.github.io/projects/peptide-shaker.html"/>
      <cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="peptide-shaker@googlegroups.com"/>
    </Organization>







cvParam Mapping Rules:

Path /MzIdentML/AuditCollection/Organization
SHOULD supply term MS:1000588 (contact URL) one or more times
SHOULD supply term MS:1000587 (contact address) one or more times
SHOULD supply term MS:1000589 (contact email) one or more times
SHOULD supply term MS:1000586 (contact name) one or more times







Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1000586" name="contact name" value="test"/>
<cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="test"/>
<cvParam cvRef="PSI-MS" accession="MS:1000588" name="contact URL" value="test"/>
<cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="test"/>










Element <Parent>






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





Type:
ParentOrganizationType





Attributes:



Attribute NameData TypeUseDefinition


organization_refxsd:stringrequiredA reference to the organization this contact belongs to.








Subelements:
none






Example Context:










Element <ParentTolerance>






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





Type:
ToleranceType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam1unboundedA single entry from an ontology or a controlled vocabulary.








Example Context:

      <ParentTolerance>
        <cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="10.0" name="search tolerance plus value" />
        <cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="10.0" name="search tolerance minus value" />
      </ParentTolerance>







cvParam Mapping Rules:

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







Example cvParams:

<cvParam accession="MS:1001412" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="10.0" name="search tolerance plus value" />
<cvParam accession="MS:1001413" cvRef="PSI-MS" unitCvRef="UO" unitName="parts per million" unitAccession="UO:0000169" value="10.0" name="search tolerance minus value" />










Element <Peptide>






Definition:
One (poly)peptide (a sequence with modifications). The combination of Peptide sequence and modifications MUST be unique in the file.





Type:
PeptideType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


PeptideSequence11The amino acid sequence of the (poly)peptide. If a substitution modification has been found, the original sequence
should be reported. 


Modification0unboundedA molecule modification specification. If n modifications have been found on a peptide, there should be n instances of Modification. If multiple modifications are provided as cvParams, it is assumed that the modification is ambiguous i.e. one modification or another. A cvParam MUST be provided with the identification of the modification sourced from a suitable CV e.g. UNIMOD. If the modification is not present in the CV (and this will be checked by the semantic validator within a given tolerance window), there is a “unknown modification” CV term that MUST be used instead. A neutral loss should be defined as an additional CVParam within Modification. If more complex information should be given about neutral losses (such as presence/absence on particular product ions), this can additionally be encoded within the FragmentationArray. 


SubstitutionModification0unboundedA modification where one residue is substituted by another (amino acid change). 


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.


userParam0unboundedA single user-defined parameter.








Example Context:

    <Peptide id="KIMTPIECAMTMMSHIPSVMK_15.99491461956-ATAA-10_15.99491461956-ATAA-12_15.99491461956-ATAA-13_15.99491461956-ATAA-20_15.99491461956-ATAA-3">
      <PeptideSequence>KLMTPIECAMTMMSHIPSVMK</PeptideSequence>
      <Modification monoisotopicMassDelta="57.021464" residues="C" location="8" >
        <cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"/>
      </Modification>
      <Modification monoisotopicMassDelta="15.994915" residues="M" location="10" >
        <cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/>
  ...
</Peptide>







cvParam Mapping Rules:
WARNING: There are no cvParam mapping rules for this element even though cvParam is an allowed subelement.







Element <PeptideEvidence>






Definition:
PeptideEvidence links a specific Peptide element to a specific position in a DBSequence. There MUST only be one PeptideEvidence item per Peptide-to-DBSequence-position. 





Type:
PeptideEvidenceType





Attributes:



Attribute NameData TypeUseDefinition


dBSequence_refxsd:stringrequiredA reference to the protein sequence in which the specified peptide has been linked. 


endxsd:intoptionalThe index position of the last amino acid of the peptide inside the protein sequence, where the first amino acid of the protein sequence is position 1. Must be provided unless this is a de novo search. 


frameallowed_framesoptionalThe translation frame of this sequence if this is PeptideEvidence derived from nucleic acid sequence 


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


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


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


peptide_refxsd:stringrequiredA reference to the identified (poly)peptide sequence in the Peptide element. 


postxsd:string with restriction
[ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}
optionalPost 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. 


prexsd:string with restriction
[ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}
optionalPrevious 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:intoptionalStart position of the peptide inside the protein sequence, where the first amino acid of the protein sequence is position 1. Must be provided unless this is a de novo search.


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








Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.


userParam0unboundedA single user-defined parameter.








Example Context:

    <PeptideEvidence isDecoy="false" pre="R" post="A" start="636" end="656" peptide_ref="KIMTPIECAMTMMSHIPSVMK_15.99491461956-ATAA-10_15.99491461956-ATAA-12_15.99491461956-ATAA-13_15.99491461956-ATAA-20_15.99491461956-ATAA-3" dBSequence_ref="Q9P2D3" id="PepEv_1479" />







cvParam Mapping Rules:

Path /MzIdentML/SequenceCollection/PeptideEvidence
MUST supply term MS:1002642 (peptide exon nucleotide sizes) only once
MUST supply term MS:1002643 (peptide start positions on chromosome) only once
MUST supply term MS:1002640 (peptide end on chromosome) only once
MUST supply term MS:1002641 (peptide exon count) only once










Element <PeptideEvidenceRef>






Definition:
Reference to the PeptideEvidence element identified. If a specific sequence can be assigned to multiple proteins and or positions in a protein all possible PeptideEvidence elements should be referenced here.





Type:
PeptideEvidenceRefType





Attributes:



Attribute NameData TypeUseDefinition


peptideEvidence_refxsd:stringrequiredA reference to the PeptideEvidenceItem element(s).








Subelements:
none






Example Context:

            <PeptideEvidenceRef peptideEvidence_ref="PepEv_1499"/>










Element <PeptideHypothesis>






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





Type:
PeptideHypothesisType





Attributes:



Attribute NameData TypeUseDefinition


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








Subelements:



Subelement NameminOccursmaxOccursDefinition


SpectrumIdentificationItemRef1unboundedReference(s) to the SpectrumIdentificationItem element(s) that support the given PeptideEvidence element. Using these references it is possible to indicate which spectra were actually accepted as evidence for this peptide identification in the given protein.








Example Context:

            <PeptideHypothesis peptideEvidence_ref="PepEv_1864">
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_1780_1"/>
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_2217_1"/>
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_3245_1"/>
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_4362_1"/>
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_5349_1"/>
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_5621_1"/>
  ...
</PeptideHypothesis>







Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1002403" name="group representative"/>
<cvParam cvRef="PSI-MS" accession="MS:1002401" name="leading protein"/>
<cvParam cvRef="PSI-MS" accession="MS:1001093" name="sequence coverage" value="0.19"/>
<cvParam cvRef="PSI-MS" accession="MS:1002470" name="PeptideShaker protein group score" value="100.0"/>
<cvParam cvRef="PSI-MS" accession="MS:1002471" name="PeptideShaker protein group confidence" value="100.0"/>
<cvParam cvRef="PSI-MS" accession="MS:1002542" name="PeptideShaker protein confidence type" value="Confident"/>
<cvParam cvRef="PSI-MS" accession="MS:1002415" name="protein group passes threshold" value="true"/>
<cvParam cvRef="PSI-MS" accession="MS:1002404" name="count of identified proteins" value="1201"/>










Element <PeptideSequence>






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





Type:
sequence





Attributes:
none






Subelements:
none






Example Context:

      <PeptideSequence>KAVTGAPVLPVVSPLVIPEPEPEKEMPIGK</PeptideSequence>










Element <Person>






Definition:
A person's name and contact details. Any additional information such as the address, contact email etc. should be supplied using CV parameters or user parameters.





Type:
PersonType





Attributes:



Attribute NameData TypeUseDefinition


firstNamexsd:stringoptionalThe Person's first name.


idxsd:stringrequiredAn 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:stringoptionalThe Person's last/family name.


midInitialsxsd:stringoptionalThe Person's middle initial.


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








Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.


userParam0unboundedA single user-defined parameter.


Affiliation0unboundedThe organization a person belongs to.








Example Context:

    <Person firstName="test" lastName="test" id="PROVIDER">
      <cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="test"/>
      <cvParam cvRef="PSI-MS" accession="MS:1000588" name="contact URL" value="test"/>
      <cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="test"/>
      <Affiliation organization_ref="ORG_DOC_OWNER"/>
    </Person>







cvParam Mapping Rules:

Path /MzIdentML/AuditCollection/Person
SHOULD supply term MS:1000588 (contact URL) one or more times
SHOULD supply term MS:1000587 (contact address) one or more times
SHOULD supply term MS:1000589 (contact email) one or more times







Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="test"/>
<cvParam cvRef="PSI-MS" accession="MS:1000588" name="contact URL" value="test"/>
<cvParam cvRef="PSI-MS" accession="MS:1000589" name="contact email" value="test"/>










Element <ProteinAmbiguityGroup>






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





Type:
ProteinAmbiguityGroupType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


ProteinDetectionHypothesis1unboundedA single result of the ProteinDetection analysis (i.e. a protein).


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.


userParam0unboundedA single user-defined parameter.








Example Context:

        <ProteinAmbiguityGroup id="PAG_1051">
          <ProteinDetectionHypothesis id="PAG_1051_1" dBSequence_ref="Q7Z7K6_REVERSED" passThreshold="false">
            <PeptideHypothesis peptideEvidence_ref="PepEv_5108">
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_1428_1"/>
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_4047_1"/>
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_4272_1"/>
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_4444_1"/>
  ...
</ProteinAmbiguityGroup>







cvParam Mapping Rules:

Path /MzIdentML/DataCollection/AnalysisData/ProteinDetectionList/ProteinAmbiguityGroup
MAY supply a *child* term of MS:1002698 (protein cluster identification attribute) only once
  e.g.: MS:1002407 (cluster identifier) 
MAY supply a *child* term of MS:1002346 (protein group-level identification attribute) one or more times
  e.g.: MS:1001164 (Paragon:unused protscore) 
  e.g.: MS:1001165 (Paragon:total protscore) 
  e.g.: MS:1002236 (ProteoGrouper:PAG score) 
  e.g.: MS:1002370 (protein group-level local FDR) 
  e.g.: MS:1002371 (protein group-level p-value) 
  e.g.: MS:1002372 (protein group-level e-value) 
  e.g.: MS:1002373 (protein group-level q-value) 
  e.g.: MS:1002374 (protein group-level FDRScore) 
  e.g.: MS:1002375 (protein group-level combined FDRScore) 
  e.g.: MS:1002376 (protein group-level probability) 
  et al.
MAY supply term MS:1002542 (PeptideShaker protein confidence type) only once
MAY supply term MS:1002471 (PeptideShaker protein group confidence) only once
MUST supply term MS:1002415 (protein group passes threshold) only once
MAY supply term MS:1002470 (PeptideShaker protein group score) only once










Element <ProteinDetection>






Definition:
An Analysis which assembles a set of peptides (e.g. from a spectra search analysis) to proteins. 





Type:
ProteinDetectionType





Attributes:



Attribute NameData TypeUseDefinition


activityDatexsd:dateTimeoptionalWhen the protocol was applied.


idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance. 


proteinDetectionList_refxsd:stringrequiredA reference to the ProteinDetectionList in the DataCollection section. 


proteinDetectionProtocol_refxsd:stringrequiredA reference to the detection protocol used for this ProteinDetection. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


InputSpectrumIdentifications1unboundedThe lists of spectrum identifications that are input to the protein detection process. 








Example Context:

    <ProteinDetection proteinDetectionProtocol_ref="PeptideShaker_1" proteinDetectionList_ref="Protein_groups" id="PD_1">
      <InputSpectrumIdentifications spectrumIdentificationList_ref="SIL_1"/>
    </ProteinDetection>










Element <ProteinDetectionHypothesis>






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





Type:
ProteinDetectionHypothesisType





Attributes:



Attribute NameData TypeUseDefinition


dBSequence_refxsd:stringrequiredA reference to the corresponding DBSequence entry. Note - this attribute was optional in mzIdentML 1.1 but is now mandatory in mzIdentML 1.2. Consuming software should assume that the DBSequence entry referenced here is the definitive identifier for the protein. 


idxsd:stringrequiredAn 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:stringoptionalThe 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. 


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.


userParam0unboundedA single user-defined parameter.








Example Context:

          <ProteinDetectionHypothesis id="PAG_1051_1" dBSequence_ref="Q7Z7K6_REVERSED" passThreshold="false">
            <PeptideHypothesis peptideEvidence_ref="PepEv_5108">
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_1428_1"/>
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_4047_1"/>
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_4272_1"/>
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_4444_1"/>
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_5193_1"/>
  ...
</ProteinDetectionHypothesis>







cvParam Mapping Rules:

Path /MzIdentML/DataCollection/AnalysisData/ProteinDetectionList/ProteinAmbiguityGroup/ProteinDetectionHypothesis
MAY supply a *child* term of MS:1001085 (protein-level identification attribute) one or more times
  e.g.: MS:1001088 (protein description) 
  e.g.: MS:1001090 (taxonomy nomenclature) 
  e.g.: MS:1001093 (sequence coverage) 
  e.g.: MS:1001097 (distinct peptide sequences) 
  e.g.: MS:1001098 (confident distinct peptide sequences) 
  e.g.: MS:1001099 (confident peptide qualification) 
  e.g.: MS:1001100 (confident peptide sequence number) 
  e.g.: MS:1001125 (manual validation) 
  e.g.: MS:1001147 (protein ambiguity group result details) WARNING: Term has no definition!
  e.g.: MS:1001157 (SEQUEST:sp) 
  et al.
MAY supply a *child* term of MS:1001116 (single protein identification statistic) one or more times
  e.g.: MS:1001125 (manual validation) 
  e.g.: MS:1001157 (SEQUEST:sp) 
  e.g.: MS:1001158 (SEQUEST:Uniq) WARNING: Term has no definition!
  e.g.: MS:1001164 (Paragon:unused protscore) 
  e.g.: MS:1001165 (Paragon:total protscore) 
  e.g.: MS:1001166 (Paragon:score) 
  e.g.: MS:1001167 (Paragon:confidence) 
  e.g.: MS:1001168 (Paragon:expression error factor) 
  e.g.: MS:1001169 (Paragon:expression change p-value) 
  e.g.: MS:1001170 (Paragon:contrib) 
  et al.
MAY supply a *child* term of MS:1001153 (search engine specific score) one or more times
  e.g.: MS:1001147 (protein ambiguity group result details) WARNING: Term has no definition!
  e.g.: MS:1001155 (SEQUEST:xcorr) 
  e.g.: MS:1001159 (SEQUEST:expectation value) 
  e.g.: MS:1001163 (SEQUEST:consensus score) 
  e.g.: MS:1001874 (FDRScore) 
  e.g.: MS:1002052 (MS-GF:SpecEValue) 
  e.g.: MS:1002053 (MS-GF:EValue) 
  e.g.: MS:1002125 (combined FDRScore) 
  e.g.: MS:1002252 (Comet:xcorr) 
  e.g.: MS:1002257 (Comet:expectation value) 
  et al.
MAY supply a *child* term of MS:1001805 (quantification datatype) one or more times
  e.g.: MS:1001130 (peptide raw area) 
  e.g.: MS:1001131 (error on peptide area) 
  e.g.: MS:1001132 (peptide ratio) 
  e.g.: MS:1001133 (error on peptide ratio) 
  e.g.: MS:1001134 (protein ratio) 
  e.g.: MS:1001135 (error on protein ratio) 
  e.g.: MS:1001136 (p-value (protein diff from 1 randomly)) 
  e.g.: MS:1001137 (absolute quantity) 
  e.g.: MS:1001138 (error on absolute quantity) 
  e.g.: MS:1001141 (intensity of precursor ion) 
  et al.
MAY supply a *child* term of MS:1001060 (quality estimation method details) one or more times
  e.g.: MS:1001058 (quality estimation by manual validation) 
  e.g.: MS:1001194 (quality estimation with decoy database) 
  e.g.: MS:1001447 (prot:FDR threshold) 
  e.g.: MS:1001448 (pep:FDR threshold) 
  e.g.: MS:1001454 (quality estimation with implicite decoy sequences) 
  e.g.: MS:1001494 (no threshold) 
  e.g.: MS:1001574 (report only spectra assigned to identified proteins) 
  e.g.: MS:1001868 (distinct peptide-level q-value) 
  e.g.: MS:1002260 (PSM:FDR threshold) 
  e.g.: MS:1002486 (protein group-level statistical threshold) 
MUST supply a *child* term of MS:1001101 (protein group or subset relationship) one or more times
  e.g.: MS:1001591 (anchor protein) 
  e.g.: MS:1001592 (family member protein) 
  e.g.: MS:1001593 (group member with undefined relationship OR ortholog protein) 
  e.g.: MS:1001594 (sequence same-set protein) 
  e.g.: MS:1001595 (spectrum same-set protein) 
  e.g.: MS:1001596 (sequence sub-set protein) 
  e.g.: MS:1001597 (spectrum sub-set protein) 
  e.g.: MS:1001598 (sequence subsumable protein) 
  e.g.: MS:1001599 (spectrum subsumable protein) 
  e.g.: MS:1002213 (PAnalyzer:conclusive protein) 
  et al.
MAY supply a *child* term of MS:1002664 (interaction score derived from cross-linking) one or more times
  e.g.: MS:1002676 (protein-pair-level global FDR) 
  e.g.: MS:1002677 (residue-pair-level global FDR) 
MAY supply a *child* term of MS:1001143 (PSM-level search engine specific statistic) one or more times
  e.g.: MS:1001154 (SEQUEST:probability) 
  e.g.: MS:1001155 (SEQUEST:xcorr) 
  e.g.: MS:1001156 (SEQUEST:deltacn) 
  e.g.: MS:1001160 (SEQUEST:sf) 
  e.g.: MS:1001161 (SEQUEST:matched ions) 
  e.g.: MS:1001162 (SEQUEST:total ions) 
  e.g.: MS:1001171 (Mascot:score) 
  e.g.: MS:1001172 (Mascot:expectation value) 
  e.g.: MS:1001173 (Mascot:matched ions) 
  e.g.: MS:1001174 (Mascot:total ions) 
  et al.










Element <ProteinDetectionList>






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





Type:
ProteinDetectionListType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


ProteinAmbiguityGroup0unboundedA set of logically related results from a protein detection, for example to represent conflicting assignments of peptides to proteins.
			


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.


userParam0unboundedA single user-defined parameter.








Example Context:

      <ProteinDetectionList id="Protein_groups">
        <ProteinAmbiguityGroup id="PAG_0">
          <ProteinDetectionHypothesis id="PAG_0_1" dBSequence_ref="O75947" passThreshold="true">
            <PeptideHypothesis peptideEvidence_ref="PepEv_4952">
              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_5365_1"/>
            </PeptideHypothesis>
            <PeptideHypothesis peptideEvidence_ref="PepEv_1026">
  ...
</ProteinDetectionList>







cvParam Mapping Rules:

Path /MzIdentML/DataCollection/AnalysisData/ProteinDetectionList
MAY supply a *child* term of MS:1001184 (search statistics) one or more times
  e.g.: MS:1001035 (date / time search performed) 
  e.g.: MS:1001036 (search time taken) 
  e.g.: MS:1001177 (number of molecular hypothesis considered) 
MUST supply term MS:1002404 (count of identified proteins) only once
MAY supply term MS:1002406 (count of identified clusters) only once










Element <ProteinDetectionProtocol>






Definition:
The parameters and settings of a ProteinDetection process.





Type:
ProteinDetectionProtocolType





Attributes:



Attribute NameData TypeUseDefinition


analysisSoftware_refxsd:stringrequiredThe protein detection software used, given as a reference to the SoftwareCollection section. 


idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


AnalysisParams01The parameters and settings for the protein detection given as CV terms. 


Threshold11The threshold(s) applied to determine that a result is significant. If multiple terms are used it is assumed that all conditions are satisfied by the passing results.








Graphical Context:






Example Context:

    <ProteinDetectionProtocol analysisSoftware_ref="ID_software" id="PeptideShaker_1">
      <Threshold>
        <cvParam cvRef="PSI-MS" accession="MS:1002369" name="protein group-level global FDR" value="0.01"/>
      </Threshold>
    </ProteinDetectionProtocol>










Element <Provider>






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





Type:
ProviderType





Attributes:



Attribute NameData TypeUseDefinition


analysisSoftware_refxsd:stringoptionalThe Software that produced the document instance.


idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


ContactRole01The Contact that provided the document instance.








Example Context:

  <Provider id="PROVIDER">
    <ContactRole contact_ref="PROVIDER">
      <Role>
        <cvParam cvRef="PSI-MS" accession="MS:1001271" name="researcher"/>
      </Role>
    </ContactRole>
  </Provider>










Element <Residue>






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





Type:
ResidueType





Attributes:



Attribute NameData TypeUseDefinition


codecharsrequiredThe single letter code for the residue.


massxsd:floatrequiredThe residue mass in Daltons (not including any fixed modifications). 








Subelements:
none






Example Context:










Element <Role>






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





Type:
RoleType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam11A single entry from an ontology or a controlled vocabulary.








Example Context:

        <Role>
          <cvParam cvRef="PSI-MS" accession="MS:1001267" name="software vendor"/>
        </Role>







cvParam Mapping Rules:

Path /MzIdentML/Provider/ContactRole/Role
MUST supply a *child* term of MS:1001266 (role type) one or more times
  e.g.: MS:1001267 (software vendor) 
  e.g.: MS:1001268 (programmer) 
  e.g.: MS:1001269 (instrument vendor) 
  e.g.: MS:1001270 (lab personnel) 
  e.g.: MS:1001271 (researcher) 



Path /MzIdentML/AnalysisSoftwareList/AnalysisSoftware/ContactRole/Role
MUST supply a *child* term of MS:1001266 (role type) one or more times
  e.g.: MS:1001267 (software vendor) 
  e.g.: MS:1001268 (programmer) 
  e.g.: MS:1001269 (instrument vendor) 
  e.g.: MS:1001270 (lab personnel) 
  e.g.: MS:1001271 (researcher) 



Path /MzIdentML/AnalysisSampleCollection/Sample/ContactRole/Role
MUST supply a *child* term of MS:1001266 (role type) one or more times
  e.g.: MS:1001267 (software vendor) 
  e.g.: MS:1001268 (programmer) 
  e.g.: MS:1001269 (instrument vendor) 
  e.g.: MS:1001270 (lab personnel) 
  e.g.: MS:1001271 (researcher) 







Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1001267" name="software vendor"/>
<cvParam cvRef="PSI-MS" accession="MS:1001271" name="researcher"/>










Element <Sample>






Definition:
 A description of the sample analysed by mass spectrometry using CVParams or UserParams. If a composite sample has been analysed, a parent sample should be defined, which references subsamples. This represents any kind of substance used in an experimental workflow, such as whole organisms, cells, DNA, solutions, compounds and experimental substances (gels, arrays etc.).	





Type:
SampleType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


ContactRole0unboundedThe Contact that provided the document instance.


SubSample0unboundedReferences to the individual component samples within a mixed parent sample. 


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.


userParam0unboundedA single user-defined parameter.








Example Context:







cvParam Mapping Rules:
WARNING: There are no cvParam mapping rules for this element even though cvParam is an allowed subelement.







Element <SearchDatabase>






Definition:
A database for searching mass spectra. Examples include a set of amino acid sequence entries, nucleotide databases (e.g. 6 frame translated) or annotated spectra libraries. 





Type:
SearchDatabaseType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequiredAn 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:anyURIrequiredThe location of the data file.


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


numDatabaseSequencesxsd:longoptionalThe total number of sequences in the database.


numResiduesxsd:longoptionalThe number of residues in the database.


releaseDatexsd:dateTimeoptionalThe date and time the database was released to the public; omit this attribute when the date and time are unknown or not applicable (e.g. custom databases). 


versionxsd:stringoptionalThe version of the database.








Subelements:



Subelement NameminOccursmaxOccursDefinition


ExternalFormatDocumentation01A 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.


FileFormat11The format of the ExternalData file, for example "tiff" for image files. 


DatabaseName11The database name may be given as a cvParam if it maps exactly to one of the release databases listed in the CV, otherwise a userParam should be used. 


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.








Example Context:

      <SearchDatabase numDatabaseSequences="40400" location="C:\Users\hba041\My_Git_Applications\peptide-shaker.wiki\data\2016_04_05\uniprot-human-reviewed-trypsin-april-2016_concatenated_target_decoy.fasta" id="SearchDB_1">
        <FileFormat>
          <cvParam cvRef="PSI-MS" accession="MS:1001348" name="FASTA format"/>
        </FileFormat>
        <DatabaseName>
          <userParam name="uniprot-human-reviewed-trypsin-april-2016_concatenated_target_decoy.fasta"/>
        </DatabaseName>
  ...
</SearchDatabase>







cvParam Mapping Rules:

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










Element <SearchDatabaseRef>






Definition:
One of the search databases used.





Type:
SearchDatabaseRefType





Attributes:



Attribute NameData TypeUseDefinition


searchDatabase_refxsd:stringoptionalA reference to the database searched.








Subelements:
none






Example Context:

      <SearchDatabaseRef searchDatabase_ref="SearchDB_1"/>










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:
SearchModificationType





Attributes:



Attribute NameData TypeUseDefinition


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


massDeltaxsd:floatrequiredThe mass delta of the searched modification in Daltons.


residueslistOfCharsOrAnyrequiredThe residue(s) searched with the specified modification. For N or C terminal modifications that can occur on any residue, the . character should be used to specify any, otherwise the list of amino acids should be provided.








Subelements:



Subelement NameminOccursmaxOccursDefinition


SpecificityRules0unboundedThe specificity rules of the searched modification including for example the probability of a modification's presence or peptide or protein termini. Standard fixed or variable status should be provided by the attribute fixedMod.


cvParam1unboundedA single entry from an ontology or a controlled vocabulary.








Example Context:

        <SearchModification residues="E" massDelta="-18.010565" fixedMod= "false" >
          <SpecificityRules>
            <cvParam cvRef="PSI-MS" accession="MS:1001189" name="modification specificity peptide N-term"/>
          </SpecificityRules>
          <cvParam cvRef="UNIMOD" accession="UNIMOD:27" name="Glu->pyro-Glu"/>
          <cvParam cvRef="PSI-MS" accession="MS:1002504" name="modification index" value="3"/>
        </SearchModification>







cvParam Mapping Rules:

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ModificationParams/SearchModification
MAY supply term MS:1002509 (cross-link donor) only once
MAY supply term MS:1002510 (cross-link acceptor) only once
MAY supply a *child* term of UNIMOD:0 (unimod root node) only once
MAY supply a *child* term of MS:1001471 (peptide modification details) only once
  e.g.: MS:1001460 (unknown modification) 
  e.g.: MS:1001524 (fragment neutral loss) 
  e.g.: MS:1001525 (precursor neutral loss) 
  e.g.: MS:1001972 (PTM scoring algorithm version) 
  e.g.: MS:1002028 (nucleic acid base modification) 
  e.g.: MS:1002029 (original nucleic acid sequence) 
  e.g.: MS:1002030 (modified nucleic acid sequence) 
MUST supply term MS:1001460 (unknown modification) only once
MAY supply a *child* term of XLMOD:00002 (cross-linker related PTM) only once
MAY supply term MS:1002504 (modification index) only once
MAY supply a *child* term of XLMOD:00004 (cross-linker) only once
MAY supply a *child* term of MOD:00000 (protein modification) only once







Example cvParams:

<cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"/>
<cvParam cvRef="PSI-MS" accession="MS:1002504" name="modification index" value="0"/>
<cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/>










Element <SearchType>






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





Type:
ParamType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam11A single entry from an ontology or a controlled vocabulary.


userParam11A single user-defined parameter.








Example Context:

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







cvParam Mapping Rules:

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/SearchType
MUST supply term MS:1001083 (ms-ms search) only once
MUST supply term MS:1001081 (pmf search) only once
MAY supply term MS:1001010 (de novo search) only once
MAY supply term MS:1001031 (spectral library search) only once
MUST supply term MS:1001584 (combined pmf + ms-ms search) only once
MUST supply term MS:1001082 (tag search) only once







Example cvParams:

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










Element <Seq>






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





Type:
sequence





Attributes:
none






Subelements:
none






Example Context:










Element <SequenceCollection>






Definition:
The collection of sequences (DBSequence or Peptide) identified and their relationship between each other (PeptideEvidence) to be referenced elsewhere in the results. 





Type:
SequenceCollectionType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


DBSequence0unboundedA database sequence from the specified SearchDatabase (nucleic acid or amino acid). If the sequence is nucleic acid, the source nucleic acid sequence
should be given in the seq attribute rather than a translated sequence.	


Peptide0unboundedOne (poly)peptide (a sequence with modifications). The combination of Peptide sequence and modifications MUST be unique in the file.


PeptideEvidence0unboundedPeptideEvidence links a specific Peptide element to a specific position in a DBSequence. There MUST only be one PeptideEvidence item per Peptide-to-DBSequence-position. 








Graphical Context:






Example Context:

  <SequenceCollection>
    <DBSequence id="P27348" accession="P27348" searchDatabase_ref="SearchDB_1" >
      <cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="1433T_HUMAN 14-3-3 protein theta OS=Homo sapiens GN=YWHAQ PE=1 SV=1"/>
    </DBSequence>
    <DBSequence id="P27348_REVERSED" accession="P27348_REVERSED" searchDatabase_ref="SearchDB_1" >
      <cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="1433T_HUMAN 14-3-3 protein theta OS=Homo sapiens GN=YWHAQ PE=1 SV=1-REVERSED"/>
    </DBSequence>
  ...
</SequenceCollection>










Element <SiteRegexp>






Definition:
Regular expression for specifying the enzyme cleavage site.





Type:
xsd:string





Attributes:
none






Subelements:
none






Example Context:










Element <SoftwareName>






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





Type:
ParamType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam11A single entry from an ontology or a controlled vocabulary.


userParam11A single user-defined parameter.








Example Context:

      <SoftwareName>
        <cvParam cvRef="PSI-MS" accession="MS:1002458" name="PeptideShaker"/>
      </SoftwareName>







cvParam Mapping Rules:

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







Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1002458" name="PeptideShaker"/>










Element <SourceFile>






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





Type:
SourceFileType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequiredAn 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:anyURIrequiredThe location of the data file.


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








Subelements:



Subelement NameminOccursmaxOccursDefinition


ExternalFormatDocumentation01A 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.


FileFormat11The format of the ExternalData file, for example "tiff" for image files. 


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.


userParam0unboundedA single user-defined parameter.








Example Context:

      <SourceFile location="C:\Users\hba041\My_Git_Applications\peptide-shaker.wiki\data\2016_04_05\.PeptideShaker_unzip_temp\searchgui_out_PeptideShaker_temp\qExactive01819.t.xml" id="SourceFile_2">
        <FileFormat>
          <cvParam cvRef="PSI-MS" accession="MS:1001401" name="X!Tandem xml format"/>
        </FileFormat>
      </SourceFile>







cvParam Mapping Rules:

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










Element <SpecificityRules>






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





Type:
SpecificityRulesType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam1unboundedA single entry from an ontology or a controlled vocabulary.








Example Context:

          <SpecificityRules>
            <cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"/>
          </SpecificityRules>







cvParam Mapping Rules:

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ModificationParams/SearchModification/SpecificityRules
MUST supply a *child* term of MS:1001056 (modification specificity rule) only once
  e.g.: MS:1001189 (modification specificity peptide N-term) 
  e.g.: MS:1001190 (modification specificity peptide C-term) 
  e.g.: MS:1001875 (modification motif) 
  e.g.: MS:1001876 (modification probability) 
  e.g.: MS:1002057 (modification specificity protein N-term) 
  e.g.: MS:1002058 (modification specificity protein C-term) 







Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"/>
<cvParam cvRef="UNIMOD" accession="UNIMOD:1" name="Acetyl"/>
<cvParam cvRef="PSI-MS" accession="MS:1002504" name="modification index" value="2"/>
<cvParam cvRef="PSI-MS" accession="MS:1001189" name="modification specificity peptide N-term"/>
<cvParam cvRef="UNIMOD" accession="UNIMOD:27" name="Glu->pyro-Glu"/>
<cvParam cvRef="UNIMOD" accession="UNIMOD:28" name="Gln->pyro-Glu"/>
<cvParam cvRef="UNIMOD" accession="UNIMOD:385" name="Ammonia-loss"/>










Element <SpectraData>






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





Type:
SpectraDataType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequiredAn 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:anyURIrequiredThe location of the data file.


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








Subelements:



Subelement NameminOccursmaxOccursDefinition


ExternalFormatDocumentation01A 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.


FileFormat11The format of the ExternalData file, for example "tiff" for image files. 


SpectrumIDFormat11The format of the spectrum identifier within the source file








Example Context:

      <SpectraData location="C:\Users\hba041\My_Git_Applications\peptide-shaker.wiki\data\2016_04_05\qExactive01819.mgf" id="qExactive01819.mgf" name="qExactive01819.mgf">
        <FileFormat>
          <cvParam cvRef="PSI-MS" accession="MS:1001062" name="Mascot MGF format"/>
        </FileFormat>
        <SpectrumIDFormat>
          <cvParam cvRef="PSI-MS" accession="MS:1000774" name="multiple peak list nativeID format"/>
        </SpectrumIDFormat>
  ...
</SpectraData>










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:
SpectrumIdentificationType





Attributes:



Attribute NameData TypeUseDefinition


activityDatexsd:dateTimeoptionalWhen the protocol was applied.


idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance. 


spectrumIdentificationList_refxsd:stringrequiredA reference to the SpectrumIdentificationList produced by this analysis in the DataCollection section. 


spectrumIdentificationProtocol_refxsd:stringrequiredA reference to the search protocol used for this SpectrumIdentification. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


InputSpectra1unboundedOne of the spectra data sets used.


SearchDatabaseRef1unboundedOne of the search databases used.








Example Context:

    <SpectrumIdentification spectrumIdentificationList_ref="SIL_1" spectrumIdentificationProtocol_ref="SearchProtocol_1" id="SpecIdent_1">
      <InputSpectra spectraData_ref="qExactive01819.mgf"/>
      <SearchDatabaseRef searchDatabase_ref="SearchDB_1"/>
    </SpectrumIdentification>










Element <SpectrumIdentificationItem>






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





Type:
SpectrumIdentificationItemType





Attributes:



Attribute NameData TypeUseDefinition


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


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


chargeStatexsd:intrequiredThe charge state of the identified peptide.


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


idxsd:stringrequiredAn 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.		


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


namexsd:stringoptionalThe 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. 


peptide_refxsd:stringrequiredA reference to the identified (poly)peptide sequence in the Peptide element. 


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. 


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








Subelements:



Subelement NameminOccursmaxOccursDefinition


PeptideEvidenceRef0unboundedReference to the PeptideEvidence element identified. If a specific sequence can be assigned to multiple proteins and or positions in a protein all possible PeptideEvidence elements should be referenced here.


Fragmentation01The product ions identified in this result.


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.


userParam0unboundedA single user-defined parameter.








Graphical Context:






Example Context:

          <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="TSRPENAIIYNNNEDFQVGQAK" calculatedMassToCharge="1254.6093159770621" experimentalMassToCharge="1254.610100434848" chargeState="2" id="SII_810_1">
            <PeptideEvidenceRef peptideEvidence_ref="PepEv_5683"/>
            <Fragmentation>
              <IonType charge="1" index="3 5 6 7 8 9 10 11 12 14 15 17 18">
                <FragmentArray measure_ref="Measure_MZ" values="345.1880493 571.2817383 685.3267212 756.3624878 869.4454956 982.5328369 1145.584717 1259.631592 1373.695923 1616.779907 1731.780884 2006.913086 2105.992188"/>
                <FragmentArray measure_ref="Measure_Int" values="8469.0126953125 3977.8522949219 1782.3315429688 5673.8774414063 21878.765625 22688.71484375 8875.0830078125 6355.658203125 2438.638671875 5115.9819335938 14359.912109375 6059.7827148438 5840.6997070313"/>
                <FragmentArray measure_ref="Measure_Error" values="-4.50630921022821E-5 -0.001712999912115265 3.4245894778450747E-4 -0.0010047257620726668 -0.002060902892139893 0.0012164199779363116 -0.010232012572259919 -0.006284453712169125 0.01511910514796 0.013582576038061234 -0.012383447791989965 -0.007172866062091998 0.00351522094797474"/>
  ...
</SpectrumIdentificationItem>







cvParam Mapping Rules:

Path /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult/SpectrumIdentificationItem
MUST supply a *child* term of MS:1002549 (PTM localization distinct peptide-level statistic) one or more times
  e.g.: MS:1002550 (peptide:phosphoRS score) 
  e.g.: MS:1002551 (peptide:Ascore) 
  e.g.: MS:1002552 (peptide:H-Score) 
  e.g.: MS:1002553 (peptide:D-Score) 
  e.g.: MS:1002554 (peptide:MD-Score) 
MUST supply a *child* term of MS:1002538 (PTM localization confidence metric) one or more times
  e.g.: MS:1002539 (PeptideShaker PTM confidence type) 
MUST supply a *child* term of MS:1001968 (PTM localization PSM-level statistic) one or more times
  e.g.: MS:1001969 (phosphoRS score) 
  e.g.: MS:1001970 (phosphoRS sequence probability) 
  e.g.: MS:1001971 (phosphoRS site probability) 
  e.g.: MS:1001974 (DeBunker:score) 
  e.g.: MS:1001978 (MSQuant:PTM-score) 
  e.g.: MS:1001979 (MaxQuant:PTM Score) 
  e.g.: MS:1001980 (MaxQuant:Phospho (STY) Probabilities) 
  e.g.: MS:1001981 (MaxQuant:Phospho (STY) Score Diffs) 
  e.g.: MS:1001982 (MaxQuant:P-site localization probability) 
  e.g.: MS:1001983 (MaxQuant:PTM Delta Score) 
  et al.
MUST supply a *child* term of MS:1002555 (PTM localization score threshold) one or more times
  e.g.: MS:1002556 (Ascore threshold) 
  e.g.: MS:1002557 (D-Score threshold) 
  e.g.: MS:1002558 (MD-Score threshold) 
  e.g.: MS:1002559 (H-Score threshold) 
  e.g.: MS:1002560 (DeBunker:score threshold) 
  e.g.: MS:1002561 (Mascot:PTM site assignment confidence threshold) 
  e.g.: MS:1002562 (MSQuant:PTM-score threshold) 
  e.g.: MS:1002563 (MaxQuant:PTM Score threshold) 
  e.g.: MS:1002564 (MaxQuant:P-site localization probability threshold) 
  e.g.: MS:1002565 (MaxQuant:PTM Delta Score threshold) 
  et al.
MAY supply a *child* term of MS:1002484 (peptide-level statistical threshold) one or more times
  e.g.: MS:1001448 (pep:FDR threshold) 
  e.g.: MS:1001868 (distinct peptide-level q-value) 
MUST supply a *child* term of MS:1001143 (PSM-level search engine specific statistic) one or more times
  e.g.: MS:1001154 (SEQUEST:probability) 
  e.g.: MS:1001155 (SEQUEST:xcorr) 
  e.g.: MS:1001156 (SEQUEST:deltacn) 
  e.g.: MS:1001160 (SEQUEST:sf) 
  e.g.: MS:1001161 (SEQUEST:matched ions) 
  e.g.: MS:1001162 (SEQUEST:total ions) 
  e.g.: MS:1001171 (Mascot:score) 
  e.g.: MS:1001172 (Mascot:expectation value) 
  e.g.: MS:1001173 (Mascot:matched ions) 
  e.g.: MS:1001174 (Mascot:total ions) 
  et al.
MAY supply a *child* term of MS:1001405 (spectrum identification result details) one or more times
  e.g.: MS:1000016 (scan start time) 
  e.g.: MS:1000796 (spectrum title) 
  e.g.: MS:1000797 (peak list scans) 
  e.g.: MS:1000798 (peak list raw scans) 
  e.g.: MS:1000903 (product ion series ordinal) 
  e.g.: MS:1000904 (product ion m/z delta) 
  e.g.: MS:1000926 (product interpretation rank) 
  e.g.: MS:1001030 (number of peptide seqs compared to each spectrum) 
  e.g.: MS:1001035 (date / time search performed) 
  e.g.: MS:1001036 (search time taken) 
  et al.







Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1002466" name="PeptideShaker PSM score" value="4.77"/>
<cvParam cvRef="PSI-MS" accession="MS:1002467" name="PeptideShaker PSM confidence" value="57.81"/>
<cvParam cvRef="PSI-MS" accession="MS:1002469" name="PeptideShaker peptide confidence" value="50.0"/>
<cvParam cvRef="PSI-MS" accession="MS:1002468" name="PeptideShaker peptide score" value="3.748162098248999"/>
<cvParam cvRef="PSI-MS" accession="MS:1002500" name="peptide passes threshold" value="false"/>
<cvParam cvRef="PSI-MS" accession="MS:1002520" name="peptide group ID" value="EIPAAEPV"/>
<cvParam cvRef="PSI-MS" accession="MS:1001330" name="X!Tandem:expect" value="0.51"/>
<cvParam cvRef="PSI-MS" accession="MS:1001117" name="theoretical mass" value="824.4279840168801" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton"/>
<cvParam cvRef="PSI-MS" accession="MS:1002540" name="PeptideShaker PSM confidence type" value="Doubtful"/>
<cvParam cvRef="PSI-MS" accession="MS:1000796" name="spectrum title" value="qExactive01819.4140.4140.2 File:"qExactive01819.raw", NativeID:"controllerType=0 controllerNumber=1 scan=4140""/>
<cvParam cvRef="PSI-MS" accession="MS:1000894" name="retention time" value="1162.20342" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>










Element <SpectrumIdentificationItemRef>






Definition:
Reference(s) to the SpectrumIdentificationItem element(s) that support the given PeptideEvidence element. Using these references it is possible to indicate which spectra were actually accepted as evidence for this peptide identification in the given protein.





Type:
SpectrumIdentificationItemRefType





Attributes:



Attribute NameData TypeUseDefinition


spectrumIdentificationItem_refxsd:stringrequiredA reference to the SpectrumIdentificationItem element(s).








Subelements:
none






Example Context:

              <SpectrumIdentificationItemRef spectrumIdentificationItem_ref="SII_5365_1"/>










Element <SpectrumIdentificationList>






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





Type:
SpectrumIdentificationListType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance. 


numSequencesSearchedxsd:longoptionalThe number of database sequences searched against. 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 


SpectrumIdentificationResult1unboundedAll 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.


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.


userParam0unboundedA single user-defined parameter.








Graphical Context:






Example Context:

      <SpectrumIdentificationList id="SIL_1">
        <FragmentationTable>
          <Measure id="Measure_MZ">
            <cvParam cvRef="PSI-MS" accession="MS:1001225" name="product ion m/z" unitCvRef="PSI-MS" unitAccession="MS:1000040" unitName="m/z" />
          </Measure>
          <Measure id="Measure_Int">
            <cvParam cvRef="PSI-MS" accession="MS:1001226" name="product ion intensity" unitCvRef="PSI-MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
  ...
</SpectrumIdentificationList>







cvParam Mapping Rules:

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










Element <SpectrumIdentificationProtocol>






Definition:
The parameters and settings of a SpectrumIdentification analysis.





Type:
SpectrumIdentificationProtocolType





Attributes:



Attribute NameData TypeUseDefinition


analysisSoftware_refxsd:stringrequiredThe search algorithm used, given as a reference to the SoftwareCollection section. 


idxsd:stringrequiredAn 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:stringoptionalThe 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. 


ModificationParams01The specification of static/variable modifications (e.g. Oxidation of Methionine) that are to be considered in the spectra search. 


Enzymes01The list of enzymes used in experiment


MassTable0unboundedThe masses of residues used in the search.


FragmentTolerance01The tolerance of the search given as a plus and minus value with units. 


ParentTolerance01The tolerance of the search given as a plus and minus value with units. 


Threshold11The threshold(s) applied to determine that a result is significant. If multiple terms are used it is assumed that all conditions are satisfied by the passing results.


DatabaseFilters01The specification of filters applied to the database searched.
			


DatabaseTranslation01A specification of how a nucleic acid sequence database was translated for searching. 








Graphical Context:






Example Context:

    <SpectrumIdentificationProtocol analysisSoftware_ref="ID_software" id="SearchProtocol_1">
      <SearchType>
        <cvParam cvRef="PSI-MS" accession="MS:1001083" name="ms-ms search"/>
      </SearchType>
      <AdditionalSearchParams>
        <cvParam cvRef="PSI-MS" accession="MS:1001211" name="parent mass type mono"/>
        <cvParam cvRef="PSI-MS" accession="MS:1001256" name="fragment mass type mono"/>
  ...
</SpectrumIdentificationProtocol>










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:
SpectrumIdentificationResultType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance. 


spectraData_refxsd:stringrequiredA reference to a spectra data set (e.g. a spectra file).


spectrumIDxsd:stringrequiredThe 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


SpectrumIdentificationItem1unboundedAn identification of a single (poly)peptide, resulting from querying an input spectra, along with the set of confidence values for that identification.
PeptideEvidence elements should be given for all mappings of the corresponding Peptide sequence within protein sequences. 


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.


userParam0unboundedA single user-defined parameter.








Example Context:

        <SpectrumIdentificationResult spectraData_ref="qExactive01819.mgf" spectrumID="index=4012" id="SIR_810">
          <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="TSRPENAIIYNNNEDFQVGQAK" calculatedMassToCharge="1254.6093159770621" experimentalMassToCharge="1254.610100434848" chargeState="2" id="SII_810_1">
            <PeptideEvidenceRef peptideEvidence_ref="PepEv_5683"/>
            <Fragmentation>
              <IonType charge="1" index="3 5 6 7 8 9 10 11 12 14 15 17 18">
                <FragmentArray measure_ref="Measure_MZ" values="345.1880493 571.2817383 685.3267212 756.3624878 869.4454956 982.5328369 1145.584717 1259.631592 1373.695923 1616.779907 1731.780884 2006.913086 2105.992188"/>
                <FragmentArray measure_ref="Measure_Int" values="8469.0126953125 3977.8522949219 1782.3315429688 5673.8774414063 21878.765625 22688.71484375 8875.0830078125 6355.658203125 2438.638671875 5115.9819335938 14359.912109375 6059.7827148438 5840.6997070313"/>
  ...
</SpectrumIdentificationResult>







cvParam Mapping Rules:

Path /MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/SpectrumIdentificationResult
MAY supply term MS:1000894 (retention time) only once
MAY supply a *child* term of MS:1001405 (spectrum identification result details) one or more times
  e.g.: MS:1000016 (scan start time) 
  e.g.: MS:1000796 (spectrum title) 
  e.g.: MS:1000797 (peak list scans) 
  e.g.: MS:1000798 (peak list raw scans) 
  e.g.: MS:1000903 (product ion series ordinal) 
  e.g.: MS:1000904 (product ion m/z delta) 
  e.g.: MS:1000926 (product interpretation rank) 
  e.g.: MS:1001030 (number of peptide seqs compared to each spectrum) 
  e.g.: MS:1001035 (date / time search performed) 
  e.g.: MS:1001036 (search time taken) 
  et al.










Element <SpectrumIDFormat>






Definition:
The format of the spectrum identifier within the source file





Type:
SpectrumIDFormatType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam11A single entry from an ontology or a controlled vocabulary.








Example Context:

        <SpectrumIDFormat>
          <cvParam cvRef="PSI-MS" accession="MS:1000774" name="multiple peak list nativeID format"/>
        </SpectrumIDFormat>







cvParam Mapping Rules:

Path /MzIdentML/DataCollection/Inputs/SpectraData/SpectrumIDFormat
MUST supply a *child* term of MS:1000767 (native spectrum identifier format) only once
  e.g.: MS:1000768 (Thermo nativeID format) 
  e.g.: MS:1000769 (Waters nativeID format) 
  e.g.: MS:1000770 (WIFF nativeID format) 
  e.g.: MS:1000771 (Bruker/Agilent YEP nativeID format) 
  e.g.: MS:1000772 (Bruker BAF nativeID format) 
  e.g.: MS:1000773 (Bruker FID nativeID format) 
  e.g.: MS:1000774 (multiple peak list nativeID format) 
  e.g.: MS:1000775 (single peak list nativeID format) 
  e.g.: MS:1000776 (scan number only nativeID format) 
  e.g.: MS:1000777 (spectrum identifier nativeID format) 
  et al.
MUST supply a *child* term of MS:1001529 (spectra data details) only once
  e.g.: MS:1001530 (mzML unique identifier) 
  e.g.: MS:1001531 (spectrum from ProteinScape database nativeID format) 
  e.g.: MS:1001532 (spectrum from database string nativeID format) 







Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1000774" name="multiple peak list nativeID format"/>










Element <SubSample>






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





Type:
SubSampleType





Attributes:



Attribute NameData TypeUseDefinition


sample_refxsd:stringrequiredA reference to the child sample.








Subelements:
none






Example Context:










Element <SubstitutionModification>






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





Type:
SubstitutionModificationType





Attributes:



Attribute NameData TypeUseDefinition


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


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


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


originalResiduexsd:string with restriction
[ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}
requiredThe original residue before replacement.


replacementResiduexsd:string with restriction
[ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}
requiredThe residue that replaced the originalResidue.








Subelements:
none






Example Context:










Element <Threshold>






Definition:
Depending on context:

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

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






Type:
ParamListType





Attributes:
none






Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam1unboundedA single entry from an ontology or a controlled vocabulary.


userParam1unboundedA single user-defined parameter.








Example Context:

      <Threshold>
        <cvParam cvRef="PSI-MS" accession="MS:1001364" name="distinct peptide-level global FDR" value="1.0"/>
        <cvParam cvRef="PSI-MS" accession="MS:1002350" name="PSM-level global FDR" value="1.0"/>
        <cvParam cvRef="PSI-MS" accession="MS:1002567" name="phosphoRS score threshold" value="95.0"/>
        <cvParam cvRef="PSI-MS" accession="MS:1002557" name="D-Score threshold" value="95.0"/>
      </Threshold>







cvParam Mapping Rules:

Path /MzIdentML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/Threshold
MUST supply a *child* term of MS:1002703 (peptide sequence-level result list statistic) one or more times
  e.g.: MS:1001364 (peptide sequence-level global FDR) 
  e.g.: MS:1002462 (peptide sequence-level global FNR) 
  e.g.: MS:1002463 (peptide sequence-level global confidence) 
MAY supply a *child* term of MS:1001302 (search engine specific input parameter) one or more times
  e.g.: MS:1001005 (SEQUEST:CleavesAt) WARNING: Term has no definition!
  e.g.: MS:1001007 (SEQUEST:OutputLines) 
  e.g.: MS:1001009 (SEQUEST:DescriptionLines) 
  e.g.: MS:1001026 (SEQUEST:NormalizeXCorrValues) WARNING: Term has no definition!
  e.g.: MS:1001028 (SEQUEST:SequenceHeaderFilter) 
  e.g.: MS:1001032 (SEQUEST:SequencePartialFilter) WARNING: Term has no definition!
  e.g.: MS:1001037 (SEQUEST:ShowFragmentIons) 
  e.g.: MS:1001038 (SEQUEST:Consensus) 
  e.g.: MS:1001042 (SEQUEST:LimitTo) 
  e.g.: MS:1001046 (SEQUEST:sort by dCn) 
  et al.
MAY supply a *child* term of MS:1002347 (PSM-level identification statistic) one or more times
  e.g.: MS:1001154 (SEQUEST:probability) 
  e.g.: MS:1001155 (SEQUEST:xcorr) 
  e.g.: MS:1001156 (SEQUEST:deltacn) 
  e.g.: MS:1001160 (SEQUEST:sf) 
  e.g.: MS:1001161 (SEQUEST:matched ions) 
  e.g.: MS:1001162 (SEQUEST:total ions) 
  e.g.: MS:1001171 (Mascot:score) 
  e.g.: MS:1001172 (Mascot:expectation value) 
  e.g.: MS:1001173 (Mascot:matched ions) 
  e.g.: MS:1001174 (Mascot:total ions) 
  et al.
MUST supply a *child* term of MS:1002363 (search engine specific score for proteins) one or more times
  e.g.: MS:1001157 (SEQUEST:sp) 
  e.g.: MS:1001158 (SEQUEST:Uniq) WARNING: Term has no definition!
  e.g.: MS:1001164 (Paragon:unused protscore) 
  e.g.: MS:1001165 (Paragon:total protscore) 
  e.g.: MS:1001166 (Paragon:score) 
  e.g.: MS:1001167 (Paragon:confidence) 
  e.g.: MS:1001168 (Paragon:expression error factor) 
  e.g.: MS:1001169 (Paragon:expression change p-value) 
  e.g.: MS:1001170 (Paragon:contrib) 
  e.g.: MS:1001372 (SEQUEST:Sequences) WARNING: Term has no definition!
  et al.
MUST supply a *child* term of MS:1002573 (spectrum identification statistical threshold) one or more times
  e.g.: MS:1001448 (pep:FDR threshold) 
  e.g.: MS:1001868 (distinct peptide-level q-value) 
  e.g.: MS:1002260 (PSM:FDR threshold) 
MAY supply a *child* term of MS:1002358 (search engine specific peptide sequence-level identification statistic) one or more times
  e.g.: MS:1001396 (Phenyx:PepPvalue) 
  e.g.: MS:1002360 (distinct peptide-level FDRScore) 
  e.g.: MS:1002361 (distinct peptide-level combined FDRScore) 
  e.g.: MS:1002468 (PeptideShaker peptide score) 
  e.g.: MS:1002499 (peptide level score) 
  e.g.: MS:1002541 (PeptideShaker peptide confidence type) 
MUST supply a *child* term of MS:1002701 (PSM-level result list statistic) one or more times
  e.g.: MS:1002350 (PSM-level global FDR) 
  e.g.: MS:1002464 (PSM-level global FNR) 
  e.g.: MS:1002465 (PSM-level global confidence) 
  e.g.: MS:1002501 (no PSM threshold) 
MAY supply a *child* term of MS:1002555 (PTM localization score threshold) one or more times
  e.g.: MS:1002556 (Ascore threshold) 
  e.g.: MS:1002557 (D-Score threshold) 
  e.g.: MS:1002558 (MD-Score threshold) 
  e.g.: MS:1002559 (H-Score threshold) 
  e.g.: MS:1002560 (DeBunker:score threshold) 
  e.g.: MS:1002561 (Mascot:PTM site assignment confidence threshold) 
  e.g.: MS:1002562 (MSQuant:PTM-score threshold) 
  e.g.: MS:1002563 (MaxQuant:PTM Score threshold) 
  e.g.: MS:1002564 (MaxQuant:P-site localization probability threshold) 
  e.g.: MS:1002565 (MaxQuant:PTM Delta Score threshold) 
  et al.
MUST supply a *child* term of MS:1001153 (search engine specific score) one or more times
  e.g.: MS:1001147 (protein ambiguity group result details) WARNING: Term has no definition!
  e.g.: MS:1001155 (SEQUEST:xcorr) 
  e.g.: MS:1001159 (SEQUEST:expectation value) 
  e.g.: MS:1001163 (SEQUEST:consensus score) 
  e.g.: MS:1001874 (FDRScore) 
  e.g.: MS:1002052 (MS-GF:SpecEValue) 
  e.g.: MS:1002053 (MS-GF:EValue) 
  e.g.: MS:1002125 (combined FDRScore) 
  e.g.: MS:1002252 (Comet:xcorr) 
  e.g.: MS:1002257 (Comet:expectation value) 
  et al.
MAY supply a *child* term of MS:1001060 (quality estimation method details) one or more times
  e.g.: MS:1001058 (quality estimation by manual validation) 
  e.g.: MS:1001194 (quality estimation with decoy database) 
  e.g.: MS:1001447 (prot:FDR threshold) 
  e.g.: MS:1001448 (pep:FDR threshold) 
  e.g.: MS:1001454 (quality estimation with implicite decoy sequences) 
  e.g.: MS:1001494 (no threshold) 
  e.g.: MS:1001574 (report only spectra assigned to identified proteins) 
  e.g.: MS:1001868 (distinct peptide-level q-value) 
  e.g.: MS:1002260 (PSM:FDR threshold) 
  e.g.: MS:1002486 (protein group-level statistical threshold) 
MUST supply term MS:1001494 (no threshold) one or more times
MAY supply a *child* term of MS:1002484 (peptide-level statistical threshold) one or more times
  e.g.: MS:1001448 (pep:FDR threshold) 
  e.g.: MS:1001868 (distinct peptide-level q-value) 



Path /MzIdentML/AnalysisProtocolCollection/ProteinDetectionProtocol/Threshold
MUST supply a *child* term of MS:1001302 (search engine specific input parameter) one or more times
  e.g.: MS:1001005 (SEQUEST:CleavesAt) WARNING: Term has no definition!
  e.g.: MS:1001007 (SEQUEST:OutputLines) 
  e.g.: MS:1001009 (SEQUEST:DescriptionLines) 
  e.g.: MS:1001026 (SEQUEST:NormalizeXCorrValues) WARNING: Term has no definition!
  e.g.: MS:1001028 (SEQUEST:SequenceHeaderFilter) 
  e.g.: MS:1001032 (SEQUEST:SequencePartialFilter) WARNING: Term has no definition!
  e.g.: MS:1001037 (SEQUEST:ShowFragmentIons) 
  e.g.: MS:1001038 (SEQUEST:Consensus) 
  e.g.: MS:1001042 (SEQUEST:LimitTo) 
  e.g.: MS:1001046 (SEQUEST:sort by dCn) 
  et al.
MAY supply a *child* term of MS:1002706 (protein group-level result list statistic) one or more times
  e.g.: MS:1002369 (protein group-level global FDR) 
  e.g.: MS:1002460 (protein group-level global FNR) 
MUST supply a *child* term of MS:1002572 (protein detection statistical threshold) one or more times
  e.g.: MS:1001447 (prot:FDR threshold) 
  e.g.: MS:1002486 (protein group-level statistical threshold) 
MAY supply a *child* term of MS:1002701 (PSM-level result list statistic) one or more times
  e.g.: MS:1002350 (PSM-level global FDR) 
  e.g.: MS:1002464 (PSM-level global FNR) 
  e.g.: MS:1002465 (PSM-level global confidence) 
  e.g.: MS:1002501 (no PSM threshold) 
MUST supply a *child* term of MS:1001153 (search engine specific score) one or more times
  e.g.: MS:1001147 (protein ambiguity group result details) WARNING: Term has no definition!
  e.g.: MS:1001155 (SEQUEST:xcorr) 
  e.g.: MS:1001159 (SEQUEST:expectation value) 
  e.g.: MS:1001163 (SEQUEST:consensus score) 
  e.g.: MS:1001874 (FDRScore) 
  e.g.: MS:1002052 (MS-GF:SpecEValue) 
  e.g.: MS:1002053 (MS-GF:EValue) 
  e.g.: MS:1002125 (combined FDRScore) 
  e.g.: MS:1002252 (Comet:xcorr) 
  e.g.: MS:1002257 (Comet:expectation value) 
  et al.
MAY supply a *child* term of MS:1002555 (PTM localization score threshold) one or more times
  e.g.: MS:1002556 (Ascore threshold) 
  e.g.: MS:1002557 (D-Score threshold) 
  e.g.: MS:1002558 (MD-Score threshold) 
  e.g.: MS:1002559 (H-Score threshold) 
  e.g.: MS:1002560 (DeBunker:score threshold) 
  e.g.: MS:1002561 (Mascot:PTM site assignment confidence threshold) 
  e.g.: MS:1002562 (MSQuant:PTM-score threshold) 
  e.g.: MS:1002563 (MaxQuant:PTM Score threshold) 
  e.g.: MS:1002564 (MaxQuant:P-site localization probability threshold) 
  e.g.: MS:1002565 (MaxQuant:PTM Delta Score threshold) 
  et al.
MAY supply term MS:1001494 (no threshold) only once
MAY supply a *child* term of MS:1002485 (protein-level statistical threshold) one or more times
  e.g.: MS:1001447 (prot:FDR threshold) 







Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1001364" name="distinct peptide-level global FDR" value="1.0"/>
<cvParam cvRef="PSI-MS" accession="MS:1002350" name="PSM-level global FDR" value="1.0"/>
<cvParam cvRef="PSI-MS" accession="MS:1002567" name="phosphoRS score threshold" value="95.0"/>
<cvParam cvRef="PSI-MS" accession="MS:1002557" name="D-Score threshold" value="95.0"/>
<cvParam cvRef="PSI-MS" accession="MS:1002369" name="protein group-level global FDR" value="0.01"/>










Element <TranslationTable>






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





Type:
TranslationTableType





Attributes:



Attribute NameData TypeUseDefinition


idxsd:stringrequiredAn 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:stringoptionalThe potentially ambiguous common identifier, such as a human-readable name for the instance. 








Subelements:



Subelement NameminOccursmaxOccursDefinition


cvParam0unboundedA single entry from an ontology or a controlled vocabulary.








Example Context:







cvParam Mapping Rules:

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










Element <userParam>






Definition:
In case more information about the ions annotation has to be conveyed, that has no fit in FragmentArray. Note: It is suggested that the value attribute takes the form of a list of the same size as FragmentArray values. However, there is no formal encoding and it cannot be expeceted that other software will process or impart that information properly.





Type:
UserParamType





Attributes:



Attribute NameData TypeUseDefinition


namexsd:stringrequiredThe name of the parameter.


typexsd:stringoptionalThe datatype of the parameter, where appropriate (e.g.: xsd:float).


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


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


unitNamexsd:stringoptionalThe name of the unit.


valuexsd:stringoptionalThe user-entered value of the parameter.








Subelements:
none






Example Context:

          <userParam name="uniprot-human-reviewed-trypsin-april-2016_concatenated_target_decoy.fasta"/>