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 Name	Data Type	Use	Definition
creationDate	xsd:dateTime	optional	The date on which the file was produced.
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.
version	versionRegex	required	The 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 Name	minOccurs	maxOccurs	Definition
cvList	1	1	The list of controlled vocabularies used in the file.
AnalysisSoftwareList	0	1	The software packages used to perform the analyses.
Provider	0	1	The Provider of the mzIdentML record in terms of the contact and software.
AuditCollection	0	1	The complete set of Contacts (people and organisations) for this file.
AnalysisSampleCollection	0	1	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.
SequenceCollection	0	1	The collection of sequences (DBSequence or Peptide) identified and their relationship between each other (PeptideEvidence) to be referenced elsewhere in the results.
AnalysisCollection	1	1	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).
AnalysisProtocolCollection	1	1	The collection of protocols which include the parameters and settings of the performed analyses.
DataCollection	1	1	The collection of input and output data sets of the analyses.
BibliographicReference	0	unbounded	Any bibliographic references associated with the file

Graphical Context:

Example Context:

<MzIdentML id="1234" 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 Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	1	unbounded	A single user-defined parameter.

Example Context:

<AdditionalSearchParams>
  <cvParam cvRef="PSI-MS" accession="MS:1001211" name="parent mass type mono"></cvParam>
  <cvParam cvRef="PSI-MS" accession="MS:1001256" name="fragment mass type mono"></cvParam>
  <cvParam cvRef="PSI-MS" accession="MS:1002490" name="peptide-level scoring"></cvParam>
  <cvParam cvRef="PSI-MS" accession="MS:1002496" name="group PSMs by sequence"></cvParam>
</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>
<cvParam cvRef="PSI-MS" accession="MS:1001256" name="fragment mass type mono"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002490" name="peptide-level scoring"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002496" name="group PSMs by sequence"></cvParam>

Element <Affiliation>

Definition:

The organization a person belongs to.

Type:

AffiliationType

Attributes:

Attribute Name	Data Type	Use	Definition
organization_ref	xsd:string	required	A reference to the organization this contact belongs to.

Subelements:

none

Example Context:

<Affiliation organization_ref="ORG_DOC_OWNER"></Affiliation>

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 Name	Data Type	Use	Definition
code	chars	required	The single letter code of the ambiguous residue e.g. X.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	1	unbounded	A 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)

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 Name	minOccurs	maxOccurs	Definition
SpectrumIdentification	1	unbounded	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.
ProteinDetection	0	1	An Analysis which assembles a set of peptides (e.g. from a spectra search analysis) to proteins.

Example Context:

<AnalysisCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.2">
  <SpectrumIdentification spectrumIdentificationProtocol_ref="SearchProtocol_1" spectrumIdentificationList_ref="SII_LIST_1" id="SpecIdent_1">
    <InputSpectra spectraData_ref="SD_COMBINED_SE_0"></InputSpectra>
    <SearchDatabaseRef searchDatabase_ref="SearchDB_1"></SearchDatabaseRef>
  </SpectrumIdentification>
</AnalysisCollection>

Element <AnalysisData>

Definition:

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

Type:

AnalysisDataType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
SpectrumIdentificationList	1	unbounded	Represents the set of all search results from SpectrumIdentification.
ProteinDetectionList	0	1	The protein list resulting from a protein detection process.

Example Context:

<AnalysisData>
<SpectrumIdentificationList xmlns="http://psidev.info/psi/pi/mzIdentML/1.2" id="SII_LIST_1">
  <SpectrumIdentificationResult spectrumID="index=6451" spectraData_ref="SD_COMBINED_SE_0" id="SIR_8947">
    <SpectrumIdentificationItem chargeState="2" experimentalMassToCharge="679.817322" calculatedMassToCharge="679.818488" peptide_ref="AVMDDFAAFVEK_##Oxidation(M):3" rank="1" passThreshold="false" id="SIR_8947_SII_1">
      <PeptideEvidenceRef peptideEvidence_ref="AVMDDFAAFVEK_generic|A_ENSP00000401820|p:known_378_389"></PeptideEvidenceRef>
      <PeptideEvidenceRef peptideEvidence_ref="AVMDDFAAFVEK_generic|A_ENSP00000421027|p:putative_420_431"></PeptideEvidenceRef>
      <PeptideEvidenceRef peptideEvidence_ref="AVMDDFAAFVEK_generic|A_ENSP00000483421|p:known_357_368"></PeptideEvidenceRef>
  ...
</AnalysisData>

Element <AnalysisParams>

Definition:

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

Type:

ParamListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	1	unbounded	A 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 Name	minOccurs	maxOccurs	Definition
SpectrumIdentificationProtocol	1	unbounded	The parameters and settings of a SpectrumIdentification analysis.
ProteinDetectionProtocol	0	1	The parameters and settings of a ProteinDetection process.

Example Context:

<AnalysisProtocolCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.2">
  <SpectrumIdentificationProtocol analysisSoftware_ref="ID_software" id="SearchProtocol_1">
    <SearchType>
      <cvParam cvRef="PSI-MS" accession="MS:1001083" name="ms-ms search"></cvParam>
    </SearchType>
    <AdditionalSearchParams>
      <cvParam cvRef="PSI-MS" accession="MS:1001211" name="parent mass type mono"></cvParam>
  ...
</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 Name	minOccurs	maxOccurs	Definition
Sample	1	unbounded	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 Name	Data Type	Use	Definition
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.
uri	xsd:anyURI	optional	URI of the analysis software e.g. manufacturer's website
version	xsd:string	optional	The version of Software used.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
ContactRole	0	1	The Contact that provided the document instance.
SoftwareName	1	1	The name of the analysis software package, sourced from a CV if available.
Customizations	0	1	Any customizations to the software, such as alternative scoring mechanisms implemented, should be documented here as free text.

Example Context:

<AnalysisSoftware id="FalseDiscoveryRateGlobal_2015-02-05 15-38-39" name="FalseDiscoveryRateGlobal_2015-02-05 15-38-39">
  <SoftwareName>
    <cvParam cvRef="PSI-MS" accession="MS:1002237" name="mzidLib"></cvParam>
  </SoftwareName>
</AnalysisSoftware>

Element <AnalysisSoftwareList>

Definition:

The software packages used to perform the analyses.

Type:

AnalysisSoftwareListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
AnalysisSoftware	1	unbounded	The software used for performing the analyses.

Example Context:

<AnalysisSoftwareList xmlns="http://psidev.info/psi/pi/mzIdentML/1.2">
  <AnalysisSoftware version="" id="ID_software" name="OMSSA">
    <SoftwareName>
      <cvParam cvRef="PSI-MS" accession="MS:1001475" name="OMSSA"></cvParam>
    </SoftwareName>
  </AnalysisSoftware>
  <AnalysisSoftware id="Omssa2mzid_2014-12-08 16-58-29" name="Omssa2mzid_2014-12-08 16-58-29">
  ...
</AnalysisSoftwareList>

Element <AuditCollection>

Definition:

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

Type:

AuditCollectionType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Person	1	1	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.
Organization	1	1	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.

Example Context:

<AuditCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.2">
  <Person lastName="secondName" firstName="firstname" id="PERSON_DOC_OWNER">
    <cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="address"></cvParam>
    <Affiliation organization_ref="ORG_DOC_OWNER"></Affiliation>
  </Person>
  <Organization id="ORG_DOC_OWNER" name="myworkplace">
    <cvParam cvRef="PSI-MS" accession="MS:1000586" name="contact name" value="address"></cvParam>
  ...
</AuditCollection>

Element <BibliographicReference>

Definition:

Any bibliographic references associated with the file

Type:

BibliographicReferenceType

Attributes:

Attribute Name	Data Type	Use	Definition
authors	xsd:string	optional	The names of the authors of the reference.
doi	xsd:string	optional	The DOI of the referenced publication.
editor	xsd:string	optional	The editor(s) of the reference.
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
issue	xsd:string	optional	The issue name or number.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.
pages	xsd:string	optional	The page numbers.
publication	xsd:string	optional	The name of the journal, book etc.
publisher	xsd:string	optional	The publisher of the publication.
title	xsd:string	optional	The title of the BibliographicReference.
volume	xsd:string	optional	The volume name or number.
year	xsd:int	optional	The 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 Name	Data Type	Use	Definition
contact_ref	xsd:string	required	When a ContactRole is used, it specifies which Contact the role is associated with.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Role	1	1	The roles (lab equipment sales, contractor, etc.) the Contact fills.

Example Context:

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

Element <cv>

Definition:

A source controlled vocabulary from which cvParams will be obtained.

Type:

cvType

Attributes:

Attribute Name	Data Type	Use	Definition
fullName	xsd:string	required	The full name of the CV.
id	xsd:string	required	The unique identifier of this cv within the document to be referenced by cvParam elements.
uri	xsd:anyURI	required	The URI of the source CV.
version	xsd:string	optional	The 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 Name	minOccurs	maxOccurs	Definition
cv	1	unbounded	A 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 Name	Data Type	Use	Definition
accession	xsd:string	required	The accession or ID number of this CV term in the source CV.
cvRef	xsd:string	required	A reference to the cv element from which this term originates.
name	xsd:string	required	The name of the parameter.
unitAccession	xsd:string	optional	An accession number identifying the unit within the OBO foundry Unit CV.
unitCvRef	xsd:string	optional	If a unit term is referenced, this attribute MUST refer to the CV 'id' attribute defined in the cvList in this file.
unitName	xsd:string	optional	The name of the unit.
value	xsd:string	optional	The user-entered value of the parameter.

Subelements:

none

Example Context:

<cvParam cvRef="PSI-MS" accession="MS:1002520" name="peptide group ID" value="CCPQCCSSGCSQNLCGPLCVTTPYYCTR_##Carbamidomethyl(C):1##Carbamidomethyl(C):2##Carbamidomethyl(C):5##Carbamidomethyl(C):6##Carbamidomethyl(C):10##Carbamidomethyl(C):15##Carbamidomethyl(C):19##Carbamidomethyl(C):26"></cvParam>

Element <DatabaseFilters>

Definition:

The specification of filters applied to the database searched.

Type:

DatabaseFiltersType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Filter	1	unbounded	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.

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 Name	minOccurs	maxOccurs	Definition
cvParam	1	1	A single entry from an ontology or a controlled vocabulary.
userParam	1	1	A single user-defined parameter.

Example Context:

<DatabaseName>
  <userParam name="fawaz_PXD000652_combined_concatenated_target_decoy.fasta"></userParam>
</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 userParams:

<userParam name="fawaz_PXD000652_combined_concatenated_target_decoy.fasta"></userParam>

Element <DatabaseTranslation>

Definition:

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

Type:

DatabaseTranslationType

Attributes:

Attribute Name	Data Type	Use	Definition
frames	listOfAllowedFrames	optional	The frames in which the nucleic acid sequence has been translated as a space separated list

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
TranslationTable	1	unbounded	The 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 Name	minOccurs	maxOccurs	Definition
Inputs	1	1	The inputs to the analyses including the databases searched, the spectral data and the source file converted to mzIdentML.
AnalysisData	1	1	Data sets generated by the analyses, including peptide and protein lists.

Graphical Context:

Example Context:

<DataCollection>
<Inputs xmlns="http://psidev.info/psi/pi/mzIdentML/1.2">
  <SourceFile location="example_files/55merge_omssa.omx" id="SourceFile_1">
    <FileFormat>
      <cvParam cvRef="PSI-MS" accession="MS:1001400" name="OMSSA xml format"></cvParam>
    </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 Name	Data Type	Use	Definition
accession	xsd:string	required	The unique accession of this sequence.
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
length	xsd:int	optional	The length of the sequence as a number of bases or residues.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.
searchDatabase_ref	xsd:string	required	The source database of this sequence.

Subelements:

Subelement Name	maxOccurs	Definition
Seq	1	The actual sequence of amino acids or nucleic acid.
cvParam	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	unbounded	A single user-defined parameter.

Example Context:

<DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000043743_REVERSED|p:genscan" id="dbseq_generic|B_GENSCAN00000043743_REVERSED|p:genscan"></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

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 Name	Data Type	Use	Definition
cTermGain	xsd:string with restriction [A-Za-z0-9 ]+	optional	Element formula gained at CTerm.
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
minDistance	xsd:int	optional	Minimal distance for another cleavage (minimum: 1).
missedCleavages	xsd:int	optional	The number of missed cleavage sites allowed by the search. The attribute MUST be provided if an enzyme has been used.
nTermGain	xsd:string with restriction [A-Za-z0-9 ]+	optional	Element formula gained at NTerm.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.
semiSpecific	xsd:boolean	optional	Set 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 Name	minOccurs	maxOccurs	Definition
SiteRegexp	0	1	Regular expression for specifying the enzyme cleavage site.
EnzymeName	0	1	The name of the enzyme from a CV.

Example Context:

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

Element <EnzymeName>

Definition:

The name of the enzyme from a CV.

Type:

ParamListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	1	unbounded	A single user-defined parameter.

Example Context:

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

Element <Enzymes>

Definition:

The list of enzymes used in experiment

Type:

EnzymesType

Attributes:

Attribute Name	Data Type	Use	Definition
independent	xsd:boolean	optional	If there are multiple enzymes specified, this attribute is set to true if cleavage with different enzymes is performed independently.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Enzyme	1	unbounded	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.

Example Context:

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

Element <Exclude>

Definition:

All sequences fulfilling the specifed criteria are excluded.

Type:

ParamListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	1	unbounded	A 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 Name	minOccurs	maxOccurs	Definition
cvParam	1	1	A single entry from an ontology or a controlled vocabulary.

Example Context:

<FileFormat>
  <cvParam cvRef="PSI-MS" accession="MS:1001062" name="Mascot MGF format"></cvParam>
</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>
<cvParam cvRef="PSI-MS" accession="MS:1001348" name="FASTA format"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1001062" name="Mascot MGF format"></cvParam>

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 Name	minOccurs	maxOccurs	Definition
FilterType	1	1	The type of filter e.g. database taxonomy filter, pi filter, mw filter
Include	0	1	All sequences fulfilling the specifed criteria are included.
Exclude	0	1	All 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 Name	minOccurs	maxOccurs	Definition
cvParam	1	1	A single entry from an ontology or a controlled vocabulary.
userParam	1	1	A 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 Name	Data Type	Use	Definition
measure_ref	xsd:string	required	A reference to the Measure defined in the FragmentationTable
values	listOfFloats	required	The values of this particular measure, corresponding to the index defined in ion type

Subelements:

none

Example Context:

Element <Fragmentation>

Definition:

The product ions identified in this result.

Type:

FragmentationType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
IonType	1	unbounded	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

Example Context:

Element <FragmentationTable>

Definition:

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

Type:

FragmentationTableType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Measure	1	unbounded	References to CV terms defining the measures about product ions to be reported in SpectrumIdentificationItem

Example Context:

Element <FragmentTolerance>

Definition:

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

Type:

ToleranceType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

<FragmentTolerance>
  <cvParam cvRef="PSI-MS" accession="MS:1001412" name="search tolerance plus value" value="0.7" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"></cvParam>
  <cvParam cvRef="PSI-MS" accession="MS:1001413" name="search tolerance minus value" value="0.7" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"></cvParam>
</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 cvRef="PSI-MS" accession="MS:1001412" name="search tolerance plus value" value="0.7" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1001413" name="search tolerance minus value" value="0.7" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"></cvParam>

Element <Include>

Definition:

All sequences fulfilling the specifed criteria are included.

Type:

ParamListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	1	unbounded	A 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 Name	minOccurs	maxOccurs	Definition
SourceFile	0	unbounded	A file from which this mzIdentML instance was created.
SearchDatabase	0	unbounded	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.
SpectraData	1	unbounded	A data set containing spectra data (consisting of one or more spectra).

Example Context:

<Inputs xmlns="http://psidev.info/psi/pi/mzIdentML/1.2">
  <SourceFile location="example_files/55merge_omssa.omx" id="SourceFile_1">
    <FileFormat>
      <cvParam cvRef="PSI-MS" accession="MS:1001400" name="OMSSA xml format"></cvParam>
    </FileFormat>
  </SourceFile>
  <SearchDatabase numDatabaseSequences="299106" location="fawaz_PXD000652_combined_concatenated_target_decoy.fasta" id="SearchDB_1">
  ...
</Inputs>

Element <InputSpectra>

Definition:

One of the spectra data sets used.

Type:

InputSpectraType

Attributes:

Attribute Name	Data Type	Use	Definition
spectraData_ref	xsd:string	optional	A reference to the SpectraData element which locates the input spectra to an external file.

Subelements:

none

Example Context:

<InputSpectra spectraData_ref="SD_COMBINED_SE_0"></InputSpectra>

Element <InputSpectrumIdentifications>

Definition:

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

Type:

InputSpectrumIdentificationsType

Attributes:

Attribute Name	Data Type	Use	Definition
spectrumIdentificationList_ref	xsd:string	required	A reference to the list of spectrum identifications that were input to the process.

Subelements:

none

Example Context:

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 Name	Data Type	Use	Definition
charge	xsd:int	required	The charge of the identified fragmentation ions.
index	listOfIntegers	optional	The index of ions identified as integers, following standard notation for a-c, x-z e.g. if b3 b5 and b6 have been identified, the index would store "3 5 6". For internal ions, the index contains pairs defining the start and end point - see specification document for examples. For immonium ions, the index is the position of the identified ion within the peptide sequence - if the peptide contains the same amino acid in multiple positions that cannot be distinguished, all positions should be given. 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 Name	minOccurs	maxOccurs	Definition
FragmentArray	0	unbounded	An array of values for a given type of measure and for a particular ion type, in parallel to the index of ions identified.
userParam	0	unbounded	A single user-defined parameter.
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

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

Element <MassTable>

Definition:

The masses of residues used in the search.

Type:

MassTableType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
msLevel	listOfIntegers	required	The MS spectrum that the MassTable refers to e.g. "1" for MS1 "2" for MS2 or "1 2" for MS1 or MS2.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

Subelement Name	maxOccurs	Definition
Residue	unbounded	The specification of a single residue within the mass table.
AmbiguousResidue	unbounded	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.
cvParam	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	unbounded	A 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 Name	Data Type	Use	Definition
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

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

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 â€œunknown modificationâ€ 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 Name	Data Type	Use	Definition
avgMassDelta	xsd:double	optional	Atomic mass delta considering the natural distribution of isotopes in Daltons.
location	xsd:int	optional	Location of the modification within the peptide - position in peptide sequence, counted from the N-terminus residue, starting at position 1. Specific modifications to the N-terminus should be given the location 0. Modification to the C-terminus should be given as peptide length + 1. If the modification location is unknown e.g. for PMF data, this attribute should be omitted.
monoisotopicMassDelta	xsd:double	optional	Atomic mass delta when assuming only the most common isotope of elements in Daltons.
residues	listOfChars	optional	Specification of the residue (amino acid) on which the modification occurs. If multiple values are given, it is assumed that the exact residue modified is unknown i.e. the modification is to ONE of the residues listed. Multiple residues would usually only be specified for PMF data.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

<Modification location="1" residues="E" monoisotopicMassDelta="-18.01056">
  <cvParam cvRef="UNIMOD" accession="UNIMOD:27" name="Glu->pyro-Glu"></cvParam>
</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:35" name="Oxidation"></cvParam>
<cvParam cvRef="UNIMOD" accession="UNIMOD:37" name="Trimethyl"></cvParam>
<cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"></cvParam>
<cvParam cvRef="UNIMOD" accession="UNIMOD:27" name="Glu->pyro-Glu"></cvParam>
<cvParam cvRef="UNIMOD" accession="UNIMOD:1" name="Acetyl"></cvParam>
<cvParam cvRef="UNIMOD" accession="UNIMOD:385" name="Ammonia-loss"></cvParam>
<cvParam cvRef="UNIMOD" accession="UNIMOD:28" name="Gln->pyro-Glu"></cvParam>
<cvParam cvRef="UNIMOD" accession="UNIMOD:575" name="Gly->Val"></cvParam>

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 Name	minOccurs	maxOccurs	Definition
SearchModification	1	unbounded	Specification of a search modification as parameter for a spectra search. Contains the name of the modification, the mass, the specificity and whether it is a static modification.

Example Context:

<ModificationParams>
  <SearchModification fixedMod="true" massDelta="57.021465" residues="C">
    <cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"></cvParam>
  </SearchModification>
  <SearchModification fixedMod="false" massDelta="15.994915" residues="M">
    <cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"></cvParam>
  </SearchModification>
  ...
</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 Name	Data Type	Use	Definition
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

Subelement Name	maxOccurs	Definition
cvParam	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	unbounded	A single user-defined parameter.
Parent	1	The containing organization (the university or business which a lab belongs to, etc.)

Example Context:

<Organization id="ORG_DOC_OWNER" name="myworkplace">
  <cvParam cvRef="PSI-MS" accession="MS:1000586" name="contact name" value="address"></cvParam>
</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="address"></cvParam>

Element <Parent>

Definition:

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

Type:

ParentOrganizationType

Attributes:

Attribute Name	Data Type	Use	Definition
organization_ref	xsd:string	required	A 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 Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

<ParentTolerance>
  <cvParam cvRef="PSI-MS" accession="MS:1001412" name="search tolerance plus value" value="10.0" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"></cvParam>
  <cvParam cvRef="PSI-MS" accession="MS:1001413" name="search tolerance minus value" value="10.0" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"></cvParam>
</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 cvRef="PSI-MS" accession="MS:1001412" name="search tolerance plus value" value="10.0" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1001413" name="search tolerance minus value" value="10.0" unitAccession="UO:0000221" unitName="dalton" unitCvRef="UO"></cvParam>

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 Name	Data Type	Use	Definition
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
PeptideSequence	1	1	The amino acid sequence of the (poly)peptide. If a substitution modification has been found, the original sequence should be reported.
Modification	0	unbounded	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 â€œunknown modificationâ€ 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.
SubstitutionModification	0	unbounded	A modification where one residue is substituted by another (amino acid change).
cvParam	0	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	0	unbounded	A single user-defined parameter.

Example Context:

<Peptide id="CCPQCCSSGCSQNLCGPLCVTTPYYCTR_##Carbamidomethyl(C):1##Carbamidomethyl(C):2##Carbamidomethyl(C):5##Carbamidomethyl(C):6##Carbamidomethyl(C):10##Carbamidomethyl(C):15##Carbamidomethyl(C):19##Carbamidomethyl(C):26">
  <PeptideSequence>CCPQCCSSGCSQNLCGPLCVTTPYYCTR</PeptideSequence>
  <Modification location="1" residues="C" monoisotopicMassDelta="57.02147">
    <cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"></cvParam>
  </Modification>
  <Modification location="2" residues="C" monoisotopicMassDelta="57.02147">
    <cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"></cvParam>
  ...
</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 Name	Data Type	Use	Definition
dBSequence_ref	xsd:string	required	A reference to the protein sequence in which the specified peptide has been linked.
end	xsd:int	optional	The index position of the last amino acid of the peptide inside the protein sequence, where the first amino acid of the protein sequence is position 1. Must be provided unless this is a de novo search.
frame	allowed_frames	optional	The translation frame of this sequence if this is PeptideEvidence derived from nucleic acid sequence
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
isDecoy	xsd:boolean	optional	Set to true if the peptide is matched to a decoy sequence.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.
peptide_ref	xsd:string	required	A reference to the identified (poly)peptide sequence in the Peptide element.
post	xsd:string with restriction [ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}	optional	Post flanking residue. If the peptide is C-terminal, post="-" and not post="". If for any reason it is unknown (e.g. denovo), post="?" should be used.
pre	xsd:string with restriction [ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}	optional	Previous flanking residue. If the peptide is N-terminal, pre="-" and not pre="". If for any reason it is unknown (e.g. denovo), pre="?" should be used.
start	xsd:int	optional	Start 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_ref	xsd:string	optional	A reference to the translation table used if this is PeptideEvidence derived from nucleic acid sequence

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	0	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	0	unbounded	A single user-defined parameter.

Example Context:

<PeptideEvidence dBSequence_ref="dbseq_generic|B_GENSCAN00000036974_REVERSED|p:genscan" peptide_ref="CRCQYSGVNNLCHTSSHCPNQGSTCENVDTCLKPDEPK_##Carbamidomethyl(C):1##Carbamidomethyl(C):3##Carbamidomethyl(C):12##Carbamidomethyl(C):18##Carbamidomethyl(C):25##Carbamidomethyl(C):31##Ammonia-loss(C):1" start="494" end="531" pre="R" post="L" isDecoy="true" id="CRCQYSGVNNLCHTSSHCPNQGSTCENVDTCLKPDEPK_generic|B_GENSCAN00000036974_REVERSED|p:genscan_494_531"></PeptideEvidence>

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 Name	Data Type	Use	Definition
peptideEvidence_ref	xsd:string	required	A reference to the PeptideEvidenceItem element(s).

Subelements:

none

Example Context:

<PeptideEvidenceRef peptideEvidence_ref="GEGGAQDGSGTEGVGATGAAGGRGAQGAPGGTGGAGSGSGLHHQQDSGYQGASGSGGAQSGGR_generic|A_ENSP00000352272_REVERSED|p:known_125_187"></PeptideEvidenceRef>

Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1002356" name="PSM-level combined FDRScore" value="3.9523759266648643E-7"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002359" name="peptide sequence-level local FDR" value="0.0"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1001868" name="distinct peptide-level q-value" value="0.0"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002360" name="distinct peptide-level FDRScore" value="3.0117913560694526E-7"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002500" name="peptide passes threshold" value="true"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002520" name="peptide group ID" value="AVMDDFAAFVEK_##Oxidation(M):3"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002439" name="final PSM list"></cvParam>

Example userParams:

<userParam name="search engines identifying PSM" value="12"></userParam>

Element <PeptideHypothesis>

Definition:

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

Type:

PeptideHypothesisType

Attributes:

Attribute Name	Data Type	Use	Definition
peptideEvidence_ref	xsd:string	required	A reference to the PeptideEvidence element on which this hypothesis is based.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
SpectrumIdentificationItemRef	1	unbounded	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.

Example Context:

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>GEGGAQDGSGTEGVGATGAAGGRGAQGAPGGTGGAGSGSGLHHQQDSGYQGASGSGGAQSGGR</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 Name	Data Type	Use	Definition
firstName	xsd:string	optional	The Person's first name.
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
lastName	xsd:string	optional	The Person's last/family name.
midInitials	xsd:string	optional	The Person's middle initial.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

Subelement Name	maxOccurs	Definition
cvParam	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	unbounded	A single user-defined parameter.
Affiliation	unbounded	The organization a person belongs to.

Example Context:

<Person lastName="secondName" firstName="firstname" id="PERSON_DOC_OWNER">
  <cvParam cvRef="PSI-MS" accession="MS:1000587" name="contact address" value="address"></cvParam>
  <Affiliation organization_ref="ORG_DOC_OWNER"></Affiliation>
</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="address"></cvParam>

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 Name	Data Type	Use	Definition
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
ProteinDetectionHypothesis	1	unbounded	A single result of the ProteinDetection analysis (i.e. a protein).
cvParam	0	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	0	unbounded	A single user-defined parameter.

Example Context:

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 Name	Data Type	Use	Definition
activityDate	xsd:dateTime	optional	When the protocol was applied.
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.
proteinDetectionList_ref	xsd:string	required	A reference to the ProteinDetectionList in the DataCollection section.
proteinDetectionProtocol_ref	xsd:string	required	A reference to the detection protocol used for this ProteinDetection.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
InputSpectrumIdentifications	1	unbounded	The lists of spectrum identifications that are input to the protein detection process.

Example Context:

Element <ProteinDetectionHypothesis>

Definition:

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

Type:

ProteinDetectionHypothesisType

Attributes:

Attribute Name	Data Type	Use	Definition
dBSequence_ref	xsd:string	required	A 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.
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.
passThreshold	xsd:boolean	required	Set 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 Name	minOccurs	maxOccurs	Definition
PeptideHypothesis	1	unbounded	Peptide evidence on which this ProteinHypothesis is based by reference to a PeptideEvidence element.
cvParam	0	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	0	unbounded	A single user-defined parameter.

Example Context:

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 Name	Data Type	Use	Definition
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

Subelement Name	maxOccurs	Definition
ProteinAmbiguityGroup	unbounded	A set of logically related results from a protein detection, for example to represent conflicting assignments of peptides to proteins.
cvParam	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	unbounded	A single user-defined parameter.

Example Context:

<ProteinDetectionList id="PDL_1" >
</ProteinDetectionList>

cvParam Mapping Rules:

Path /MzIdentML/DataCollection/AnalysisData/ProteinDetectionList
MAY supply a *child* term of MS:1001184 (search statistics) one or more times
  e.g.: MS:1001035 (date / time search performed) 
  e.g.: MS:1001036 (search time taken) 
  e.g.: MS:1001177 (number of molecular hypothesis considered) 
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 Name	Data Type	Use	Definition
analysisSoftware_ref	xsd:string	required	The protein detection software used, given as a reference to the SoftwareCollection section.
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
AnalysisParams	0	1	The parameters and settings for the protein detection given as CV terms.
Threshold	1	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.

Graphical Context:

Example Context:

Element <Provider>

Definition:

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

Type:

ProviderType

Attributes:

Attribute Name	Data Type	Use	Definition
analysisSoftware_ref	xsd:string	optional	The Software that produced the document instance.
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
ContactRole	0	1	The Contact that provided the document instance.

Example Context:

<Provider xmlns="http://psidev.info/psi/pi/mzIdentML/1.2" id="PROVIDER">
  <ContactRole contact_ref="PERSON_DOC_OWNER">
    <Role>
      <cvParam cvRef="PSI-MS" accession="MS:1001271" name="researcher"></cvParam>
    </Role>
  </ContactRole>
</Provider>

Element <Residue>

Definition:

The specification of a single residue within the mass table.

Type:

ResidueType

Attributes:

Attribute Name	Data Type	Use	Definition
code	chars	required	The single letter code for the residue.
mass	xsd:float	required	The 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 Name	minOccurs	maxOccurs	Definition
cvParam	1	1	A single entry from an ontology or a controlled vocabulary.

Example Context:

<Role>
  <cvParam cvRef="PSI-MS" accession="MS:1001271" name="researcher"></cvParam>
</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:1001271" name="researcher"></cvParam>

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 Name	Data Type	Use	Definition
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

Subelement Name	maxOccurs	Definition
ContactRole	unbounded	The Contact that provided the document instance.
SubSample	unbounded	References to the individual component samples within a mixed parent sample.
cvParam	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	unbounded	A 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 Name	Data Type	Use	Definition
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
location	xsd:anyURI	required	The location of the data file.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.
numDatabaseSequences	xsd:long	optional	The total number of sequences in the database.
numResidues	xsd:long	optional	The number of residues in the database.
releaseDate	xsd:dateTime	optional	The 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).
version	xsd:string	optional	The version of the database.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
ExternalFormatDocumentation	0	1	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.
FileFormat	1	1	The format of the ExternalData file, for example "tiff" for image files.
DatabaseName	1	1	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.
cvParam	0	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

<SearchDatabase numDatabaseSequences="299106" location="fawaz_PXD000652_combined_concatenated_target_decoy.fasta" id="SearchDB_1">
  <FileFormat>
    <cvParam cvRef="PSI-MS" accession="MS:1001348" name="FASTA format"></cvParam>
  </FileFormat>
  <DatabaseName>
    <userParam name="fawaz_PXD000652_combined_concatenated_target_decoy.fasta"></userParam>
  </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 Name	Data Type	Use	Definition
searchDatabase_ref	xsd:string	optional	A reference to the database searched.

Subelements:

none

Example Context:

<SearchDatabaseRef searchDatabase_ref="SearchDB_1"></SearchDatabaseRef>

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 Name	Data Type	Use	Definition
fixedMod	xsd:boolean	required	True, if the modification is static (i.e. occurs always).
massDelta	xsd:float	required	The mass delta of the searched modification in Daltons.
residues	listOfCharsOrAny	required	The 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 Name	minOccurs	maxOccurs	Definition
SpecificityRules	0	unbounded	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.
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

<SearchModification fixedMod="true" massDelta="57.021465" residues="C">
  <cvParam cvRef="UNIMOD" accession="UNIMOD:4" name="Carbamidomethyl"></cvParam>
</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>
<cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"></cvParam>

Element <SearchType>

Definition:

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

Type:

ParamType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	1	A single entry from an ontology or a controlled vocabulary.
userParam	1	1	A single user-defined parameter.

Example Context:

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

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 Name	maxOccurs	Definition
DBSequence	unbounded	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.
Peptide	unbounded	One (poly)peptide (a sequence with modifications). The combination of Peptide sequence and modifications MUST be unique in the file.
PeptideEvidence	unbounded	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.

Graphical Context:

Example Context:

<SequenceCollection xmlns="http://psidev.info/psi/pi/mzIdentML/1.2">
  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|A_ENSP00000462078|p:known" id="dbseq_generic|A_ENSP00000462078|p:known"></DBSequence>
  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|A_ENSP00000290100|p:known" id="dbseq_generic|A_ENSP00000290100|p:known"></DBSequence>
  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|A_ENSP00000468798|p:known" id="dbseq_generic|A_ENSP00000468798|p:known"></DBSequence>
  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|A_ENSP00000481360|p:known" id="dbseq_generic|A_ENSP00000481360|p:known"></DBSequence>
  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|B_GENSCAN00000011570|p:genscan" id="dbseq_generic|B_GENSCAN00000011570|p:genscan"></DBSequence>
  <DBSequence searchDatabase_ref="SearchDB_1" accession="generic|A_ENSP00000397445|p:known" id="dbseq_generic|A_ENSP00000397445|p:known"></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 Name	minOccurs	maxOccurs	Definition
cvParam	1	1	A single entry from an ontology or a controlled vocabulary.
userParam	1	1	A single user-defined parameter.

Example Context:

<SoftwareName>
  <cvParam cvRef="PSI-MS" accession="MS:1002237" name="mzidLib"></cvParam>
</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:1001475" name="OMSSA"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002237" name="mzidLib"></cvParam>

Element <SourceFile>

Definition:

A file from which this mzIdentML instance was created.

Type:

SourceFileType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
location	xsd:anyURI	required	The location of the data file.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
ExternalFormatDocumentation	0	1	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.
FileFormat	1	1	The format of the ExternalData file, for example "tiff" for image files.
cvParam	0	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	0	unbounded	A single user-defined parameter.

Example Context:

<SourceFile location="example_files/55merge_omssa.omx" id="SourceFile_1">
  <FileFormat>
    <cvParam cvRef="PSI-MS" accession="MS:1001400" name="OMSSA xml format"></cvParam>
  </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 Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.

Example Context:

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)

Element <SpectraData>

Definition:

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

Type:

SpectraDataType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
location	xsd:anyURI	required	The location of the data file.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
ExternalFormatDocumentation	0	1	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.
FileFormat	1	1	The format of the ExternalData file, for example "tiff" for image files.
SpectrumIDFormat	1	1	The format of the spectrum identifier within the source file

Example Context:

<SpectraData location="/home/fawaz/mgf/HV_map_B1.mgf" id="SD_COMBINED_SE_0">
  <FileFormat>
    <cvParam cvRef="PSI-MS" accession="MS:1001062" name="Mascot MGF format"></cvParam>
  </FileFormat>
  <SpectrumIDFormat>
    <cvParam cvRef="PSI-MS" accession="MS:1000774" name="multiple peak list nativeID format"></cvParam>
  </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 Name	Data Type	Use	Definition
activityDate	xsd:dateTime	optional	When the protocol was applied.
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.
spectrumIdentificationList_ref	xsd:string	required	A reference to the SpectrumIdentificationList produced by this analysis in the DataCollection section.
spectrumIdentificationProtocol_ref	xsd:string	required	A reference to the search protocol used for this SpectrumIdentification.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
InputSpectra	1	unbounded	One of the spectra data sets used.
SearchDatabaseRef	1	unbounded	One of the search databases used.

Example Context:

<SpectrumIdentification spectrumIdentificationProtocol_ref="SearchProtocol_1" spectrumIdentificationList_ref="SII_LIST_1" id="SpecIdent_1">
  <InputSpectra spectraData_ref="SD_COMBINED_SE_0"></InputSpectra>
  <SearchDatabaseRef searchDatabase_ref="SearchDB_1"></SearchDatabaseRef>
</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 Name	Data Type	Use	Definition
calculatedMassToCharge	xsd:double	optional	The theoretical mass-to-charge value calculated for the peptide in Daltons / charge.
calculatedPI	xsd:float	optional	The calculated isoelectric point of the (poly)peptide, with relevant modifications included. Do not supply this value if the PI cannot be calcuated properly.
chargeState	xsd:int	required	The charge state of the identified peptide.
experimentalMassToCharge	xsd:double	required	The mass-to-charge value measured in the experiment in Daltons / charge.
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
massTable_ref	xsd:string	optional	A reference should be given to the MassTable used to calculate the sequenceMass only if more than one MassTable has been given.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.
passThreshold	xsd:boolean	required	Set 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_ref	xsd:string	required	A reference to the identified (poly)peptide sequence in the Peptide element.
rank	xsd:int	required	For 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_ref	xsd:string	optional	A reference should be provided to link the SpectrumIdentificationItem to a Sample if more than one sample has been described in the AnalysisSampleCollection.

Subelements:

Subelement Name	maxOccurs	Definition
PeptideEvidenceRef	unbounded	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.
Fragmentation	1	The product ions identified in this result.
cvParam	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	unbounded	A single user-defined parameter.

Graphical Context:

Example Context:

<SpectrumIdentificationItem chargeState="4" experimentalMassToCharge="1123.974121" calculatedMassToCharge="1123.968707" peptide_ref="CRCQYSGVNNLCHTSSHCPNQGSTCENVDTCLKPDEPK_##Carbamidomethyl(C):1##Carbamidomethyl(C):3##Carbamidomethyl(C):12##Carbamidomethyl(C):18##Carbamidomethyl(C):25##Carbamidomethyl(C):31##Ammonia-loss(C):1" rank="1" passThreshold="false" id="SIR_7191_SII_1">
  <PeptideEvidenceRef peptideEvidence_ref="CRCQYSGVNNLCHTSSHCPNQGSTCENVDTCLKPDEPK_generic|A_ENSP00000376692_REVERSED|p:novel_575_612"></PeptideEvidenceRef>
  <PeptideEvidenceRef peptideEvidence_ref="CRCQYSGVNNLCHTSSHCPNQGSTCENVDTCLKPDEPK_generic|B_GENSCAN00000036974_REVERSED|p:genscan_494_531"></PeptideEvidenceRef>
  <PeptideEvidenceRef peptideEvidence_ref="CRCQYSGVNNLCHTSSHCPNQGSTCENVDTCLKPDEPK_generic|A_ENSP00000471297_REVERSED|p:putative_641_678"></PeptideEvidenceRef>
  <PeptideEvidenceRef peptideEvidence_ref="CRCQYSGVNNLCHTSSHCPNQGSTCENVDTCLKPDEPK_generic|A_ENSP00000319883_REVERSED|p:known_633_670"></PeptideEvidenceRef>
  <PeptideEvidenceRef peptideEvidence_ref="CRCQYSGVNNLCHTSSHCPNQGSTCENVDTCLKPDEPK_generic|A_ENSP00000472280_REVERSED|p:putative_622_659"></PeptideEvidenceRef>
  <cvParam cvRef="PSI-MS" accession="MS:1002356" name="PSM-level combined FDRScore" value="0.4294078446305645"></cvParam>
  ...
</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.

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 Name	Data Type	Use	Definition
spectrumIdentificationItem_ref	xsd:string	required	A reference to the SpectrumIdentificationItem element(s).

Subelements:

none

Example Context:

Element <SpectrumIdentificationList>

Definition:

Represents the set of all search results from SpectrumIdentification.

Type:

SpectrumIdentificationListType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.
numSequencesSearched	xsd:long	optional	The number of database sequences searched against. This value should be provided unless a de novo search has been performed.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
FragmentationTable	0	1	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
SpectrumIdentificationResult	1	unbounded	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.
cvParam	0	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	0	unbounded	A single user-defined parameter.

Graphical Context:

Example Context:

<SpectrumIdentificationList xmlns="http://psidev.info/psi/pi/mzIdentML/1.2" id="SII_LIST_1">
  <SpectrumIdentificationResult spectrumID="index=6451" spectraData_ref="SD_COMBINED_SE_0" id="SIR_8947">
    <SpectrumIdentificationItem chargeState="2" experimentalMassToCharge="679.817322" calculatedMassToCharge="679.818488" peptide_ref="AVMDDFAAFVEK_##Oxidation(M):3" rank="1" passThreshold="false" id="SIR_8947_SII_1">
      <PeptideEvidenceRef peptideEvidence_ref="AVMDDFAAFVEK_generic|A_ENSP00000401820|p:known_378_389"></PeptideEvidenceRef>
      <PeptideEvidenceRef peptideEvidence_ref="AVMDDFAAFVEK_generic|A_ENSP00000421027|p:putative_420_431"></PeptideEvidenceRef>
      <PeptideEvidenceRef peptideEvidence_ref="AVMDDFAAFVEK_generic|A_ENSP00000483421|p:known_357_368"></PeptideEvidenceRef>
      <PeptideEvidenceRef peptideEvidence_ref="AVMDDFAAFVEK_generic|A_ENSP00000480485|p:known_357_368"></PeptideEvidenceRef>
  ...
</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 Name	Data Type	Use	Definition
analysisSoftware_ref	xsd:string	required	The search algorithm used, given as a reference to the SoftwareCollection section.
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
SearchType	1	1	The type of search performed e.g. PMF, Tag searches, MS-MS
AdditionalSearchParams	0	1	The search parameters other than the modifications searched.
ModificationParams	0	1	The specification of static/variable modifications (e.g. Oxidation of Methionine) that are to be considered in the spectra search.
Enzymes	0	1	The list of enzymes used in experiment
MassTable	0	unbounded	The masses of residues used in the search.
FragmentTolerance	0	1	The tolerance of the search given as a plus and minus value with units.
ParentTolerance	0	1	The tolerance of the search given as a plus and minus value with units.
Threshold	1	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.
DatabaseFilters	0	1	The specification of filters applied to the database searched.
DatabaseTranslation	0	1	A 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"></cvParam>
  </SearchType>
  <AdditionalSearchParams>
    <cvParam cvRef="PSI-MS" accession="MS:1001211" name="parent mass type mono"></cvParam>
    <cvParam cvRef="PSI-MS" accession="MS:1001256" name="fragment mass type mono"></cvParam>
  ...
</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 Name	Data Type	Use	Definition
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.
spectraData_ref	xsd:string	required	A reference to a spectra data set (e.g. a spectra file).
spectrumID	xsd:string	required	The locally unique id for the spectrum in the spectra data set specified by SpectraData_ref. External guidelines are provided on the use of consistent identifiers for spectra in different external formats.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
SpectrumIdentificationItem	1	unbounded	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.
cvParam	0	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	0	unbounded	A single user-defined parameter.

Example Context:

<SpectrumIdentificationResult spectrumID="index=7665" spectraData_ref="SD_COMBINED_SE_0" id="SIR_7191">
  <SpectrumIdentificationItem chargeState="4" experimentalMassToCharge="1123.974121" calculatedMassToCharge="1123.968707" peptide_ref="CRCQYSGVNNLCHTSSHCPNQGSTCENVDTCLKPDEPK_##Carbamidomethyl(C):1##Carbamidomethyl(C):3##Carbamidomethyl(C):12##Carbamidomethyl(C):18##Carbamidomethyl(C):25##Carbamidomethyl(C):31##Ammonia-loss(C):1" rank="1" passThreshold="false" id="SIR_7191_SII_1">
    <PeptideEvidenceRef peptideEvidence_ref="CRCQYSGVNNLCHTSSHCPNQGSTCENVDTCLKPDEPK_generic|A_ENSP00000376692_REVERSED|p:novel_575_612"></PeptideEvidenceRef>
    <PeptideEvidenceRef peptideEvidence_ref="CRCQYSGVNNLCHTSSHCPNQGSTCENVDTCLKPDEPK_generic|B_GENSCAN00000036974_REVERSED|p:genscan_494_531"></PeptideEvidenceRef>
    <PeptideEvidenceRef peptideEvidence_ref="CRCQYSGVNNLCHTSSHCPNQGSTCENVDTCLKPDEPK_generic|A_ENSP00000471297_REVERSED|p:putative_641_678"></PeptideEvidenceRef>
    <PeptideEvidenceRef peptideEvidence_ref="CRCQYSGVNNLCHTSSHCPNQGSTCENVDTCLKPDEPK_generic|A_ENSP00000319883_REVERSED|p:known_633_670"></PeptideEvidenceRef>
    <PeptideEvidenceRef peptideEvidence_ref="CRCQYSGVNNLCHTSSHCPNQGSTCENVDTCLKPDEPK_generic|A_ENSP00000472280_REVERSED|p:putative_622_659"></PeptideEvidenceRef>
  ...
</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 Name	minOccurs	maxOccurs	Definition
cvParam	1	1	A 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"></cvParam>
</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"></cvParam>

Element <SubSample>

Definition:

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

Type:

SubSampleType

Attributes:

Attribute Name	Data Type	Use	Definition
sample_ref	xsd:string	required	A 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 Name	Data Type	Use	Definition
avgMassDelta	xsd:double	optional	Atomic mass delta considering the natural distribution of isotopes in Daltons. This should only be reported if the original amino acid is known i.e. it is not "X"
location	xsd:int	optional	Location of the modification within the peptide - position in peptide sequence, counted from the N-terminus residue, starting at position 1. Specific modifications to the N-terminus should be given the location 0. Modification to the C-terminus should be given as peptide length + 1.
monoisotopicMassDelta	xsd:double	optional	Atomic mass delta when assuming only the most common isotope of elements in Daltons. This should only be reported if the original amino acid is known i.e. it is not "X"
originalResidue	xsd:string with restriction [ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}	required	The original residue before replacement.
replacementResidue	xsd:string with restriction [ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}	required	The 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 Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	1	unbounded	A single user-defined parameter.

Example Context:

<Threshold>
  <cvParam cvRef="PSI-MS" accession="MS:1001494" name="no threshold"></cvParam>
</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:1001494" name="no threshold"></cvParam>

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 Name	Data Type	Use	Definition
id	xsd:string	required	An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	0	unbounded	A 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 Name	Data Type	Use	Definition
name	xsd:string	required	The name of the parameter.
type	xsd:string	optional	The datatype of the parameter, where appropriate (e.g.: xsd:float).
unitAccession	xsd:string	optional	An accession number identifying the unit within the OBO foundry Unit CV.
unitCvRef	xsd:string	optional	If a unit term is referenced, this attribute MUST refer to the CV 'id' attribute defined in the cvList in this file.
unitName	xsd:string	optional	The name of the unit.
value	xsd:string	optional	The user-entered value of the parameter.

Subelements:

none

Example Context:

<userParam name="fawaz_PXD000652_combined_concatenated_target_decoy.fasta"></userParam>

Element <MzIdentML>

Element <AdditionalSearchParams>

Element <Affiliation>

Element <AmbiguousResidue>

Element <AnalysisCollection>

Element <AnalysisData>

Element <AnalysisParams>

Element <AnalysisProtocolCollection>

Element <AnalysisSampleCollection>

Element <AnalysisSoftware>

Element <AnalysisSoftwareList>

Element <AuditCollection>

Element <BibliographicReference>

Element <ContactRole>

Element <Customizations>

Element <cv>

Element <cvList>

Element <cvParam>

Element <DatabaseFilters>

Element <DatabaseName>

Element <DatabaseTranslation>

Element <DataCollection>

Element <DBSequence>

Element <Enzyme>

Element <EnzymeName>

Element <Enzymes>

Element <Exclude>

Element <ExternalFormatDocumentation>

Element <FileFormat>

Element <Filter>

Element <FilterType>

Element <FragmentArray>

Element <Fragmentation>

Element <FragmentationTable>

Element <FragmentTolerance>

Element <Include>

Element <Inputs>

Element <InputSpectra>

Element <InputSpectrumIdentifications>

Element <IonType>

Element <MassTable>

Element <Measure>

Element <Modification>

Element <ModificationParams>

Element <Organization>

Element <Parent>

Element <ParentTolerance>

Element <Peptide>

Element <PeptideEvidence>

Element <PeptideEvidenceRef>

Element <PeptideHypothesis>

Element <PeptideSequence>

Element <Person>

Element <ProteinAmbiguityGroup>

Element <ProteinDetection>

Element <ProteinDetectionHypothesis>

Element <ProteinDetectionList>

Element <ProteinDetectionProtocol>

Element <Provider>

Element <Residue>

Element <Role>

Element <Sample>

Element <SearchDatabase>

Element <SearchDatabaseRef>

Element <SearchModification>

Element <SearchType>

Element <Seq>

Element <SequenceCollection>

Element <SiteRegexp>

Element <SoftwareName>

Element <SourceFile>

Element <SpecificityRules>

Element <SpectraData>

Element <SpectrumIdentification>

Element <SpectrumIdentificationItem>

Element <SpectrumIdentificationItemRef>

Element <SpectrumIdentificationList>

Element <SpectrumIdentificationProtocol>

Element <SpectrumIdentificationResult>

Element <SpectrumIDFormat>