Element <MzQuantML>

Definition:

Root element of the instance document.

Type:

MzQuantMLType

Attributes:

Attribute Name	Data Type	Use	Definition
creationDate	xsd:dateTime	optional	The date on which the file was produced.
id	xsd:ID	required	The unique identifier for the mzQuantML file or experiment.
name	xsd:string	optional	Optional name for the file or experiment.
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.
Provider	0	1	The provider of the document in terms of the Contact and the software the produced the document instance.
AuditCollection	0	1	The complete set of Contacts (people and organisations) for this file.
AnalysisSummary	1	1	Summary information about the analysis in terms of the type of analysis, any global scores or metrics and global thresholds used.
InputFiles	1	1	All the raw files, identification files and databases used in the quantitation.
SoftwareList	1	1	List and descriptions of software used to acquire and/or process the data in this file.
DataProcessingList	1	1	List and descriptions of data processing applied to this data.
BibliographicReference	0	unbounded	Represents bibliographic references.
AssayList	1	1	The list of assays represented by the file, where each assay captures the concept of one sample analysed - this can be one or more raw files.
StudyVariableList	0	1	The list of experimental conditions used to group results.
RatioList	0	1	The definition of ratios of study variables or assays, referenced elsewhere in the document.
ProteinGroupList	0	1	The list of all groups of proteins with conflicting evidence for which quantitation values are being reported along with quantitative values about those protein groups. If quantitation is done on individual proteins only, ProteinGroupsList should not be included.
ProteinList	0	1	The list of all individual proteins (i.e. ungrouped) for which quantitation values are being reported. If quantitation is done on protein groups, the constituent proteins should be listed here with no QuantLayers.
PeptideConsensusList	0	unbounded	The list of all peptides for which quantitation values are reported.
SmallMoleculeList	0	1	List of small molecules and associated data values.
FeatureList	0	unbounded	All the features identified on a single raw file or raw file group.

Graphical Context:

Example Context:

<MzQuantML creationDate="2012-12-03T00:00:00.000+01:00" version="1.0.0" id="MZQ_SPC_EX1" xsi:schemaLocation="http://psidev.info/psi/pi/mzQuantML/1.0.0-rc3 ../../../schema/mzQuantML_1_0_0-rc3.xsd" xmlns="http://psidev.info/psi/pi/mzQuantML/1.0.0-rc3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
    <CvList>
        <Cv fullName="Proteomics Standards Initiative Protein Modifications" version="1.010.7" uri="http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mod/data/PSI-MOD.obo" id="MOD"/>
        <Cv fullName="Proteomics Standards Initiative Mass Spectrometry Vocabulary" version="3.41.0" uri="http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" id="MS"/>
        <Cv fullName="UNIMOD CV for modifications" version="" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"/>
        <Cv fullName="Unit Ontology" version="" uri="http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/phenotype/unit.obo" id="UO"/>
    </CvList>
  ...
</MzQuantML>

Element <Affiliation>

Definition:

The organization a person belongs to.

Type:

AffiliationType

Attributes:

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

Subelements:

none

Example Context:

<Affiliation organization_ref="ORG_UOL"/>

Element <AnalysisSummary>

Definition:

Summary information about the analysis in terms of the type of analysis, any global scores or metrics and global thresholds used.

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:

  <AnalysisSummary>
    <cvParam cvRef="PSI-MS" accession="MS:1002018" name="MS1 label-based analysis"/>
    <cvParam cvRef="PSI-MS" accession="MS:1001835" name="SILAC quantitation analysis"/>
    <cvParam cvRef="PSI-MS" accession="MS:1002001" name="MS1 label-based raw feature quantitation" value="true"/>
    <cvParam cvRef="PSI-MS" accession="MS:1002002" name="MS1 label-based peptide level quantitation" value="true"/>
    <cvParam cvRef="PSI-MS" accession="MS:1002003" name="MS1 label-based protein level quantitation" value="false"/>
    <cvParam cvRef="PSI-MS" accession="MS:1002004" name="MS1 label-based proteingroup level quantitation" value="false"/>
  ...
</AnalysisSummary>

cvParam Mapping Rules:

Path /MzQuantML/AnalysisSummary
MUST supply a *child* term of MS:1001833 (quantitation analysis summary) only once
  e.g.: MS:1001835 (SILAC quantitation analysis) 
  e.g.: MS:1001837 (iTRAQ quantitation analysis) 
  e.g.: MS:1001838 (SRM quantitation analysis) 
  e.g.: MS:1001839 (metabolic labeling 14N / 15N quantitation analysis) 
  e.g.: MS:1002001 (MS1 label-based raw feature quantitation) 
  e.g.: MS:1002002 (MS1 label-based peptide level quantitation) 
  e.g.: MS:1002003 (MS1 label-based protein level quantitation) 
  e.g.: MS:1002004 (MS1 label-based proteingroup level quantitation) 
  e.g.: MS:1002010 (TMT quantitation analysis) 
  e.g.: MS:1002015 (spectral count peptide level quantitation) 
  et al.

Example cvParams:

<cvParam accession="MS:1001834" cvRef="PSI-MS" name="LC-MS label-free quantitation analysis"/>
<cvParam accession="MS:1002019" cvRef="PSI-MS" value="false" name="label-free raw feature quantitation"/>
<cvParam accession="MS:1002020" cvRef="PSI-MS" value="true" name="label-free peptide level quantitation"/>
<cvParam accession="MS:1002021" cvRef="PSI-MS" value="true" name="label-free protein level quantitation"/>
<cvParam accession="MS:1002022" cvRef="PSI-MS" value="false" name="label-free proteingroup level quantitation"/>
<cvParam accession="MS:1002018" cvRef="PSI-MS" name="MS1 label-based analysis"/>
<cvParam accession="MS:1002001" cvRef="PSI-MS" value="true" name="MS1 label-based raw feature quantitation"/>
<cvParam accession="MS:1002002" cvRef="PSI-MS" value="true" name="MS1 label-based peptide level quantitation"/>
<cvParam accession="MS:1002003" cvRef="PSI-MS" value="true" name="MS1 label-based protein level quantitation"/>
<cvParam accession="MS:1002004" cvRef="PSI-MS" value="false" name="MS1 label-based proteingroup level quantitation"/>
<cvParam cvRef="PSI-MS" accession="MS:1001835" name="SILAC quantitation analysis"/>
<cvParam accession="MS:1002023" cvRef="PSI-MS" name="MS2 tag-based analysis"/>
<cvParam accession="MS:1002024" cvRef="PSI-MS" value="true" name="MS2 tag-based feature level quantitation"/>
<cvParam accession="MS:1002025" cvRef="PSI-MS" value="true" name="MS2 tag-based peptide level quantitation"/>
<cvParam accession="MS:1002026" cvRef="PSI-MS" value="true" name="MS2 tag-based protein level quantitation"/>
<cvParam accession="MS:1002027" cvRef="PSI-MS" value="false" name="MS2 tag-based proteingroup level quantitation"/>
<cvParam accession="MS:1001836" cvRef="PSI-MS" name="spectral counting quantitation analysis"/>
<cvParam accession="MS:1002015" cvRef="PSI-MS" value="false" name="spectral count peptide level quantitation"/>
<cvParam accession="MS:1002016" cvRef="PSI-MS" value="true" name="spectral count protein level quantitation"/>
<cvParam accession="MS:1002017" cvRef="PSI-MS" value="false" name="spectral count proteingroup level quantitation"/>

Element <Assay>

Definition:

Describes a single analysis of a sample (e.g. with the channel mapping in iTRAQ), which could constitute multiple raw files e.g. if pre-separation steps have occurred.

Type:

AssayType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.
name	xsd:string	optional	Human readable name for the assay.
rawFilesGroup_ref	xsd:IDREF	optional	A reference to the RawFilesGroup that the Assay is linked to.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Label	1	1	A specification of labels or tags used to define the assay within the raw file, such as heavy labelling or iTRAQ tag mass. The Label and Modification is mandatory so a specific term is provided under Modification for unlabeled sample for label-free and, for example, so-called light samples in a labelling experiment.
IdentificationFile_refs	0	1	One or more identification files used within this assay.
cvParam	0	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	0	unbounded	A single user-defined parameter.

Example Context:

    <Assay id="a_3151552639304580883" rawFilesGroup_ref="rfg_15787140749886983179">
      <Label>
        <Modification massDelta="8.0141988132" >
          <cvParam cvRef="PSI-MOD" accession="MOD:00582" name="6x(13)C,2x(15)N labeled L-lysine" value="Lys8"/>
        </Modification>
        <Modification massDelta="10.0082686" >
          <cvParam cvRef="PSI-MOD" accession="MOD:00587" name="6x(13)C,4x(15)N labeled L-arginine" value="Arg10"/>
  ...
</Assay>

cvParam Mapping Rules:

Path /MzQuantML/AssayList/Assay
MAY supply a *child* term of MS:1002110 (assay attribute) one or more times

Element <AssayList>

Definition:

The list of assays represented by the file, where each assay captures the concept of one sample analysed - this can be one or more raw files.

Type:

AssayListType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Assay	1	unbounded	Describes a single analysis of a sample (e.g. with the channel mapping in iTRAQ), which could constitute multiple raw files e.g. if pre-separation steps have occurred.

Graphical Context:

Example Context:

<AssayList id="AssayList1">
    <Assay rawFilesGroup_ref="raw1" name="114" id="_114">
        <Label>
            <Modification massDelta="145.0">
                <cvParam accession="MOD:01522" cvRef="PSI-MOD" value="114" name="iTRAQ4plex-114 reporter fragment"/>
            </Modification>
        </Label>
  ...
</AssayList>

Depending on context:
1: Quant layer for reporting data values about protein groups related to different assays i.e. the column index MUST refer to Assays defined in the file.
2: Quant layer for reporting data values about proteins related to different assays i.e. the column index MUST refer to Assays defined in the file.
3: Quant layer for reporting data values about peptides related to different assays i.e. the column index MUST refer to Assays defined in the file.
4: Quant layer for reporting data values about small molecules related to different assays i.e. the column index MUST refer to Assays defined in the file.

Type:

QuantLayerType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
DataType	1	1	Type of data in the column e.g. cvParam = "Intensity\|RawAbundance\|NormalisedAbundance".
ColumnIndex	1	1	Space separated unique identifiers for each column of data, MUST refer to an object in the file i.e. Ratio elements.
DataMatrix	1	1	A matrix of data stored in rows and columns, as defined in the parent QuantLayer.

Example Context:

<AssayQuantLayer id="Pep_AQL1">
    <DataType>
        <cvParam accession="MS:1001891" cvRef="PSI-MS" name="Progenesis:peptide normalised abundance"/>
    </DataType>
    <ColumnIndex>ass_0 ass_1 ass_2 ass_3 ass_4 ass_5 ass_6 ass_7 ass_8 ass_9 ass_10 ass_11</ColumnIndex>
    <DataMatrix>
        <Row object_ref="pep_GAPEIDVLEGETDTK_2_21711">9079.67 6680.893 6869.919 7069.431 6872.01 7488.588 5045.095 7063.636 6636.347 3902.41 4320.357 4045.954</Row>
  ...
</AssayQuantLayer>

Element <Assay_refs>

Definition:	Reference to the assays that are contained within this study variable.
Type:	xsd:IDREFS
Attributes:	none
Subelements:	none
Example Context:	<Assay_refs>ASS_0 ASS_1 ASS_2 ASS_3 ASS_4</Assay_refs>

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	0	unbounded	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	0	unbounded	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.

Graphical Context:

Example Context:

<AuditCollection>
    <Person lastName="Mayer" firstName="Gerhard" id="PERS_GM" name="Gerhard Mayer">
        <Affiliation organization_ref="ORG_MPC"/>
    </Person>
    <Organization id="ORG_Univ_Bochum" name="University of Bochum"/>
    <Organization id="ORG_MPC" name="MPC - Medizinisches Proteom Center, Bochum">
        <ParentOrganization organization_ref="ORG_Univ_Bochum"/>
  ...
</AuditCollection>

Element <BibliographicReference>

Definition:

Represents bibliographic references.

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:ID	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:

<BibliographicReference doi="doi:10.1089/omi.2012.0042" title="A software toolkit and interface for performing stable isotope labelling and top3 quantification using Progenesis LC-MS" pages="489-495" issue="9" volume="16" year="2012" publication="OMICS: A Journal of Integrative Biology" authors="D. Qi, P. Brownridge, D. Xia, K. Mackay, F. F. Gonzalez-Galarza, J. Kenyani, V. Harman, R. J. Beynon and A. R. Jones" id="BF_DQ1"/>

Element <Column>

Definition:

The datatype and index position of one column of data in the DataMatrix.

Type:

ColumnType

Attributes:

Attribute Name	Data Type	Use	Definition
index	xsd:nonNegativeInteger	required	The column position within the data matrix - incrementing positive integers starting from zero.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
DataType	1	1	Type of data in the column e.g. cvParam = "Intensity\|RawAbundance\|NormalisedAbundance".

Example Context:

        <Column index="0">
          <DataType>
            <cvParam cvRef="PSI-MS" accession="MS:1001141" name="intensity of precursor ion"/>
          </DataType>
        </Column>        <Column index="1">

Element <ColumnDefinition>

Definition:

Definition of the data types in each column.

Type:

ColumnDefinitionType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Column	1	unbounded	The datatype and index position of one column of data in the DataMatrix.

Example Context:

      <ColumnDefinition>
        <Column index="0">
          <DataType>
            <cvParam cvRef="PSI-MS" accession="MS:1001141" name="intensity of precursor ion"/>
          </DataType>
        </Column>        <Column index="1">
          <DataType>
  ...
</ColumnDefinition>

Element <ColumnIndex>

Definition:	Depending on context: 1: Space separated unique identifiers for each column of data, MUST refer to an object in the file i.e. StudyVariable or Assay, depending on the context where the QuantLayer resides. 2: Space separated unique identifiers for each column of data, MUST refer to an object in the file i.e. Ratio elements.
Type:	xsd:IDREFS
Attributes:	none
Subelements:	none
Example Context:	<ColumnIndex>RATIO_vIa_30min_vs_vIb_120min RATIO_20a_30min_vs_20b_120min RATIO_40a_30min_vs_40b_120min RATIO_60a_30min_vs_60b_120min RATIO_80a_30min_vs_80b_120min RATIO_Ia_30min_vs_Ib_120min</ColumnIndex>

Element <ContactRole>

Definition:

The role of the Contact that provided the document instance.

Type:

ContactRoleType

Attributes:

Attribute Name	Data Type	Use	Definition
contact_ref	xsd:IDREF	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="PERS_GM">
    <Role>
        <cvParam cvRef="MS" accession="MS:1001271" name="researcher"/>
    </Role>
</ContactRole>

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:ID	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="PSI-MS" fullName="Proteomics Standards Initiative Mass Spectrometry Vocabularies"  uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.40.0"/>

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 fullName="Proteomics Standards Initiative Protein Modifications" version="1.010.7" uri="http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mod/data/PSI-MOD.obo" id="MOD"/>
    <Cv fullName="Proteomics Standards Initiative Mass Spectrometry Vocabulary" version="3.41.0" uri="http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" id="MS"/>
    <Cv fullName="UNIMOD CV for modifications" version="" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"/>
    <Cv fullName="Unit Ontology" version="" uri="http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/phenotype/unit.obo" id="UO"/>
</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:IDREF	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 accession="MS:1001524" cvRef="PSI-MS" unitCvRef="UO" unitName="dalton" unitAccession="UO:0000221" value="63.998285" name="fragment neutral loss"/>

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>
        <cvParam cvRef="PSI-MS" accession="MS:1001013" name="database name" value="SwissProtHuman554TD_20080526.fasta"/>
      </DatabaseName>

cvParam Mapping Rules:

Path /MzQuantML/InputFiles/SearchDatabase/DatabaseName
SHOULD supply a *child* term of MS:1001013 (database name) only once
  e.g.: MS:1001084 (database nr) 
  e.g.: MS:1001104 (database UniProtKB/Swiss-Prot) 
  e.g.: MS:1001142 (database IPI_human) 
  e.g.: MS:1001285 (database IPI_mouse) 
  e.g.: MS:1001286 (database IPI_rat) 
  e.g.: MS:1001287 (database IPI_zebrafish) 
  e.g.: MS:1001288 (database IPI_chicken) 
  e.g.: MS:1001289 (database IPI_cow) 
  e.g.: MS:1001290 (database IPI_arabidopsis) 
  e.g.: MS:1002060 (database UniProtKB/TrEMBL)

Example cvParams:

<cvParam cvRef="PSI-MS" accession="MS:1001013" name="database name" value="SwissProtHuman554TD_20080526.fasta"/>
<cvParam cvRef="MS" accession="MS:1001084" name="database nr"/>

Example userParams:

<userParam name="sgd_orfs_plus_ups_prots.fasta"/>
<userParam name="itraq_db.fasta"/>
<userParam name="Pseudomonas.fasta"/>

Element <DataMatrix>

Definition:

A matrix of data stored in rows and columns, as defined in the parent QuantLayer.

Type:

DataMatrixType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Row	1	unbounded	One row of data in a data matrix.

Example Context:

<DataMatrix>
    <Row object_ref="pep_GAPEIDVLEGETDTK_2_21711">9079.67 6680.893 6869.919 7069.431 6872.01 7488.588 5045.095 7063.636 6636.347 3902.41 4320.357 4045.954</Row>
    <Row object_ref="pep_QSTTFADCPVVPADPDILLAK_2_48178">3299.727 576.473 43.736 1858.257 657.126 933.167 2811.395 1563.02 2621.453 3516.591 2474.139 1086.323</Row>
    <Row object_ref="pep_QKYDADVLDK_3_2006">48572.697 36224.374 49154.991 48022.429 42519.467 43865.915 33691.767 30520.391 29488.844 31172.178 23221.642 20119.87</Row>
    <Row object_ref="pep_GLGNPLLYDGVER_2_13819">14041.079 10370.307 11493.51 12698.35 9696.061 10021.047 9707.69 10754.69 10504.175 8528.331 7383.964 6172.554</Row>
    <Row object_ref="pep_LFAGMSPEMAK_2_5761">25030.664 17899.384 19336.846 26564.901 19449.275 22901.059 15937.055 21527.449 16656.611 13495.235 12320.256 12043.633</Row>
    <Row object_ref="pep_FSPVSTASYR_2_7384">15736.005 12792.928 12804.118 14132.755 14456.028 15512.023 8811.88 11793.098 10181.587 7227.684 7532.051 6258.705</Row>
  ...
</DataMatrix>

Element <DataProcessing>

Definition:

Description of the way in which a particular software package was used to analyse data and for example produce different quant layers or lists in the file.

Type:

DataProcessingType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.
order	xsd:positiveInteger	required	This attributes allows a series of consecutive steps to be placed in the correct order, start counting from 1.
software_ref	xsd:IDREF	required	This attribute MUST reference the appropriate SoftwareType.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
InputObject_refs	0	1	References to raw file groups, FeatureList, PeptideConsensusList, ProteinList or ProteinGroupList or QuantLayers that were inputs to the data processing step.
OutputObject_refs	0	1	References to raw file groups, FeatureList, PeptideConsensusList, ProteinList or ProteinGroupList or QuantLayers that were the outputs of the data processing step.
ProcessingMethod	1	unbounded	Description of one step within the data processing pipeline.

Example Context:

<DataProcessing order="1" software_ref="x-Tracker" id="DP1">
    <ProcessingMethod order="1">
        <userParam value="load identification" name="Plugin type"/>
        <userParam value="loadMzIdentML" name="Plugin name"/>
        <userParam value="examples/paper_iTraq4plex/loadMzIdentML.xtp" name="Plugin configuration file"/>
    </ProcessingMethod>
    <ProcessingMethod order="2">
  ...
</DataProcessing>

Element <DataProcessingList>

Definition:

List and descriptions of data processing applied to this data.

Type:

DataProcessingListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
DataProcessing	1	unbounded	Description of the way in which a particular software package was used to analyse data and for example produce different quant layers or lists in the file.

Graphical Context:

Example Context:

<DataProcessingList>
    <DataProcessing order="1" software_ref="x-Tracker" id="DP1">
        <ProcessingMethod order="1">
            <userParam value="load identification" name="Plugin type"/>
            <userParam value="loadMzIdentML" name="Plugin name"/>
            <userParam value="examples/paper_iTraq4plex/loadMzIdentML.xtp" name="Plugin configuration file"/>
        </ProcessingMethod>
  ...
</DataProcessingList>

Element <DataType>

Definition:

Type:

cvParamRefType

Attributes:

none

Subelements:

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

Example Context:

<DataType>
    <cvParam accession="MS:1001890" cvRef="PSI-MS" name="Progenesis:protein normalised abundance"/>
</DataType>

cvParam Mapping Rules:

Path /MzQuantML/SmallMoleculeList/GlobalQuantLayer/ColumnDefinition/Column/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Path /MzQuantML/ProteinGroupList/AssayQuantLayer/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Path /MzQuantML/ProteinGroupList/GlobalQuantLayer/ColumnDefinition/Column/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Path /MzQuantML/FeatureList/MS2AssayQuantLayer/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Path /MzQuantML/PeptideConsensusList/AssayQuantLayer/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Path /MzQuantML/ProteinGroupList/StudyVariableQuantLayer/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Path /MzQuantML/ProteinList/GlobalQuantLayer/ColumnDefinition/Column/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Path /MzQuantML/SmallMoleculeList/StudyVariableQuantLayer/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Path /MzQuantML/FeatureList/FeatureQuantLayer/ColumnDefinition/Column/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Path /MzQuantML/FeatureList/MS2StudyVariableQuantLayer/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Path /MzQuantML/ProteinList/StudyVariableQuantLayer/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Path /MzQuantML/SmallMoleculeList/AssayQuantLayer/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Path /MzQuantML/PeptideConsensusList/StudyVariableQuantLayer/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Path /MzQuantML/ProteinList/AssayQuantLayer/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Path /MzQuantML/PeptideConsensusList/GlobalQuantLayer/ColumnDefinition/Column/DataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Example cvParams:

<cvParam accession="MS:1001890" cvRef="PSI-MS" name="Progenesis:protein normalised abundance"/>
<cvParam accession="MS:1001892" cvRef="PSI-MS" name="Progenesis:protein raw abundance"/>
<cvParam accession="MS:1001171" cvRef="PSI-MS" name="Mascot:score"/>
<cvParam accession="MS:1001891" cvRef="PSI-MS" name="Progenesis:peptide normalised abundance"/>
<cvParam accession="MS:1001893" cvRef="PSI-MS" name="Progenesis:peptide raw abundance"/>
<cvParam accession="MS:1001903" cvRef="PSI-MS" name="MaxQuant:feature intensity"/>
<cvParam accession="MS:1001897" cvRef="PSI-MS" name="MaxQuant:peptide counts (unique)"/>
<cvParam cvRef="PSI-MS" accession="MS:1001141" name="intensity of precursor ion"/>
<cvParam cvRef="PSI-MS" accession="MS:1001105" name="peptide result details"/>
<cvParam accession="MS:1001847" cvRef="PSI-MS" name="reporter ion intensity"/>
<cvParam accession="MS:1001905" cvRef="PSI-MS" name="emPAI value"/>
<cvParam cvRef="MS" accession="MS:1001860" name="protein value: mean of peptide ratios"/>
<cvParam cvRef="MS" accession="MS:1001842" name="peptide PSM count"/>
<cvParam cvRef="MS" accession="MS:1001852" name="normalized protein value"/>

Element <DBIdentificationRef>

Definition:

External database references for the small molecule identification.

Type:

DBIdentificationRefType

Attributes:

Attribute Name	Data Type	Use	Definition
id_ref	xsd:string	required	Reference to the unique identifier of this object in the referenced external file.
searchDatabase_ref	xsd:IDREF	required	Reference to the SearchDatabase object in this file from which this identification was made.

Subelements:

none

Example Context:

Element <DenominatorDataType>

Definition:

Type:

cvParamRefType

Attributes:

none

Subelements:

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

Example Context:

      <DenominatorDataType>
        <cvParam accession="MS:1001847" cvRef="PSI-MS" name="reporter ion intensity"/>
      </DenominatorDataType>

cvParam Mapping Rules:

Path /MzQuantML/RatioList/Ratio/DenominatorDataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Example cvParams:

<cvParam accession="MS:1001903" cvRef="PSI-MS" name="MaxQuant:feature intensity"/>
<cvParam accession="MS:1001847" cvRef="PSI-MS" name="reporter ion intensity"/>
<cvParam cvRef="MS" accession="MS:1001842" name="peptide PSM count"/>

Element <EvidenceRef>

Definition:

Evidence associated with the PeptideConsensus, including mandatory associations to features and optional references to identifications that have been assigned to the feature.

Type:

EvidenceRefType

Attributes:

Attribute Name	Data Type	Use	Definition
assay_refs	xsd:IDREFS	required	A reference to the Assay to which the referenced Feature belongs (e.g. in label-free analyses) or has been assigned (e.g. in label-based analyses). Multiple values MUST only be given for MS2-tag approaches where the same feature quantifies multiple assays.
feature_ref	xsd:IDREF	required	The feature to which this identification has been assigned.
id_refs	listOfStrings	optional	One or more reference to the unique identifiers for objects identifying the relevant Peptide in an external file. This attribute MUST be present if an identificationFile_ref is given.
identificationFile_ref	xsd:IDREF	optional	Reference to the IdentificationFile object in this file. This attribute MUST be present if id_refs are given.

Subelements:

none

Example Context:

<EvidenceRef feature_ref="raw1-PA0958-LFPQTATGFQLQSSEFEGLDLEAGHFTEGK_000000000000000000000000000000-3-1095.8101_Scan_Number_4715" identificationFile_ref="id_file1" id_refs="Scan Number: 4715" assay_refs="assay1"/>

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 <Feature>

Definition:

A region on a (potentially) two-dimensional map of MS1 scans, defined by the retention time, mass over charge and optionally a mass trace. Quantitative values about features can be added in the associated QuantLayers. For techniques that analyse data from single scans e.g. MS2 tagging approaches, a Feature corresponds with the mz of the parent ions only.

Type:

FeatureType

Attributes:

Attribute Name	Data Type	Use	Definition
charge	integerOrNullType	required	The assumed charge of the feature, used to calculate the m/z value. If the charge is unknown the null type MUST be used.
chromatogram_refs	xsd:string	optional	The identifier(s) of the chromatogram from which this feature was detected, for example required for SRM analyses. Multiple values can be provided separated by spaces following the XSD:IDREFS style.
id	xsd:ID	required	Unique identifier for the feature.
mz	xsd:double	required	The monoisotopic peak on the mass over charge axis in daltons over charge.
rawFile_ref	xsd:IDREF	optional	An optional reference to a RawFile element inside a RawFileGroup. The reference MUST be used if multiple RawFiles are provided within a RawFilesGroup, e.g. if pre-fractionation has occurred, and SHOULD not be used otherwise.
rt	doubleOrNullType	required	The centre point of the feature on the retention time axis in minutes. If the retention time is unknown, the value should be null.
spectrum_refs	xsd:string	optional	An optional identifier for an individual spectrum from which this feature was detected, required only for techniques where rt mapping is not appropriate. Multiple values can be provided separated by spaces following the XSD:IDREFS style.

Subelements:

Subelement Name	maxOccurs	Definition
MassTrace	1	The coordinates defining the feature in RT and MZ space, given as boundary points or a series of rectangles, as encoded by the MassTraceEncoding cvParam on the FeatureList.
cvParam	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	unbounded	A single user-defined parameter.

Example Context:

    <Feature id="f_14215451996852426123" rt="5002.86467743247" mz="580.976424828825" charge="3">
      <userParam name="map_index" value="0"/>
      <userParam name="feature_index" value="0"/>
    </Feature>

cvParam Mapping Rules:

Path /MzQuantML/FeatureList/Feature
MAY supply a *child* term of MS:1001828 (feature attribute) one or more times
  e.g.: MS:1001829 (SRM transition ID) 
  e.g.: MS:1002121 (spectral count feature)

Example userParams:

<userParam name="map_index" value="0"/>
<userParam name="feature_index" value="0"/>

Element <FeatureList>

Definition:

All the features identified on a single raw file or raw file group.

Type:

FeatureListType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.
rawFilesGroup_ref	xsd:IDREF	required	Reference to the raw file or group of raw files from which this feature list was generated.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Feature	1	unbounded	A region on a (potentially) two-dimensional map of MS1 scans, defined by the retention time, mass over charge and optionally a mass trace. Quantitative values about features can be added in the associated QuantLayers. For techniques that analyse data from single scans e.g. MS2 tagging approaches, a Feature corresponds with the mz of the parent ions only.
FeatureQuantLayer	0	unbounded	All the data values about features in one raw file or raw file group, such as feature raw intensity, feature RT window size etc.
MS2AssayQuantLayer	0	unbounded	Quant layer for reporting data values about MS2 features (e.g. iTRAQ) related to different assays i.e. the column index MUST refer to Assays defined in the file.
MS2StudyVariableQuantLayer	0	unbounded	Quant layer for reporting data values about MS2 features (e.g. iTRAQ) related to different study variables i.e. the column index MUST refer to StudyVariables defined in the file.
MS2RatioQuantLayer	0	1	Quant layer for reporting data values about MS2 features (e.g. iTRAQ) related to different ratios i.e. the column index MUST refer to Ratio elements defined in the file.
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:

<FeatureList id="featureList_raw1" rawFilesGroup_ref="raw1">
    <Feature spectrum_refs="Scan Number: 1656" charge="2" mz="411.6925" rt="null" id="raw1-PA0958-SADFIGGR_00000000-2-411.6925_Scan_Number_1656"/>
    <Feature spectrum_refs="Scan Number: 1205" charge="2" mz="474.7568" rt="null" id="raw1-PA0958-YVVQSGPAK_000000000-2-474.7568_Scan_Number_1205"/>
    <Feature spectrum_refs="Scan Number: 3667" charge="2" mz="573.2433" rt="null" id="raw1-PA0958-LIVDYPLSIL_0000000000-2-573.2433_Scan_Number_3667"/>
    <Feature spectrum_refs="Scan Number: 3612" charge="2" mz="573.2534" rt="null" id="raw1-PA0958-LIVDYPLSIL_0000000000-2-573.2534_Scan_Number_3612"/>
    <Feature spectrum_refs="Scan Number: 1995" charge="2" mz="687.29" rt="null" id="raw1-PA0958-GELYATYAGETAK_0000000000000-2-687.29_Scan_Number_1995"/>
    <Feature spectrum_refs="Scan Number: 1877" charge="2" mz="687.3034" rt="null" id="raw1-PA0958-GELYATYAGETAK_0000000000000-2-687.3034_Scan_Number_1877"/>
  ...
</FeatureList>

cvParam Mapping Rules:

Path /MzQuantML/FeatureList
MAY supply a *child* term of MS:1001825 (feature list attribute) one or more times
  e.g.: MS:1001826 (mass trace reporting: rectangles) 
  e.g.: MS:1001827 (mass trace reporting: polygons) 
  e.g.: MS:1002122 (counts reporting)

Element <FeatureQuantLayer>

Definition:

All the data values about features in one raw file or raw file group, such as feature raw intensity, feature RT window size etc.

Type:

GlobalQuantLayerType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
ColumnDefinition	1	1	Definition of the data types in each column.
DataMatrix	1	1	A matrix of data stored in rows and columns, as defined in the parent QuantLayer.

Example Context:

    <FeatureQuantLayer id="q_14611336223554821348">
      <ColumnDefinition>
        <Column index="0">
          <DataType>
            <cvParam cvRef="PSI-MS" accession="MS:1001141" name="intensity of precursor ion"/>
          </DataType>
        </Column>        <Column index="1">
  ...
</FeatureQuantLayer>

Element <Feature_refs>

Definition:	Optional references to features on which quantification values about the SmallMolecule in the QuantLayer were based.
Type:	xsd:IDREFS
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="MS" accession="MS:1000914" name="tab delimited text file"/>
</FileFormat>

cvParam Mapping Rules:

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

Path /MzQuantML/InputFiles/MethodFiles/MethodFile/FileFormat
MAY supply a *child* term of MS:1002128 (method file format attribute) only once

Path /MzQuantML/InputFiles/IdentificationFiles/IdentificationFile/FileFormat
MUST supply a *child* term of MS:1001040 (intermediate analysis format) only once
  e.g.: MS:1000742 (Bioworks SRF file) 
  e.g.: MS:1000914 (tab delimited text file) 
  e.g.: MS:1001107 (data stored in database) 
  e.g.: MS:1001199 (Mascot DAT file) 
  e.g.: MS:1001200 (Sequest out file) 
  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 file) 
  et al.

Path /MzQuantML/InputFiles/SourceFile/FileFormat
MUST supply a *child* term of MS:1001040 (intermediate analysis format) only once
  e.g.: MS:1000742 (Bioworks SRF file) 
  e.g.: MS:1000914 (tab delimited text file) 
  e.g.: MS:1001107 (data stored in database) 
  e.g.: MS:1001199 (Mascot DAT file) 
  e.g.: MS:1001200 (Sequest out file) 
  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 file) 
  et al.

Path /MzQuantML/InputFiles/SearchDatabase/FileFormat
MUST supply a *child* term of MS:1001347 (database file formats) only once
  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)

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000914" name="tab delimited text file"/>

Element <GlobalQuantLayer>

Definition:

Depending on context:
1: Global values corresponding to the ProteinGroup such as the total intensity of the protein group in all assays, Anova etc.
2: Global values corresponding to the Protein such as the total intensity of the protein in all assays, Anova etc.
3: Global values corresponding to the Peptide such as the total intensity of peptide in all assays, Anova in a quantitative peptidome experiment etc.
4: Global values corresponding to the small molecule such as the total intensity of the molecule in all assays, Anova etc.

Type:

GlobalQuantLayerType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
ColumnDefinition	1	1	Definition of the data types in each column.
DataMatrix	1	1	A matrix of data stored in rows and columns, as defined in the parent QuantLayer.

Example Context:

<GlobalQuantLayer id="Pep_GQL1">
    <ColumnDefinition>
        <Column index="0">
            <DataType>
                <cvParam accession="MS:1001171" cvRef="PSI-MS" name="Mascot:score"/>
            </DataType>
        </Column>
  ...
</GlobalQuantLayer>

Element <IdentificationFile>

Definition:

A single identification file associated with this analysis.

Type:

IdentificationFileType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	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.
searchDatabase_ref	xsd:IDREF	optional	Reference to the SearchDatabase object in this file from which this identification was made.

Subelements:

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

Example Context:

<IdentificationFile searchDatabase_ref="SD1" location="file://progenesis-post-processor/progenesis-post-processor/src/main/resources/examples/out_CPTAC_Progen_mzid_toyexample.csv" name="out_CPTAC_Progen_mzid_toyexample.csv" id="idfile_1"/>

cvParam Mapping Rules:

Path /MzQuantML/InputFiles/IdentificationFiles/IdentificationFile
MAY supply a *child* term of MS:1002127 (identification file attribute) one or more times

Element <IdentificationFiles>

Definition:

All identification files associated with this quantitation analysis to be referenced elsewhere.

Type:

IdentificationFilesType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
IdentificationFile	1	unbounded	A single identification file associated with this analysis.

Example Context:

<IdentificationFiles>
    <IdentificationFile searchDatabase_ref="SD1" location="file://progenesis-post-processor/progenesis-post-processor/src/main/resources/examples/out_CPTAC_Progen_mzid_toyexample.csv" name="out_CPTAC_Progen_mzid_toyexample.csv" id="idfile_1"/>
</IdentificationFiles>

Element <IdentificationFile_refs>

Definition:	One or more identification files used within this assay.
Type:	xsd:IDREFS
Attributes:	none
Subelements:	none
Example Context:

Element <IdentificationRef>

Definition:

Depending on context:
1: Reference for the identification evidence for peptides from the referenced external file and unique identifier e.g. a link to an mzIdentML file and ID for the ProteinAmbiguityGroup.
2: Reference for the identification evidence for peptides from the referenced external file and unique identifier e.g. a link to an mzIdentML file and ID for the ProteinDetectionHypothesis.

Type:

IdentificationRefType

Attributes:

Attribute Name	Data Type	Use	Definition
id_refs	listOfStrings	required	One or more reference to the unique identifiers for objects identifying the relevant Peptide, Protein or Protein group in an external file.
identificationFile_ref	xsd:IDREF	required	Reference to the IdentificationFile object in this file.

Subelements:

none

Example Context:

Element <InputFiles>

Definition:

All the raw files, identification files and databases used in the quantitation.

Type:

InputFilesType

Attributes:

none

Subelements:

Subelement Name	maxOccurs	Definition
RawFilesGroup	unbounded	The raw file or collection of raw files that together form one unit of analysis. This is mandatory unless raw files were not used for quantitation e.g. spectral counting. Multiple raw files should only be provided within a group if they have been used for sample pre-fractionation which are later summed together.
MethodFiles	1	All methods files associated with this quantitation analysis to be referenced elsewhere, for example used to describe TraML files used in SRM analysis.
IdentificationFiles	1	All identification files associated with this quantitation analysis to be referenced elsewhere.
SearchDatabase	unbounded	A database used for searching mass spectra. Examples include a set of amino acid sequence entries, or annotated spectra libraries.
SourceFile	unbounded	A file from which this MzQuantML instance was created, including potentially MzQuantML files for earlier stages in a workflow.

Graphical Context:

Example Context:

<InputFiles>
    <RawFilesGroup id="RF_GRP1">
        <RawFile location="file:///C:/Users/Gerhard/Documents/SW_Projekte/OwnProjects/ConvertSpecCnts2MzQuant/ConvertSpectCnts2MzQuant/resources/input/MTQ2_1661_60b_GB4_01_5706.mzML" id="RF_1"/>
    </RawFilesGroup>
    <RawFilesGroup id="RF_GRP2">
        <RawFile location="file:///C:/Users/Gerhard/Documents/SW_Projekte/OwnProjects/ConvertSpecCnts2MzQuant/ConvertSpectCnts2MzQuant/resources/input/MTQ2_1662_80b_GB5_01_5707.mzML" id="RF_2"/>
    </RawFilesGroup>
  ...
</InputFiles>

Element <InputObject_refs>

Definition:	References to raw file groups, FeatureList, PeptideConsensusList, ProteinList or ProteinGroupList or QuantLayers that were inputs to the data processing step.
Type:	xsd:IDREFS
Attributes:	none
Subelements:	none
Example Context:	<InputObject_refs>AQL_MEANS_OF_GROUPS</InputObject_refs>

Element <Label>

Definition:

A specification of labels or tags used to define the assay within the raw file, such as heavy labelling or iTRAQ tag mass. The Label and Modification is mandatory so a specific term is provided under Modification for unlabeled sample for label-free and, for example, so-called light samples in a labelling experiment.

Type:

LabelType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Modification	1	unbounded	The modification searched for or used to define the label or tag for quantification. It SHOULD be sourced from UniMod, PSI-MS or PSI-MOD.

Example Context:

      <Label>
        <Modification massDelta="8.0141988132" >
          <cvParam cvRef="PSI-MOD" accession="MOD:00582" name="6x(13)C,2x(15)N labeled L-lysine" value="Lys8"/>
        </Modification>
        <Modification massDelta="10.0082686" >
          <cvParam cvRef="PSI-MOD" accession="MOD:00587" name="6x(13)C,4x(15)N labeled L-arginine" value="Arg10"/>
        </Modification>
  ...
</Label>

Element <MassTrace>

Definition:	The coordinates defining the feature in RT and MZ space, given as boundary points or a series of rectangles, as encoded by the MassTraceEncoding cvParam on the FeatureList.
Type:	psi-mzq:listOfDoubles
Attributes:	none
Subelements:	none
Example Context:	<MassTrace>76.344 1129.574 76.916 1131.074</MassTrace>
Example cvParams:	<cvParam accession="MS:1001826" cvRef="PSI-MS" name="mass trace reporting: rectangles"/>

Element <MethodFile>

Definition:

A single methods file associated with this analysis e.g. a TraML file used for SRM analysis.

Type:

MethodFileType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	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	0	1	The format of the ExternalData file, for example "tiff" for image files.

Example Context:

Element <MethodFiles>

Definition:

All methods files associated with this quantitation analysis to be referenced elsewhere, for example used to describe TraML files used in SRM analysis.

Type:

MethodFilesType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
MethodFile	1	unbounded	A single methods file associated with this analysis e.g. a TraML file used for SRM analysis.

Example Context:

Element <Modification>

Definition:

The modification searched for or used to define the label or tag for quantification. It SHOULD be sourced from UniMod, PSI-MS or PSI-MOD.

Type:

ModParamType

Attributes:

Attribute Name	Data Type	Use	Definition
massDelta	xsd:float	optional	The mass delta of the modification in Daltons
residues	listOfChars	optional	The residue(s) to which the modification has been applied.

Subelements:

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

Example Context:

<Modification monoisotopicMassDelta="15.994915" location="13">
    <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
    <cvParam accession="MS:1001524" cvRef="PSI-MS" unitCvRef="UO" unitName="dalton" unitAccession="UO:0000221" value="63.998285" name="fragment neutral loss"/>
</Modification>

cvParam Mapping Rules:

Path /MzQuantML/PeptideConsensusList/PeptideConsensus/Modification
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) 
MAY supply a *child* term of MOD:00000 (protein modification) only once

Path /MzQuantML/AssayList/Assay/Label/Modification
MUST supply a *child* term of UNIMOD:0 (unimod root node) only once
MUST 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:1002038 (unlabeled sample) only once
MUST supply a *child* term of MOD:00000 (protein modification) only once

Path /MzQuantML/SmallMoleculeList/SmallMolecule/Modification
MAY supply a *child* term of MS:1002119 (small molecule modification attribute) only once

Example cvParams:

<cvParam accession="MS:1002038" cvRef="PSI-MS" name="unlabeled sample"/>
<cvParam accession="MOD:00582" cvRef="PSI-MOD" value="Lys8" name="6x(13)C,2x(15)N labeled L-lysine"/>
<cvParam accession="MOD:00587" cvRef="PSI-MOD" value="Arg10" name="6x(13)C,4x(15)N labeled L-arginine"/>
<cvParam accession="MOD:01522" cvRef="PSI-MOD" value="114" name="iTRAQ4plex-114 reporter fragment"/>
<cvParam accession="MOD:01523" cvRef="PSI-MOD" value="115" name="iTRAQ4plex-115 reporter fragment"/>
<cvParam accession="MOD:01524" cvRef="PSI-MOD" value="116" name="iTRAQ4plex-116 reporter fragment"/>
<cvParam accession="MOD:01525" cvRef="PSI-MOD" value="117" name="iTRAQ4plex-117, mTRAQ heavy, reporter fragment"/>
<cvParam accession="UNIMOD:214" cvRef="UNIMOD" name="iTRAQ4plex"/>
<cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
<cvParam accession="MS:1001524" cvRef="PSI-MS" unitCvRef="UO" unitName="dalton" unitAccession="UO:0000221" value="63.998285" name="fragment neutral loss"/>

Element <MS2AssayQuantLayer>

Definition:

Quant layer for reporting data values about MS2 features (e.g. iTRAQ) related to different assays i.e. the column index MUST refer to Assays defined in the file.

Type:

QuantLayerType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
DataType	1	1	Type of data in the column e.g. cvParam = "Intensity\|RawAbundance\|NormalisedAbundance".
ColumnIndex	1	1	Space separated unique identifiers for each column of data, MUST refer to an object in the file i.e. Ratio elements.
DataMatrix	1	1	A matrix of data stored in rows and columns, as defined in the parent QuantLayer.

Example Context:

<MS2AssayQuantLayer id="MS2AssayQuantLayer_raw1_reporter_ion_intensity">
    <DataType>
        <cvParam accession="MS:1001847" cvRef="PSI-MS" name="reporter ion intensity"/>
    </DataType>
    <ColumnIndex>_114 _115 _116 _117</ColumnIndex>
    <DataMatrix>
        <Row object_ref="raw1-sp_P00924_ENO1_YEAST-SVYDSR_00000000-2-435.7178_SIR_62">3.118874006098781 2.628302416711611 1.9418652317472234 1.8073460629379474</Row>
  ...
</MS2AssayQuantLayer>

Element <MS2RatioQuantLayer>

Definition:

Quant layer for reporting data values about MS2 features (e.g. iTRAQ) related to different ratios i.e. the column index MUST refer to Ratio elements defined in the file.

Type:

RatioQuantLayerType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
ColumnIndex	1	1	Space separated unique identifiers for each column of data, MUST refer to an object in the file i.e. Ratio elements.
DataMatrix	1	1	A matrix of data stored in rows and columns, as defined in the parent QuantLayer.

Example Context:

Element <MS2StudyVariableQuantLayer>

Definition:

Quant layer for reporting data values about MS2 features (e.g. iTRAQ) related to different study variables i.e. the column index MUST refer to StudyVariables defined in the file.

Type:

QuantLayerType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
DataType	1	1	Type of data in the column e.g. cvParam = "Intensity\|RawAbundance\|NormalisedAbundance".
ColumnIndex	1	1	Space separated unique identifiers for each column of data, MUST refer to an object in the file i.e. Ratio elements.
DataMatrix	1	1	A matrix of data stored in rows and columns, as defined in the parent QuantLayer.

Example Context:

Element <NumeratorDataType>

Definition:

Type:

cvParamRefType

Attributes:

none

Subelements:

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

Example Context:

      <NumeratorDataType>
        <cvParam accession="MS:1001847" cvRef="PSI-MS" name="reporter ion intensity"/>
      </NumeratorDataType>

cvParam Mapping Rules:

Path /MzQuantML/RatioList/Ratio/NumeratorDataType
MUST supply a *child* term of MS:1001805 (quantification datatype) only once
  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.
MUST supply a *child* term of MS:1001405 (spectrum identification result details) only once
  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) 
  e.g.: MS:1001088 (protein description) 
  et al.

Example cvParams:

<cvParam accession="MS:1001903" cvRef="PSI-MS" name="MaxQuant:feature intensity"/>
<cvParam accession="MS:1001847" cvRef="PSI-MS" name="reporter ion intensity"/>
<cvParam cvRef="MS" accession="MS:1001842" name="peptide PSM count"/>

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:ID	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.
ParentOrganization	1	The containing organization (the university or business which a lab belongs to, etc.)

Example Context:

<Organization id="ORG_MPC" name="MPC - Medizinisches Proteom Center, Bochum">
    <ParentOrganization organization_ref="ORG_Univ_Bochum"/>
</Organization>

cvParam Mapping Rules:

Path /MzQuantML/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

Element <OutputObject_refs>

Definition:	References to raw file groups, FeatureList, PeptideConsensusList, ProteinList or ProteinGroupList or QuantLayers that were the outputs of the data processing step.
Type:	xsd:IDREFS
Attributes:	none
Subelements:	none
Example Context:

Element <ParentOrganization>

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:IDREF	required	A reference to the organization this contact belongs to.

Subelements:

none

Example Context:

<ParentOrganization organization_ref="ORG_Univ_Bochum"/>

Element <PeptideConsensus>

Definition:

An element representing a peptide in different assays that may or may not have been identified. If it has been identified, the sequence and modification(s) SHOULD be reported. Within the parent list, it is allowed for there to be multiple instances of the same peptide sequence, for example capturing different charge states or different modifications, if they are differentially quantified. If peptides with different charge states are aggregated, they should be represented by a single PeptideConsensus element.

Type:

PeptideConsensusType

Attributes:

Attribute Name	Data Type	Use	Definition
charge	listOfIntegers	required	The charge of this instance of Peptide. If more than one value is provided, it is assumed that this Peptide element is summarising multiple charge states of the Peptide.
id	xsd:ID	required	The unique identifier for the object within the file.
searchDatabase_ref	xsd:IDREF	optional	The search database from which this peptide was identified

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
PeptideSequence	0	1	The amino acid sequence of the (poly)peptide. If a substitution modification has been found, the original sequence should be reported. The peptide sequence is mandatory unless this is a PeptideConsensus that has not been assigned to a peptide sequence.
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 an _unknown modification_CV term that MUST be used instead. A neutral loss should be defined as an additional CVParam within Modification.
EvidenceRef	1	unbounded	Evidence associated with the PeptideConsensus, including mandatory associations to features and optional references to identifications that have been assigned to the feature.
cvParam	0	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	0	unbounded	A single user-defined parameter.

Example Context:

<PeptideConsensus searchDatabase_ref="Pseudomonas" charge="3" id="PA0958-LFPQTATGFQLQSSEFEGLDLEAGHFTEGK_000000000000000000000000000000">
    <PeptideSequence>LFPQTATGFQLQSSEFEGLDLEAGHFTEGK</PeptideSequence>
    <EvidenceRef feature_ref="raw1-PA0958-LFPQTATGFQLQSSEFEGLDLEAGHFTEGK_000000000000000000000000000000-3-1095.76_Scan_Number_4429" identificationFile_ref="id_file1" id_refs="Scan Number: 4429" assay_refs="assay1"/>
    <EvidenceRef feature_ref="raw1-PA0958-LFPQTATGFQLQSSEFEGLDLEAGHFTEGK_000000000000000000000000000000-3-1095.8_Scan_Number_4619" identificationFile_ref="id_file1" id_refs="Scan Number: 4619" assay_refs="assay1"/>
    <EvidenceRef feature_ref="raw1-PA0958-LFPQTATGFQLQSSEFEGLDLEAGHFTEGK_000000000000000000000000000000-3-1095.8101_Scan_Number_4715" identificationFile_ref="id_file1" id_refs="Scan Number: 4715" assay_refs="assay1"/>
    <EvidenceRef feature_ref="raw1-PA0958-LFPQTATGFQLQSSEFEGLDLEAGHFTEGK_000000000000000000000000000000-3-1095.86_Scan_Number_4377" identificationFile_ref="id_file1" id_refs="Scan Number: 4377" assay_refs="assay1"/>
    <EvidenceRef feature_ref="raw1-PA0958-LFPQTATGFQLQSSEFEGLDLEAGHFTEGK_000000000000000000000000000000-3-1095.86_Scan_Number_4477" identificationFile_ref="id_file1" id_refs="Scan Number: 4477" assay_refs="assay1"/>
  ...
</PeptideConsensus>

cvParam Mapping Rules:

Path /MzQuantML/PeptideConsensusList/PeptideConsensus
MAY supply a *child* term of MS:1002116 (peptide consensus attribute) only once

Element <PeptideConsensusList>

Definition:

The list of all peptides for which quantitation values are reported.

Type:

PeptideConsensusListType

Attributes:

Attribute Name	Data Type	Use	Definition
finalResult	xsd:boolean	required	Multiple peptide lists are allowed for reporting the evidence trail to create a final peptide list, but the final result e.g. to be loaded into a database, MUST be flagged with finalResult=true
id	xsd:ID	required	The unique identifier for the object within the file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
PeptideConsensus	1	unbounded	An element representing a peptide in different assays that may or may not have been identified. If it has been identified, the sequence and modification(s) SHOULD be reported. Within the parent list, it is allowed for there to be multiple instances of the same peptide sequence, for example capturing different charge states or different modifications, if they are differentially quantified. If peptides with different charge states are aggregated, they should be represented by a single PeptideConsensus element.
GlobalQuantLayer	0	unbounded	Global values corresponding to the small molecule such as the total intensity of the molecule in all assays, Anova etc.
AssayQuantLayer	0	unbounded	Quant layer for reporting data values about small molecules related to different assays i.e. the column index MUST refer to Assays defined in the file.
StudyVariableQuantLayer	0	unbounded	Quant layer for reporting data values about small molecules related to different study variables i.e. the column index MUST refer to StudyVariables defined in the file.
RatioQuantLayer	0	1	Quant layer for reporting data values about small molecules related to different ratios i.e. the column index MUST refer to Ratio elements defined in the file.
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:

<PeptideConsensusList finalResult="true" id="PepList1">
    <PeptideConsensus searchDatabase_ref="SD1" charge="2" id="pep_GAPEIDVLEGETDTK_2_21711">
        <PeptideSequence>GAPEIDVLEGETDTK</PeptideSequence>
        <EvidenceRef feature_ref="ft_216" identificationFile_ref="idfile_1" id_refs="SII_69413_1" assay_refs="ass_0"/>
        <EvidenceRef feature_ref="ft_217" identificationFile_ref="idfile_1" id_refs="SII_69415_1" assay_refs="ass_1"/>
        <EvidenceRef feature_ref="ft_218" identificationFile_ref="idfile_1" id_refs="SII_69417_1" assay_refs="ass_2"/>
        <EvidenceRef feature_ref="ft_219" identificationFile_ref="idfile_1" id_refs="SII_69414_1" assay_refs="ass_3"/>
  ...
</PeptideConsensusList>

cvParam Mapping Rules:

Path /MzQuantML/PeptideConsensusList
MAY supply a *child* term of MS:1002115 (peptide consensus list attribute) only once

Element <PeptideConsensus_refs>

Definition:	The peptides on which the quantitative protein values in the QuantLayer(s) are based. Note this should not be used to report all peptides that can support the protein identification, only quantitation.
Type:	xsd:IDREFS
Attributes:	none
Subelements:	none
Example Context:	<PeptideConsensus_refs>pep_LKQSAEEQAQAQAQAQAAAEK pep_LLDAQLSTGGIVDPSK pep_DLLQQFR pep_LSVYTALQR pep_SIQEELQHLR pep_QLLSPGTALILLEAQAASGFLLDPVR pep_LTVEEAVR pep_YSELTTLTSQYIK pep_SFLSEKDSLLQR pep_CITDPQTGLCLLPLK pep_YLYGTGAVAGVYLPGSR pep_IDSAEWGVDLPSVEAQLGSHR pep_GYYSPYSVSGSGSTAGSR pep_LAAISEATR pep_SILDEELQR pep_EVAEADSVR pep_VTLVQTLEIQR pep_TLQEEHVTVAQLR pep_DTHDQLSEPSEVR pep_AFCGFEDPR pep_LQLEACETR pep_LQAEEVAQQK pep_VYHDPSTQEPVTYSQLQQR pep_APVPASELLDAK pep_SQVEEELFSVR pep_AQVEQELTTLR pep_HISDLYEDLR pep_WQAVLAQTDVR pep_AQAELEAQELQR pep_AQAEAQQPVFNTLR pep_SDQLTGLSLLPLSEK pep_LKAEAELLQQQK pep_LAQGHTTVAELTQR pep_SLAAEEEAAR pep_LTVDEAVR pep_LSVAAQEAAR pep_FLEVQYLTGGLIEPDTPGR pep_ARQEEVYSELQAR pep_EAQAVPATLQELEATK pep_AALAHSEIATTQAASTK pep_SSSVGSSSSYPISSAGPR pep_DAPDGPSVEAEPEYTFEGLR pep_TQLASWSDPTEETGPVAGILDTETLEK pep_YLQDLLAWVEENQR pep_GGELVYTDTEAR pep_ALVPAAELLDSGVISHELYQQLQR pep_QLQLAQEAAQK pep_QSAEEQAQAQAQAQAAAEK pep_GLLSAEVAR pep_LLDAQLATGGIVDPR pep_QEQIQAVPIANCQAAR pep_LQNVQIALDYLR pep_LTVNEAVK pep_CVEDPETGLR pep_NLVDNITGQR pep_LECLQR pep_VSLDEALQR pep_VLALPEPSPAAPTLR pep_SWSLVTFR pep_VPLDVAYAR pep_QVQVALETAQR pep_LPVDVAYQR pep_IISLETYNLFR pep_LSYTQLLK pep_GFFDPNTHENLTYLQLLER pep_LAEVEAALEK pep_QITVEELVR pep_ESADPLSAWLQDAK pep_AKLEQLFQDEVAK pep_VQSGSESVIQEYVDLR pep_DLLQPEVAVALLEAQAGTGHIIDPATSAR pep_AHLLTSGPPPDEQDFIQAYEEVR pep_ALLEEIER pep_VTQLLER pep_FLEGTSCIAGVFVDATK pep_RQEQIQAVPIANCQAAR pep_SLLAWQSLSR pep_VIYQSLEGAVQAGQLK pep_LLFNDVQTLK pep_QTNLENLDQAFSVAER pep_LLEAAAQSSK pep_LTAEDLYEAR pep_LLDPEDVDVPQPDEK pep_SAEVELQSK pep_QLAEEDLAQQR pep_DPYSGQSVSLFQALK pep_QLLEEELAR pep_QLEMSAEAER pep_LLLWSQR</PeptideConsensus_refs>

Element <PeptideSequence>

Definition:	The amino acid sequence of the (poly)peptide. If a substitution modification has been found, the original sequence should be reported. The peptide sequence is mandatory unless this is a PeptideConsensus that has not been assigned to a peptide sequence.
Type:	sequence
Attributes:	none
Subelements:	none
Example Context:	<PeptideSequence>DQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPGSETSDAK</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:ID	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="Mayer" firstName="Gerhard" id="PERS_GM" name="Gerhard Mayer">
    <Affiliation organization_ref="ORG_MPC"/>
</Person>

cvParam Mapping Rules:

Path /MzQuantML/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

Element <ProcessingMethod>

Definition:

Description of one step within the data processing pipeline.

Type:

ProcessingMethodType

Attributes:

Attribute Name	Data Type	Use	Definition
order	xsd:positiveInteger	required	This attributes allows a series of consecutive steps to be placed in the correct order, start counting from 1.

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:

<ProcessingMethod order="3">
    <userParam value="feature detection and quantitation" name="Plugin type"/>
    <userParam value="iTraqQuantitation" name="Plugin name"/>
    <userParam value="examples/paper_iTraq4plex/iTraqQuantitationPSIMOD.xtp" name="Plugin configuration file"/>
    <userParam value="mean" name="Feature to peptide inference method"/>
    <userParam value="weightedAverage" name="Peptide to protein inference method"/>
    <userParam value="sum" name="Assay to Study Variables inference method"/>
  ...
</ProcessingMethod>

cvParam Mapping Rules:

Path /MzQuantML/DataProcessingList/DataProcessing/ProcessingMethod
MAY supply a *child* term of MS:1001861 (quantification data processing) one or more times
  e.g.: MS:1001862 (normalization to mean of sum of all proteins) 
  e.g.: MS:1001863 (quantile normalization, proteins) 
  e.g.: MS:1001864 (quantile normalization, peptides) 
  e.g.: MS:1001865 (Progenesis automatic alignment) 
  e.g.: MS:1001866 (Progenesis manual alignment) 
  e.g.: MS:1001867 (Progenesis normalization) 
  e.g.: MS:1002070 (t-test) 
  e.g.: MS:1002071 (ANOVA-test) 
  e.g.: MS:1002211 (Variance stabilizing normalization)

Example cvParams:

<cvParam accession="MS:1001865" cvRef="PSI-MS" name="Progenesis automatic alignment"/>
<cvParam accession="MS:1001867" cvRef="PSI-MS" name="Progenesis normalization"/>
<cvParam accession="MS:1001861" cvRef="PSI-MS" name="quantification data processing"/>
<cvParam cvRef="MS" accession="MS:1001862" name="normalization to mean of sum of all proteins"/>

Example userParams:

<userParam name="Conversion to mzML format" value="ProteoWizard" />
<userParam name="Data filtering" value="FileFilter" />
<userParam name="Data processing action" value="SILACAnalyzer" />
<userParam name="Peak picking" value="SILACAnalyzer" />
<userParam name="Quantitation" value="SILACAnalyzer" />
<userParam value="load identification" name="Plugin type"/>
<userParam value="loadMzIdentML" name="Plugin name"/>
<userParam value="examples/paper_iTraq4plex/loadMzIdentML.xtp" name="Plugin configuration file"/>
<userParam value="mean" name="Feature to peptide inference method"/>
<userParam value="weightedAverage" name="Peptide to protein inference method"/>
<userParam value="sum" name="Assay to Study Variables inference method"/>
<userParam value="true" name="Protein ratio calculation infer from peptide ratio"/>
<userParam name="Identification mapping" value="IDMapper" />

Element <Protein>

Definition:

One protein that has been quantified in the file, including references to peptides on which the quantification is based.

Type:

ProteinType

Attributes:

Attribute Name	Data Type	Use	Definition
accession	xsd:string	required	The accession of the protein in the source database. In most use cases it is expected that accession will be unique within the ProteinList, although in rare cases there may be different entries for the same protein for example if quantifying different PTMs on the same protein.
id	xsd:ID	required	The unique identifier for the object within the file.
searchDatabase_ref	xsd:IDREF	required	The search database from which this protein was identified

Subelements:

Subelement Name	maxOccurs	Definition
IdentificationRef	unbounded	Reference for the identification evidence for peptides from the referenced external file and unique identifier e.g. a link to an mzIdentML file and ID for the ProteinDetectionHypothesis.
PeptideConsensus_refs	1	The peptides on which the quantitative protein values in the QuantLayer(s) are based. Note this should not be used to report all peptides that can support the protein identification, only quantitation.
cvParam	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	unbounded	A single user-defined parameter.

Example Context:

<Protein searchDatabase_ref="SD1" accession="IPI00421271" id="prot_275">
    <PeptideConsensus_refs>pep_LKQSAEEQAQAQAQAQAAAEK pep_LLDAQLSTGGIVDPSK pep_DLLQQFR pep_LSVYTALQR pep_SIQEELQHLR pep_QLLSPGTALILLEAQAASGFLLDPVR pep_LTVEEAVR pep_YSELTTLTSQYIK pep_SFLSEKDSLLQR pep_CITDPQTGLCLLPLK pep_YLYGTGAVAGVYLPGSR pep_IDSAEWGVDLPSVEAQLGSHR pep_GYYSPYSVSGSGSTAGSR pep_LAAISEATR pep_SILDEELQR pep_EVAEADSVR pep_VTLVQTLEIQR pep_TLQEEHVTVAQLR pep_DTHDQLSEPSEVR pep_AFCGFEDPR pep_LQLEACETR pep_LQAEEVAQQK pep_VYHDPSTQEPVTYSQLQQR pep_APVPASELLDAK pep_SQVEEELFSVR pep_AQVEQELTTLR pep_HISDLYEDLR pep_WQAVLAQTDVR pep_AQAELEAQELQR pep_AQAEAQQPVFNTLR pep_SDQLTGLSLLPLSEK pep_LKAEAELLQQQK pep_LAQGHTTVAELTQR pep_SLAAEEEAAR pep_LTVDEAVR pep_LSVAAQEAAR pep_FLEVQYLTGGLIEPDTPGR pep_ARQEEVYSELQAR pep_EAQAVPATLQELEATK pep_AALAHSEIATTQAASTK pep_SSSVGSSSSYPISSAGPR pep_DAPDGPSVEAEPEYTFEGLR pep_TQLASWSDPTEETGPVAGILDTETLEK pep_YLQDLLAWVEENQR pep_GGELVYTDTEAR pep_ALVPAAELLDSGVISHELYQQLQR pep_QLQLAQEAAQK pep_QSAEEQAQAQAQAQAAAEK pep_GLLSAEVAR pep_LLDAQLATGGIVDPR pep_QEQIQAVPIANCQAAR pep_LQNVQIALDYLR pep_LTVNEAVK pep_CVEDPETGLR pep_NLVDNITGQR pep_LECLQR pep_VSLDEALQR pep_VLALPEPSPAAPTLR pep_SWSLVTFR pep_VPLDVAYAR pep_QVQVALETAQR pep_LPVDVAYQR pep_IISLETYNLFR pep_LSYTQLLK pep_GFFDPNTHENLTYLQLLER pep_LAEVEAALEK pep_QITVEELVR pep_ESADPLSAWLQDAK pep_AKLEQLFQDEVAK pep_VQSGSESVIQEYVDLR pep_DLLQPEVAVALLEAQAGTGHIIDPATSAR pep_AHLLTSGPPPDEQDFIQAYEEVR pep_ALLEEIER pep_VTQLLER pep_FLEGTSCIAGVFVDATK pep_RQEQIQAVPIANCQAAR pep_SLLAWQSLSR pep_VIYQSLEGAVQAGQLK pep_LLFNDVQTLK pep_QTNLENLDQAFSVAER pep_LLEAAAQSSK pep_LTAEDLYEAR pep_LLDPEDVDVPQPDEK pep_SAEVELQSK pep_QLAEEDLAQQR pep_DPYSGQSVSLFQALK pep_QLLEEELAR pep_QLEMSAEAER pep_LLLWSQR</PeptideConsensus_refs>
</Protein>

cvParam Mapping Rules:

Path /MzQuantML/ProteinList/Protein
MAY supply a *child* term of MS:1000884 (protein attribute) one or more times
  e.g.: MS:1000883 (protein short name) 
  e.g.: MS:1000885 (protein accession) 
  e.g.: MS:1000886 (protein name) 
  e.g.: MS:1000933 (protein modifications) 
  e.g.: MS:1000934 (gene name)

Example userParams:

<userParam name="Molecular weight" value="69.1"/>
<userParam name="Number of peptides" value="48"/>

Element <ProteinGroup>

Definition:

A grouping of quantified proteins based on ambiguous assignment of peptide evidence to protein identification. The semantics of elements within the group, such as a leading protein or those sharing equal evidence can be reported using cvParams.

Type:

ProteinGroupType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.
searchDatabase_ref	xsd:IDREF	required	The search database from which this protein group was identified

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
IdentificationRef	0	unbounded	Reference for the identification evidence for peptides from the referenced external file and unique identifier e.g. a link to an mzIdentML file and ID for the ProteinDetectionHypothesis.
ProteinRef	1	unbounded	A reference to one of the Proteins contained within this group, along with CV terms describing the role it plays within the group, such as representative or anchor protein, same set or sub-set.
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 /MzQuantML/ProteinGroupList/ProteinGroup
MAY supply a *child* term of MS:1002113 (protein group attribute) one or more times

Element <ProteinGroupList>

Definition:

The list of all groups of proteins with conflicting evidence for which quantitation values are being reported along with quantitative values about those protein groups. If quantitation is done on individual proteins only, ProteinGroupsList should not be included.

Type:

ProteinGroupListType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
ProteinGroup	1	unbounded	A grouping of quantified proteins based on ambiguous assignment of peptide evidence to protein identification. The semantics of elements within the group, such as a leading protein or those sharing equal evidence can be reported using cvParams.
GlobalQuantLayer	0	unbounded	Global values corresponding to the small molecule such as the total intensity of the molecule in all assays, Anova etc.
AssayQuantLayer	0	unbounded	Quant layer for reporting data values about small molecules related to different assays i.e. the column index MUST refer to Assays defined in the file.
StudyVariableQuantLayer	0	unbounded	Quant layer for reporting data values about small molecules related to different study variables i.e. the column index MUST refer to StudyVariables defined in the file.
RatioQuantLayer	0	1	Quant layer for reporting data values about small molecules related to different ratios i.e. the column index MUST refer to Ratio elements defined in the file.
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:

cvParam Mapping Rules:

Path /MzQuantML/ProteinGroupList
MAY supply a *child* term of MS:1002112 (protein group list attribute) one or more times

Element <ProteinList>

Definition:

The list of all individual proteins (i.e. ungrouped) for which quantitation values are being reported. If quantitation is done on protein groups, the constituent proteins should be listed here with no QuantLayers.

Type:

ProteinListType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Protein	1	unbounded	One protein that has been quantified in the file, including references to peptides on which the quantification is based.
GlobalQuantLayer	0	unbounded	Global values corresponding to the small molecule such as the total intensity of the molecule in all assays, Anova etc.
AssayQuantLayer	0	unbounded	Quant layer for reporting data values about small molecules related to different assays i.e. the column index MUST refer to Assays defined in the file.
StudyVariableQuantLayer	0	unbounded	Quant layer for reporting data values about small molecules related to different study variables i.e. the column index MUST refer to StudyVariables defined in the file.
RatioQuantLayer	0	1	Quant layer for reporting data values about small molecules related to different ratios i.e. the column index MUST refer to Ratio elements defined in the file.
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:

<ProteinList id="ProteinList">
    <Protein searchDatabase_ref="SDB_itraq_test_db" accession="sp_P00924_ENO1_YEAST" id="DBSeq_1_sp_P00924_ENO1_YEAST"/>
    <Protein searchDatabase_ref="SDB_itraq_test_db" accession="sp_P02769_ALBU_BOVIN" id="DBSeq_1_sp_P02769_ALBU_BOVIN"/>
    <Protein searchDatabase_ref="SDB_itraq_test_db" accession="sp_P62894.2_CYC_BOVIN" id="DBSeq_1_sp_P62894.2_CYC_BOVIN"/>
    <Protein searchDatabase_ref="SDB_itraq_test_db" accession="sp_P00489_PYGM_RABIT" id="DBSeq_1_sp_P00489_PYGM_RABIT"/>
    <AssayQuantLayer id="AssayQuantLayer_Proteins_reporter_ion_intensity">
        <DataType>
  ...
</ProteinList>

cvParam Mapping Rules:

Path /MzQuantML/ProteinList
MAY supply a *child* term of MS:1002114 (protein list attribute) one or more times

Element <ProteinRef>

Definition:

A reference to one of the Proteins contained within this group, along with CV terms describing the role it plays within the group, such as representative or anchor protein, same set or sub-set.

Type:

ProteinRefType

Attributes:

Attribute Name	Data Type	Use	Definition
protein_ref	xsd:IDREF	required	Reference to one of the proteins within the ProteinList.

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:

cvParam Mapping Rules:

Path /MzQuantML/ProteinGroupList/ProteinGroup/ProteinRef
SHOULD 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)

Element <Provider>

Definition:

The provider of the document in terms of the Contact and the software the produced the document instance.

Type:

ProviderType

Attributes:

Attribute Name	Data Type	Use	Definition
analysisSoftware_ref	xsd:IDREF	optional	The Software that produced the document instance.
id	xsd:ID	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 role of the Contact that provided the document instance.

Graphical Context:

Example Context:

<Provider analysisSoftware_ref="Microsoft_Excel_2007" id="PROV_1" name="Gerhard Mayer">
    <ContactRole contact_ref="PERS_GM">
        <Role>
            <cvParam cvRef="MS" accession="MS:1001271" name="researcher"/>
        </Role>
    </ContactRole>
</Provider>

Element <Ratio>

Definition:

The setup of a ratio of study variables or assays that is referenced elsewhere in the file. It is expected that the numerator and denominator MUST both be Assays or MUST both be StudyVariables. However, StudyVariables MAY contain 1 to many Assays, thus allowing more complex ratios to be constructed if needed via use of StudyVariables with unbalanced numbers of Assays.

Type:

RatioType

Attributes:

Attribute Name	Data Type	Use	Definition
denominator_ref	xsd:IDREF	required	Reference to a StudyVariable or an Assay.
id	xsd:ID	required	The unique identifier for the object within the file.
name	xsd:string	optional	Optional name for the ratio.
numerator_ref	xsd:IDREF	required	Reference to a StudyVariable or an Assay.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
RatioCalculation	0	1	Information should be provided about how ratios are calculated if they differ from simple division of numerator by denominator
NumeratorDataType	1	1	Type of data used for the numerator of the ratio e.g. cvParam = "Intensity\|RawAbundance\|NormalisedAbundance\|PeptideCount\|ConfidenceScore\|Anova\|MaxFoldChange\|...."
DenominatorDataType	1	1	Type of data used for the denominator of the ratio e.g. cvParam = "Intensity\|RawAbundance\|NormalisedAbundance\|PeptideCount\|ConfidenceScore\|Anova\|MaxFoldChange\|...."

Example Context:

<Ratio numerator_ref="ASS_0" denominator_ref="ASS_5" id="RATIO_vIa_30min_vs_vIb_120min" name="vIa_30min_vs_vIb_120min">
    <NumeratorDataType>
        <cvParam cvRef="MS" accession="MS:1001842" name="peptide PSM count"/>
    </NumeratorDataType>
    <DenominatorDataType>
        <cvParam cvRef="MS" accession="MS:1001842" name="peptide PSM count"/>
    </DenominatorDataType>
  ...
</Ratio>

Element <RatioCalculation>

Definition:

Information should be provided about how ratios are calculated if they differ from simple division of numerator by denominator

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:

      <RatioCalculation>
        <userParam name="Simple ratio calc"/>
        <userParam name="light to medium/.../heavy"/>
        <cvParam cvRef="PSI-MS" accession="MS:1001848" name="simple ratio of two values"/>
      </RatioCalculation>

cvParam Mapping Rules:

Path /MzQuantML/RatioList/Ratio/RatioCalculation
SHOULD supply term MS:1001848 (simple ratio of two values) only once

Example cvParams:

<cvParam accession="MS:1001848" cvRef="PSI-MS" name="simple ratio of two values"/>

Example userParams:

<userParam name="Simple ratio calc"/>
<userParam name="light to medium/.../heavy"/>

Element <RatioList>

Definition:

The definition of ratios of study variables or assays, referenced elsewhere in the document.

Type:

RatioListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Ratio	1	unbounded	The setup of a ratio of study variables or assays that is referenced elsewhere in the file. It is expected that the numerator and denominator MUST both be Assays or MUST both be StudyVariables. However, StudyVariables MAY contain 1 to many Assays, thus allowing more complex ratios to be constructed if needed via use of StudyVariables with unbalanced numbers of Assays.

Graphical Context:

Example Context:

<RatioList>
    <Ratio numerator_ref="ASS_0" denominator_ref="ASS_5" id="RATIO_vIa_30min_vs_vIb_120min" name="vIa_30min_vs_vIb_120min">
        <NumeratorDataType>
            <cvParam cvRef="MS" accession="MS:1001842" name="peptide PSM count"/>
        </NumeratorDataType>
        <DenominatorDataType>
            <cvParam cvRef="MS" accession="MS:1001842" name="peptide PSM count"/>
  ...
</RatioList>

Element <RatioQuantLayer>

Definition:

Depending on context:
1: Quant layer for reporting data values about protein groups related to different ratios i.e. the column index MUST refer to Ratio elements defined in the file.
2: Quant layer for reporting data values about proteins related to different ratios i.e. the column index MUST refer to Ratio elements defined in the file.
3: Quant layer for reporting data values about peptides related to different ratios i.e. the column index MUST refer to Ratio elements defined in the file.
4: Quant layer for reporting data values about small molecules related to different ratios i.e. the column index MUST refer to Ratio elements defined in the file.

Type:

RatioQuantLayerType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
ColumnIndex	1	1	Space separated unique identifiers for each column of data, MUST refer to an object in the file i.e. Ratio elements.
DataMatrix	1	1	A matrix of data stored in rows and columns, as defined in the parent QuantLayer.

Example Context:

<RatioQuantLayer id="RatioQuantLayer_Proteins">
    <ColumnIndex>ratio_SV_A_B ratio_assay_115_114 ratio_assay_116_114 ratio_assay_117_114</ColumnIndex>
    <DataMatrix>
        <Row object_ref="DBSeq_1_sp_P00924_ENO1_YEAST">1.5688765800335178 0.8774300605025027 0.5904007385417112 0.5794867184130507</Row>
        <Row object_ref="DBSeq_1_sp_P02769_ALBU_BOVIN">0.533639611558188 1.6288166536635666 1.9181070399106477 2.8238352619946046</Row>
        <Row object_ref="DBSeq_1_sp_P62894.2_CYC_BOVIN">0.8750566475401153 1.1763661339620837 1.144083486486904 1.3894599209341105</Row>
        <Row object_ref="DBSeq_1_sp_P00489_PYGM_RABIT">0.9404534810133465 1.099880188336868 1.0193601079613397 1.2766021817677453</Row>
  ...
</RatioQuantLayer>

Element <RawFile>

Definition:

A raw mass spectrometry output file that has been analysed e.g. in mzML format. The same raw file can be referenced in multiple assays, for example if it contains multiple samples differentially labelled or tagged. Note, the name raw file does not necessarily imply that the file has not been processed, since in some quant methods, processed peak list formats such as MGF or DTA can be used, which could be referenced here.

Type:

RawFileType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	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.
methodFile_ref	xsd:IDREF	optional	An optional reference to a methods file used in association with a raw file, for example a TraML file used for SRM analysis.
name	xsd:string	optional	The potentially ambiguous common identifier, such as a human-readable name for the instance.

Subelements:

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

Example Context:

<RawFile location="file:///C:/Users/Gerhard/Documents/SW_Projekte/OwnProjects/ConvertSpecCnts2MzQuant/ConvertSpectCnts2MzQuant/resources/input/MTQ2_1654_20a_GA4_01_5698.mzML" id="RF_10"/>

cvParam Mapping Rules:

Path /MzQuantML/InputFiles/RawFilesGroup/RawFile
MAY supply a *child* term of MS:1001817 (raw file attribute) one or more times
  e.g.: MS:1001818 (one sample run) 
  e.g.: MS:1001819 (two sample run) 
  e.g.: MS:1001820 (three sample run) 
  e.g.: MS:1001821 (four sample run) 
  e.g.: MS:1001822 (eight sample run)

Element <RawFilesGroup>

Definition:

The raw file or collection of raw files that together form one unit of analysis. This is mandatory unless raw files were not used for quantitation e.g. spectral counting. Multiple raw files should only be provided within a group if they have been used for sample pre-fractionation which are later summed together.

Type:

RawFilesGroupType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	Unique identifier for the group of raw files that constitute one analysis unit.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
RawFile	1	unbounded	A raw mass spectrometry output file that has been analysed e.g. in mzML format. The same raw file can be referenced in multiple assays, for example if it contains multiple samples differentially labelled or tagged. Note, the name raw file does not necessarily imply that the file has not been processed, since in some quant methods, processed peak list formats such as MGF or DTA can be used, which could be referenced here.
cvParam	0	unbounded	A single entry from an ontology or a controlled vocabulary.
userParam	0	unbounded	A single user-defined parameter.

Example Context:

<RawFilesGroup id="RF_GRP10">
    <RawFile location="file:///C:/Users/Gerhard/Documents/SW_Projekte/OwnProjects/ConvertSpecCnts2MzQuant/ConvertSpectCnts2MzQuant/resources/input/MTQ2_1654_20a_GA4_01_5698.mzML" id="RF_10"/>
</RawFilesGroup>

cvParam Mapping Rules:

Path /MzQuantML/InputFiles/RawFilesGroup
MAY supply a *child* term of MS:1001823 (raw files group attribute) one or more times
  e.g.: MS:1001824 (merge of runs of 1D gel bands)

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="MS" accession="MS:1001271" name="researcher"/>
</Role>

cvParam Mapping Rules:

Path /MzQuantML/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)

Example cvParams:

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

Element <Row>

Definition:

One row of data in a data matrix.

Type:

RowType

Attributes:

Attribute Name	Data Type	Use	Definition
object_ref	xsd:IDREF	required	Reference to the data type represented in this row e.g. Feature, Peptide, Protein.

Subelements:

none

Example Context:

<Row object_ref="raw1-sp_P00489_PYGM_RABIT-WVDTQVVLAMPYDTPVPGYR_0000000000000000000000-3-817.4252_SIR_2585">0.11366952890220657 0.22005038249250483 1.0851682934290989E-4 0.18373924930756175</Row>

Element <SearchDatabase>

Definition:

A database used for searching mass spectra. Examples include a set of amino acid sequence entries, or annotated spectra libraries.

Type:

SearchDatabaseType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	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.
numDatabaseEntries	xsd:long	optional	The total number of entries 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	0	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 id="sdb_10827256740175179748" location="SwissProtHuman554TD_20080526.fasta">
      <DatabaseName>
        <cvParam cvRef="PSI-MS" accession="MS:1001013" name="database name" value="SwissProtHuman554TD_20080526.fasta"/>
      </DatabaseName>
    </SearchDatabase>

cvParam Mapping Rules:

Path /MzQuantML/InputFiles/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)

Element <SmallMolecule>

Definition:

An element to represent a unique identifier of a small molecule for which quantitative values are reported.

Type:

SmallMoleculeType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.

Subelements:

Subelement Name	maxOccurs	Definition
Modification	unbounded	A small molecule modification specification, given by cvParams.
DBIdentificationRef	unbounded	External database references for the small molecule identification.
Feature_refs	1	Optional references to features on which quantification values about the SmallMolecule in the QuantLayer were based.
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 /MzQuantML/SmallMoleculeList/SmallMolecule
MAY supply a *child* term of MS:1002118 (small molecule attribute) only once

Element <SmallMoleculeList>

Definition:

List of small molecules and associated data values.

Type:

SmallMoleculeListType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
SmallMolecule	1	unbounded	An element to represent a unique identifier of a small molecule for which quantitative values are reported.
GlobalQuantLayer	0	unbounded	Global values corresponding to the small molecule such as the total intensity of the molecule in all assays, Anova etc.
AssayQuantLayer	0	unbounded	Quant layer for reporting data values about small molecules related to different assays i.e. the column index MUST refer to Assays defined in the file.
StudyVariableQuantLayer	0	unbounded	Quant layer for reporting data values about small molecules related to different study variables i.e. the column index MUST refer to StudyVariables defined in the file.
RatioQuantLayer	0	1	Quant layer for reporting data values about small molecules related to different ratios i.e. the column index MUST refer to Ratio elements defined in the file.
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:

cvParam Mapping Rules:

Path /MzQuantML/SmallMoleculeList
MAY supply a *child* term of MS:1002117 (small molecule list attribute) only once

Element <Software>

Definition:

A software package used in the analysis.

Type:

SoftwareType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.
version	xsd:string	required	The software version.

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:

    <Software id="sw_14624999835377019507" version="1.6.1386">
      <cvParam cvRef="PSI-MS" accession="MS:1000615" name="ProteoWizard"/>
    </Software>

cvParam Mapping Rules:

Path /MzQuantML/SoftwareList/Software
MUST supply a *child* term of MS:1001456 (analysis software) only once
  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.
MUST supply a *child* term of MS:1001139 (quantitation software name) only once
  e.g.: MS:1000739 (WARP-LC) 
  e.g.: MS:1001488 (Mascot Distiller) 
  e.g.: MS:1001583 (MaxQuant) 
  e.g.: MS:1001830 (Progenesis LC-MS) 
  e.g.: MS:1001831 (SILACAnalyzer) 
  e.g.: MS:1001946 (PEAKS Studio) 
  e.g.: MS:1001947 (PEAKS Online) 
  e.g.: MS:1001948 (PEAKS Node) 
  e.g.: MS:1002059 (Microsoft Excel) 
  e.g.: MS:1002063 (FindPairs) 
  et al.
MAY supply term MS:1001832 (quantitation software comment or customizations) or any of its children one or more times

Example cvParams:

<cvParam accession="MS:1001830" cvRef="PSI-MS" name="Progenesis LC-MS"/>
<cvParam accession="MS:1001583" cvRef="PSI-MS" name="MaxQuant"/>
<cvParam cvRef="PSI-MS" accession="MS:1000615" name="ProteoWizard"/>
<cvParam cvRef="PSI-MS" accession="MS:1000757" name="FileFilter"/>
<cvParam cvRef="PSI-MS" accession="MS:1001831" name="SILACAnalyzer"/>
<cvParam accession="MS:1002123" cvRef="PSI-MS" name="x-Tracker"/>
<cvParam cvRef="PSI-MS" accession="MS:1002129" name="ITRAQAnalyzer"/>
<cvParam cvRef="PSI-MS" accession="MS:1002191" name="IDMapper"/>
<cvParam cvRef="MS" accession="MS:1002059" name="Microsoft Excel"/>

Element <SoftwareList>

Definition:

List and descriptions of software used to acquire and/or process the data in this file.

Type:

SoftwareListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Software	1	unbounded	A software package used in the analysis.

Graphical Context:

Example Context:

  <SoftwareList>
    <Software id="sw_14624999835377019507" version="1.6.1386">
      <cvParam cvRef="PSI-MS" accession="MS:1000615" name="ProteoWizard"/>
    </Software>
    <Software id="sw_4449351221894560547" version="1.7.0">
      <cvParam cvRef="PSI-MS" accession="MS:1000757" name="FileFilter"/>
    </Software>
  ...
</SoftwareList>

Element <SourceFile>

Definition:

A file from which this MzQuantML instance was created, including potentially MzQuantML files for earlier stages in a workflow.

Type:

SourceFileType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	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	0	1	The format of the ExternalData file, for example "tiff" for image files.

Example Context:

<SourceFile location="file:///C:/Users/Gerhard/Documents/SW_Projekte/OwnProjects/ConvertSpecCnts2MzQuant/ConvertSpectCnts2MzQuant/resources/input/counts_prot_per_sample.txt" id="SRCF_1">
    <FileFormat>
        <cvParam cvRef="MS" accession="MS:1000914" name="tab delimited text file"/>
    </FileFormat>
</SourceFile>

Element <StudyVariable>

Definition:

A logical grouping of assays into conditions or user-defined study variables such as wild-type versus disease or time points in a time course.

Type:

StudyVariableType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.
name	xsd:string	optional	A human readable name for the study variable.

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.
Assay_refs	1	1	Reference to the assays that are contained within this study variable.

Example Context:

<StudyVariable id="SV_5" name="Ib_120min">
    <cvParam cvRef="MS" accession="MS:1001814" name="generic experimental condition" value="vIb-120min gradient"/>
    <Assay_refs>ASS_5 ASS_6 ASS_7 ASS_8 ASS_9</Assay_refs>
</StudyVariable>

cvParam Mapping Rules:

Path /MzQuantML/StudyVariableList/StudyVariable
MAY supply a *child* term of MS:1001807 (study variable attribute) one or more times
  e.g.: MS:1001808 (technical replicate) 
  e.g.: MS:1001809 (biological replicate) 
  e.g.: MS:1001810 (experimental condition 'case') 
  e.g.: MS:1001811 (experimental condition 'control') 
  e.g.: MS:1001812 (experimental condition 'disease') 
  e.g.: MS:1001813 (experimental condition 'healthy') 
  e.g.: MS:1001814 (generic experimental condition) 
  e.g.: MS:1001815 (time series, time point X) 
  e.g.: MS:1001816 (dilution series, concentration X)

Example cvParams:

<cvParam accession="MS:1001808" cvRef="PSI-MS" name="technical replicate" value=""/>
<cvParam cvRef="MS" accession="MS:1001814" name="generic experimental condition" value="vIa-30min gradient"/>

Element <StudyVariableList>

Definition:

The list of experimental conditions used to group results.

Type:

StudyVariableListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
StudyVariable	1	unbounded	A logical grouping of assays into conditions or user-defined study variables such as wild-type versus disease or time points in a time course.

Graphical Context:

Example Context:

<StudyVariableList>
    <StudyVariable id="SV_0" name="Ia_30min">
        <cvParam cvRef="MS" accession="MS:1001814" name="generic experimental condition" value="vIa-30min gradient"/>
        <Assay_refs>ASS_0 ASS_1 ASS_2 ASS_3 ASS_4</Assay_refs>
    </StudyVariable>
    <StudyVariable id="SV_5" name="Ib_120min">
        <cvParam cvRef="MS" accession="MS:1001814" name="generic experimental condition" value="vIb-120min gradient"/>
  ...
</StudyVariableList>

Element <StudyVariableQuantLayer>

Definition:

Depending on context:
1: Quant layer for reporting data values about protein groups related to different study variables i.e. the column index MUST refer to StudyVariables defined in the file.
2: Quant layer for reporting data values about proteins related to different study variables i.e. the column index MUST refer to StudyVariables defined in the file.
3: Quant layer for reporting data values about peptides related to different study variables i.e. the column index MUST refer to StudyVariables defined in the file.
4: Quant layer for reporting data values about small molecules related to different study variables i.e. the column index MUST refer to StudyVariables defined in the file.

Type:

QuantLayerType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xsd:ID	required	The unique identifier for the object within the file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
DataType	1	1	Type of data in the column e.g. cvParam = "Intensity\|RawAbundance\|NormalisedAbundance".
ColumnIndex	1	1	Space separated unique identifiers for each column of data, MUST refer to an object in the file i.e. Ratio elements.
DataMatrix	1	1	A matrix of data stored in rows and columns, as defined in the parent QuantLayer.

Example Context:

<StudyVariableQuantLayer id="SV_QuantLayer_Protein_reporter_ion_intensity">
    <DataType>
        <cvParam accession="MS:1001847" cvRef="PSI-MS" name="reporter ion intensity"/>
    </DataType>
    <ColumnIndex>SV_group_A SV_group_B</ColumnIndex>
    <DataMatrix>
        <Row object_ref="DBSeq_1_sp_P00924_ENO1_YEAST">12.543762025430688 7.995378467031932</Row>
  ...
</StudyVariableQuantLayer>

Element <userParam>

Definition:

A single user-defined parameter.

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 value="examples/paper_iTraq4plex/iTraqQuantitationPSIMOD.xtp" name="Plugin configuration file"/>

Element <MzQuantML>

Element <Affiliation>

Element <AnalysisSummary>

Element <Assay>

Element <AssayList>

Element <AssayQuantLayer>

Element <Assay_refs>

Element <AuditCollection>

Element <BibliographicReference>

Element <Column>

Element <ColumnDefinition>

Element <ColumnIndex>

Element <ContactRole>

Element <Cv>

Element <CvList>

Element <cvParam>

Element <DatabaseName>

Element <DataMatrix>

Element <DataProcessing>

Element <DataProcessingList>

Element <DataType>

Element <DBIdentificationRef>

Element <DenominatorDataType>

Element <EvidenceRef>

Element <ExternalFormatDocumentation>

Element <Feature>

Element <FeatureList>

Element <FeatureQuantLayer>

Element <Feature_refs>

Element <FileFormat>

Element <GlobalQuantLayer>

Element <IdentificationFile>

Element <IdentificationFiles>

Element <IdentificationFile_refs>

Element <IdentificationRef>

Element <InputFiles>

Element <InputObject_refs>

Element <Label>

Element <MassTrace>

Element <MethodFile>

Element <MethodFiles>

Element <Modification>

Element <MS2AssayQuantLayer>

Element <MS2RatioQuantLayer>

Element <MS2StudyVariableQuantLayer>

Element <NumeratorDataType>

Element <Organization>

Element <OutputObject_refs>

Element <ParentOrganization>

Element <PeptideConsensus>

Element <PeptideConsensusList>

Element <PeptideConsensus_refs>

Element <PeptideSequence>

Element <Person>

Element <ProcessingMethod>

Element <Protein>

Element <ProteinGroup>

Element <ProteinGroupList>

Element <ProteinList>

Element <ProteinRef>

Element <Provider>

Element <Ratio>

Element <RatioCalculation>

Element <RatioList>

Element <RatioQuantLayer>

Element <RawFile>

Element <RawFilesGroup>

Element <Role>

Element <Row>

Element <SearchDatabase>

Element <SmallMolecule>

Element <SmallMoleculeList>

Element <Software>

Element <SoftwareList>

Element <SourceFile>

Element <StudyVariable>

Element <StudyVariableList>

Element <StudyVariableQuantLayer>

Element <userParam>