... </Assay> cvParam Mapping Rules: Path /MzQuantML/AssayList/Assay MAY supply a *child* term of (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: Subelements:
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> ... </AssayList>
Example Context: <ContactRole contact_ref="PERS_GM"> <Role> <cvParam accession="MS:1001271" name="researcher"/> </Role> </ContactRole> Element <Cv> Definition: A source controlled vocabulary from which cvParams will be obtained. Type: CvType Attributes:
Subelements: 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: Graphical Context: Example Context: <DataProcessingList> <DataProcessing order="1" id="DP1"> <ProcessingMethod order="1"> <userParam value="load identification" name="Plugin type"/> <userParam name="Plugin name"/> <userParam value="examples/paper_iTraq4plex/loadMzIdentML.xtp" name="Plugin configuration file"/> </ProcessingMethod> ... </DataProcessingList> Element <DataType> Definition: Depending on context: 1: Type of data in the quant layer e.g. cvParam =
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 (feature attribute) one or more times e.g.: (SRM transition ID) e.g.: (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:
Graphical Context: Example Context: <FeatureList id="featureList_raw1" rawFilesGroup_ref="raw1"> <Feature spectrum_refs="Scan Number: 1656" charge="2" mz="411.6925" rt="null" <Feature spectrum_refs="Scan Number: 1205" charge="2" mz="474.7568" rt="null" <Feature spectrum_refs="Scan Number: 3667" charge="2" mz="573.2433" rt="null" <Feature spectrum_refs="Scan Number: 3612" charge="2" mz="573.2534" rt="null" <Feature spectrum_refs="Scan Number: 1995" charge="2" mz="687.29" rt="null" <Feature spectrum_refs="Scan Number: 1877" charge="2" mz="687.3034" rt="null" ... </FeatureList> cvParam Mapping Rules: Path /MzQuantML/FeatureList MAY supply a term of (feature list attribute) one or more times e.g.: (mass trace reporting: rectangles) e.g.: (mass trace reporting: polygons) e.g.: (counts reporting) Element <FeatureQuantLayer> Definition: All the data values about features in one raw file or raw file group, such as feature raw intensity,
Subelements: Specification of a <Modification> searched for Example Context: <Modification monoisotopicMassDelta="15.994915" location="13"> <cvParam accession="UNIMOD:35" cvRef="UNIMOD" name="Oxidation"/>
Example Context: <PeptideConsensus searchDatabase_ref="SD1" charge="2" id="pep_GAPEIDVLEGETDTK_2_21711"> <PeptideSequence>GAPEIDVLEGETDTK</PeptideSequence>
Example Context: <Person firstName="Gerhard" id="PERS_GM" name="Gerhard Mayer"> <Affiliation organization_ref="ORG_MPC"/> </Person> cvParam Mapping Rules: Path /MzQuantML/AuditCollection/Person SHOULD supply term (contact URL) one or more times SHOULD supply term (contact address) one or more times SHOULD supply term (contact email) one or more times Element <ProcessingMethod> Definition: Description of one step within the data processing pipeline. Type: ProcessingMethodType Attributes: Subelements: Example Context: <ProcessingMethod order="3"> <userParam value="feature detection and quantitation" name="Plugin type"/> <userParam name="Plugin name"/>
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 (data file checksum type) one or more times e.g.: (MD5) e.g.: (SHA-1)
Example Context: cvParam Mapping Rules: Path /MzQuantML/SmallMoleculeList/SmallMolecule MAY supply a *child* term of (small molecule attribute) only once Element <SmallMoleculeList> Definition: List of small molecules and associated data values. Type: SmallMoleculeListType Attributes: Subelements: