Element <TraML>

Definition:

Container for the HUPO PSI TraML format for encoding selected reaction monitoring transitions and other target lists

Type:

TraMLType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:string	optional	An optional id for the TraML document used for referencing from external files. It is recommended to use LSIDs when possible.
version	xs:string	required	Version of the TraML format used by this document

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvList	1	1	List of controlled vocabularies used in a TraML document
SourceFileList	0	1	List and descriptions of the source files this TraML document was generated or derived from
ContactList	0	1	List of contacts referenced in the generation or validation of transitions
PublicationList	0	1	List of publications from which the transitions were collected or wherein they are published
InstrumentList	0	1	List of instruments on which transitions are validated
SoftwareList	0	1	List of software packages used in the generation of one of more transitions described in the document
ProteinList	0	1	List of proteins for which one or more transitions are intended to identify
CompoundList	0	1	List of compounds (including peptides) for which one or more transitions are intended to identify
TransitionList	0	1	List of transitions
TargetList	0	1	List of precursor m/z targets to include or exclude

Example Context:

 <TraML xmlns="http://psi.hupo.org/ms/traml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="1.0.0" xsi:schemaLocation="http://psi.hupo.org/ms/traml TraML1.0.0.xsd">   <cvList>     <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="2.29.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>     <cv id="UO" fullName="Unit Ontology" version="1.20" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>   </cvList>   <InstrumentList>     <Instrument id="microtof">       <cvParam cvRef="MS" accession="MS:1001536" name="Bruker Daltonics micrOTOF series"/>     </Instrument>   </InstrumentList>   <SoftwareList>     <Software id="XCMS-1.12" version="1.21.17">       <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="XCMS"/>     </Software>   </SoftwareList>   <TargetList>     <cvParam cvRef="MS" accession="MS:1000920" name="includes supersede excludes"/>     <TargetIncludeList>       <Target id="7">         <Precursor>           <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="4.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>         </Precursor>         <RetentionTime>           <cvParam cvRef="MS" accession="MS:1000895" name="local retention time" value="5.0" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>           <cvParam cvRef="MS" accession="MS:1000916" name="retention time window lower offset" value="6.0" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>           <cvParam cvRef="MS" accession="MS:1000917" name="retention time window upper offset" value="7.0" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>         </RetentionTime>         <ConfigurationList>           <Configuration instrumentRef="microtof">             <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="8.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>           </Configuration>         </ConfigurationList>       </Target>     </TargetIncludeList>   </TargetList> </TraML>

Example cvParams:

<TraML xmlns="http://psi.hupo.org/ms/traml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="1.0.0" xsi:schemaLocation="http://psi.hupo.org/ms/traml TraML1.0.0.xsd">   <cvList>     <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="2.29.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>     <cv id="UO" fullName="Unit Ontology" version="1.20" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>   </cvList>   <InstrumentList>     <Instrument id="microtof">       <cvParam cvRef="MS" accession="MS:1001536" name="Bruker Daltonics micrOTOF series"/>     </Instrument>   </InstrumentList>   <SoftwareList>     <Software id="XCMS-1.12" version="1.21.17">       <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="XCMS"/>     </Software>   </SoftwareList>   <TargetList>     <cvParam cvRef="MS" accession="MS:1000920" name="includes supersede excludes"/>     <TargetIncludeList>       <Target id="7">         <Precursor>           <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="4.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>         </Precursor>         <RetentionTime>           <cvParam cvRef="MS" accession="MS:1000895" name="local retention time" value="5.0" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>           <cvParam cvRef="MS" accession="MS:1000916" name="retention time window lower offset" value="6.0" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>           <cvParam cvRef="MS" accession="MS:1000917" name="retention time window upper offset" value="7.0" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>         </RetentionTime>         <ConfigurationList>           <Configuration instrumentRef="microtof">             <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="8.0" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>           </Configuration>         </ConfigurationList>       </Target>     </TargetIncludeList>   </TargetList> </TraML>

Element <cvList>

Definition:

List of controlled vocabularies used in a TraML document

Type:

cvListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cv	1	unbounded	Controlled vocabulary used in a TraML document

Example Context:

<cvList>
  <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="2.31.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
  <cv id="UO" fullName="Unit Ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
  <cv id="UNIMOD" fullName="UNIMOD CV for modifications" version="unknown" URI="http://www.unimod.org/obo/unimod.obo"/>
</cvList>

Element <SourceFileList>

Definition:

List and descriptions of the source files this TraML document was generated or derived from

Type:

SourceFileListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
SourceFile	1	unbounded	Description of the source file, including location and type.

Example Context:

<SourceFileList>
  <SourceFile id="sf1" name="OneTransition.tsv" location="file:///F:/data/Exp01">
    <cvParam cvRef="MS" accession="MS:1000914" name="tab delimited text file" value=""/>
    <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="71be39fb2700ab2f3c8b2234b91274968b6899b1"/>
  </SourceFile>
</SourceFileList>

Element <ContactList>

Definition:

List of contacts referenced in the generation or validation of transitions

Type:

ContactListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Contact	1	unbounded	Contact person referenced in the generation or validation of transitions

Example Context:

<ContactList>
  <Contact id="CS">
    <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Eric Deutsch"/>
    <cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="Institute for Systems Biology"/>
    <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="1441 NE 34th St, Seattle WA 98103, USA"/>
    <cvParam cvRef="MS" accession="MS:1000588" name="contact URL" value="http://www.systemsbiology.org/"/>
    <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="example@systemsbiology.org"/>
  ...
</ContactList>

Element <PublicationList>

Definition:

List of publications from which the transitions were collected or wherein they are published

Type:

PublicationListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Publication	1	unbounded	Reference to a publication in which one or more transitions were published

Example Context:

<PublicationList>
  <Publication id="PMID12748199">
    <cvParam cvRef="MS" accession="MS:1000879" name="PubMed identifier" value="12748199"/>
  </Publication>
</PublicationList>

Element <InstrumentList>

Definition:

List of instruments on which transitions are validated

Type:

InstrumentListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Instrument	1	unbounded	Instrument on which transitions are validated

Example Context:

<InstrumentList>
  <Instrument id="LCQ_Deca">
    <cvParam cvRef="MS" accession="MS:1000554" name="LCQ Deca"/>
  </Instrument>
  <Instrument id="QTRAP">
    <cvParam cvRef="MS" accession="MS:1000870" name="4000 QTRAP"/>
  </Instrument>
  ...
</InstrumentList>

Element <SoftwareList>

Definition:

List of software packages used in the generation of one of more transitions described in the document

Type:

SoftwareListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Software	1	unbounded	Description of a software package used in the generation of one or more transitions described in the document

Example Context:

<SoftwareList>
  <Software id="MaRiMba" version="1.0">
    <cvParam cvRef="MS" accession="MS:1000872" name="MaRiMba"/>
  </Software>
  <Software id="SSRCalc3.0" version="3.0">
    <cvParam cvRef="MS" accession="MS:1000874" name="SSRCalc"/>
  </Software>
  ...
</SoftwareList>

Element <ProteinList>

Definition:

List of proteins for which one or more transitions are intended to identify

Type:

ProteinListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Protein	1	unbounded	Protein for which one or more transitions are intended to identify

Example Context:

<ProteinList>
  <Protein id="Q12149">
    <cvParam cvRef="MS" accession="MS:1000885" name="protein accession" value="Q00613"/>
    <cvParam cvRef="MS" accession="MS:1000883" name="protein short name" value="HSF 1"/>
    <cvParam cvRef="MS" accession="MS:1000886" name="protein name" value="Heat shock factor protein 1"/>
    <Sequence>MSTEMETKAEDVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDNGKE</Sequence>
  </Protein>
  ...
</ProteinList>

Element <CompoundList>

Definition:

List of compounds (including peptides) for which one or more transitions are intended to identify

Type:

CompoundListType

Attributes:

none

Subelements:

Subelement Name	maxOccurs	Definition
cvParam	unbounded	Controlled vocabulary term adding information to the parent term
userParam	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead
Peptide	unbounded	Peptide for which one or more transitions are intended to identify
Compound	unbounded	Chemical compound other than a peptide for which one or more transitions

Example Context:

<CompoundList>
  <Peptide id="ADTHFLLNIYDQLR-M1" sequence="ADTHFLLNIYDQLR">
    <cvParam cvRef="MS" accession="MS:1000891" name="heavy labeled peptide"/>
    <cvParam cvRef="MS" accession="MS:1000893" name="peptide group label" value="G1"/>
    <cvParam cvRef="MS" accession="MS:1000863" name="predicted isoelectric point" value="5.22"/>
    <cvParam cvRef="MS" accession="MS:1001117" name="theoretical mass" value="1189.22" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton"/>
    <userParam name="isomerization potential" value="0.583" type="xsd:float"/> <!-- Additional information may be added as a userParams if it is not possible and not appropriate to encode the information as a cvParam -->
  ...
</CompoundList>

Element <TransitionList>

Definition:

List of transitions

Type:

TransitionListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Transition	1	unbounded	Information about a single transition for a peptide or other compound

Example Context:

<TransitionList>
    <Transition id="AAQVAQDEEIAR.2y8-1" peptideRef="AAQVAQDEEIAR.2">
        <Precursor>
            <cvParam unitCvRef="MS" unitName="m/z" unitAccession="MS:1000040" value="650.8288" accession="MS:1000827" name="isolation window target m/z" cvRef="MS"/>
        </Precursor>
        <Product>
            <cvParam unitCvRef="MS" unitName="m/z" unitAccession="MS:1000040" value="931.4486" accession="MS:1000827" name="isolation window target m/z" cvRef="MS"/>
  ...
</TransitionList>

Element <TargetList>

Definition:

List of precursor m/z targets to include or exclude

Type:

TargetListType

Attributes:

none

Subelements:

Subelement Name	maxOccurs	Definition
cvParam	unbounded	Controlled vocabulary term adding information to the parent term
userParam	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead
TargetIncludeList	1	List of precursor m/z targets to include
TargetExcludeList	1	List of precursor m/z targets to exclude

Example Context:

<TargetList>
  <cvParam cvRef="MS" accession="MS:1000920" name="includes supersede excludes"/>
  <TargetIncludeList>
    <Target id="PEPTIDEC2+" peptideRef="PEPTIDEC">
      <Precursor>
        <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
        <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
  ...
</TargetList>

cvParam Mapping Rules:

Path /TraML/TargetList
MUST supply a *child* term of MS:1000919 (target inclusion exclusion priority) only once
  e.g.: MS:1000920 (includes supersede excludes)
  e.g.: MS:1000921 (excludes supersede includes)

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000920" name="includes supersede excludes"/>

Element <cv>

Definition:

Controlled vocabulary used in a TraML document

Type:

cvType

Attributes:

Attribute Name	Data Type	Use	Definition
URI	xs:anyURI	required	Uniform Resource Identifier for the controlled vocabulary
fullName	xs:string	required	Full name of the controlled vocabulary
id	xs:ID	required	Identifier for the controlled vocabulary to be used for referencing within a document
version	xs:string	required	Version of controlled vocabulary in use when the document was created

Subelements:

none

Example Context:

    <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="2.29.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>

Element <SourceFile>

Definition:

Description of the source file, including location and type.

Type:

SourceFileType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	Identifier for the sourceFile to be used for referencing within a document.
location	xs:anyURI	required	URI-formatted location where the file was retrieved.
name	xs:string	required	Name of the source file, without reference to location (either URI or local path).

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	Controlled vocabulary term adding information to the parent term
userParam	0	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Example Context:

<SourceFile id="sf1" name="OneTransition.tsv" location="file:///F:/data/Exp01">
  <cvParam cvRef="MS" accession="MS:1000914" name="tab delimited text file" value=""/>
  <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="71be39fb2700ab2f3c8b2234b91274968b6899b1"/>
</SourceFile>

cvParam Mapping Rules:

Path /TraML/SourceFileList/SourceFile
MAY supply a *child* term of MS:1000561 (data file checksum type) only once
  e.g.: MS:1000568 (MD5)
  e.g.: MS:1000569 (SHA-1)
MUST supply term MS:1001459 (file format) or any of its children only once
  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.

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000914" name="tab delimited text file" value=""/>
<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="71be39fb2700ab2f3c8b2234b91274968b6899b1"/>

Element <Contact>

Definition:

Contact person referenced in the generation or validation of transitions

Type:

ContactType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	Identifier for the contact to be used for referencing within a document

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	Controlled vocabulary term adding information to the parent term
userParam	0	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Example Context:

<Contact id="CS">
  <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Eric Deutsch"/>
  <cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="Institute for Systems Biology"/>
  <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="1441 NE 34th St, Seattle WA 98103, USA"/>
  <cvParam cvRef="MS" accession="MS:1000588" name="contact URL" value="http://www.systemsbiology.org/"/>
  <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="example@systemsbiology.org"/>
</Contact>

cvParam Mapping Rules:

Path /TraML/ContactList/Contact
MAY supply a *child* term of MS:1000585 (contact attribute) one or more times
  e.g.: MS:1000586 (contact name)
  e.g.: MS:1000587 (contact address)
  e.g.: MS:1000588 (contact URL)
  e.g.: MS:1000589 (contact email)
  e.g.: MS:1000590 (contact organization)
  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)
  et al.
MUST supply term MS:1000590 (contact organization) only once
MUST supply term MS:1000586 (contact name) only once

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Eric Deutsch"/>
<cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="Institute for Systems Biology"/>
<cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="1441 NE 34th St, Seattle WA 98103, USA"/>
<cvParam cvRef="MS" accession="MS:1000588" name="contact URL" value="http://www.systemsbiology.org/"/>
<cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="example@systemsbiology.org"/>

Element <Publication>

Definition:

Reference to a publication in which one or more transitions were published

Type:

PublicationType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	Identifier for the publication to be used for referencing within a document

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	Controlled vocabulary term adding information to the parent term
userParam	0	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Example Context:

<Publication id="PMID12748199">
  <cvParam cvRef="MS" accession="MS:1000879" name="PubMed identifier" value="12748199"/>
</Publication>

cvParam Mapping Rules:

Path /TraML/PublicationList/Publication
MUST supply term MS:1000879 (PubMed identifier) only once

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000879" name="PubMed identifier" value="12748199"/>

Element <Instrument>

Definition:

Instrument on which transitions are validated

Type:

InstrumentType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	Identifier for the instrument to be used for referencing within a document

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	1	Controlled vocabulary term adding information to the parent term
userParam	0	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Example Context:

<Instrument id="1">
    <cvParam value="Positive" accession="MS:1000037" name="polarity" cvRef="MS"/>
</Instrument>

cvParam Mapping Rules:

Path /TraML/InstrumentList/Instrument
MUST supply a *child* term of MS:1000031 (instrument model) only once
  e.g.: MS:1000139 (4000 QTRAP)
  e.g.: MS:1000140 (4700 Proteomics Analyzer)
  e.g.: MS:1000141 (apex IV)
  e.g.: MS:1000142 (apex Q)
  e.g.: MS:1000143 (API 150EX)
  e.g.: MS:1000144 (API 150EX Prep)
  e.g.: MS:1000145 (API 2000)
  e.g.: MS:1000146 (API 3000)
  e.g.: MS:1000147 (API 4000)
  e.g.: MS:1000148 (autoflex II)
  et al.

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000554" name="LCQ Deca"/>
<cvParam cvRef="MS" accession="MS:1000870" name="4000 QTRAP"/>
<cvParam value="Positive" accession="MS:1000037" name="polarity" cvRef="MS"/>

Element <Software>

Definition:

Description of a software package used in the generation of one or more transitions described in the document

Type:

SoftwareType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	Identifier for the software to be used for referencing within a document
version	xs:string	required	Version of the software program described

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	1	Controlled vocabulary term adding information to the parent term
userParam	0	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Example Context:

    <Software id="ProSE" version="SE 2.11.0-dev build 3535" >
      <cvParam cvRef="MS" accession="MS:1000600" name="Proteios" />
    </Software>

cvParam Mapping Rules:

Path /TraML/SoftwareList/Software
MUST supply a *child* term of MS:1000531 (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:1000538 (massWolf)
  e.g.: MS:1000539 (Voyager Biospectrometry Workstation System)
  e.g.: MS:1000540 (FlexControl)
  e.g.: MS:1000541 (ReAdW)
  et al.

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000872" name="MaRiMba"/>
<cvParam cvRef="MS" accession="MS:1000874" name="SSRCalc"/>
<cvParam cvRef="MS" accession="MS:1000922" name="Skyline"/>
<cvParam cvRef="MS" accession="MS:1000600" name="Proteios" />

Element <Protein>

Definition:

Protein for which one or more transitions are intended to identify

Type:

ProteinType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	Identifier for the protein to be used for referencing within a document

Subelements:

Subelement Name	maxOccurs	Definition
cvParam	unbounded	Controlled vocabulary term adding information to the parent term
userParam	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead
Sequence	1	Amino acid sequence of the protein

Example Context:

<Protein id="ENSP00000332698">
  <cvParam cvRef="MS" accession="MS:1000885" name="protein accession" value="ENSP00000332698"/>
  <cvParam cvRef="MS" accession="MS:1000883" name="protein short name" value="HSF 1"/>
  <cvParam cvRef="MS" accession="MS:1000886" name="protein name" value="Heat shock factor protein 1"/>
  <Sequence>MSTEMETKAEDVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDNGKEELISNSSDALDKI</Sequence>
</Protein>

cvParam Mapping Rules:

Path /TraML/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 cvParams:

<cvParam cvRef="MS" accession="MS:1000885" name="protein accession" value="Q00613"/>
<cvParam cvRef="MS" accession="MS:1000883" name="protein short name" value="HSF 1"/>
<cvParam cvRef="MS" accession="MS:1000886" name="protein name" value="Heat shock factor protein 1"/>

Element <cvParam>

Definition:

Controlled vocabulary term adding information to the parent term

Type:

cvParamType

Attributes:

Attribute Name	Data Type	Use	Definition
accession	xs:string	required	Accession number of the controlled vocabulary term referenced
cvRef	xs:IDREF	required	Reference to a controlled vocabulary for which this cvParam is
name	xs:string	required	Name of the controlled vocabulary term referenced
unitAccession	xs:string	optional	An optional CV accession number for the unit term associated with the value, if any (e.g., 'UO:0000266' for 'electron volt').
unitCvRef	xs:IDREF	optional	If a unit term is referenced, this attribute MUST refer to the CV 'id' attribute defined in the cvList in this mzML file.
unitName	xs:string	optional	An optional CV name for the unit accession number, if any (e.g., 'electron volt' for 'UO:0000266' ).
value	xs:string	optional	Scalar value qualifying the controlled vocabulary term referenced

Subelements:

none

Example Context:

        <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="4072" unitCvRef="MS" unitAccession="MS:1000905" unitName="percent of base peak times 100"/>

Element <userParam>

Definition:

Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Type:

UserParamType

Attributes:

Attribute Name	Data Type	Use	Definition
name	xs:string	required	The name for the parameter.
type	xs:string	optional	The datatype of the parameter, where appropriate (e.g.: xsd:float).
unitAccession	xs:string	optional	An optional CV accession number for the unit term associated with the value, if any (e.g., 'UO:0000266' for 'electron volt').
unitCvRef	xs:IDREF	optional	If a unit term is referenced, this attribute MUST refer to the CV 'id' attribute defined in the cvList in this mzML file.
unitName	xs:string	optional	An optional CV name for the unit accession number, if any (e.g., 'electron volt' for 'UO:0000266' ).
value	xs:string	optional	The value for the parameter, where appropriate.

Subelements:

none

Example Context:

<userParam name="isomerization potential" value="0.583" type="xsd:float"/> <!-- Additional information may be added as a userParams if it is not possible and not appropriate to encode the information as a cvParam -->

Element <Peptide>

Definition:

Peptide for which one or more transitions are intended to identify

Type:

PeptideType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	Identifier for the peptide to be used for referencing within a document
sequence	xs:string	required	Amino acid sequence of the peptide being described

Subelements:

Subelement Name	maxOccurs	Definition
cvParam	unbounded	Controlled vocabulary term adding information to the parent term
userParam	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead
ProteinRef	unbounded	Reference to a protein which this peptide is intended to identify
Modification	unbounded	A molecule modification specification. If n modifications are present on the peptide, there should be n instances of the modification element. If multiple modifications are provided as cvParams, it is assumed the modification is ambiguous, i.e. one modification or the other. If no cvParams are provided it is assumed that the delta has not been matched to a known modification.
RetentionTimeList	1	List of retention time information entries
Evidence	1	Information about empirical mass spectrometer observations of the peptide

Example Context:

<Peptide id="ADTHFLLNIYDQLR-M1" sequence="ADTHFLLNIYDQLR">
  <cvParam cvRef="MS" accession="MS:1000891" name="heavy labeled peptide"/>
  <cvParam cvRef="MS" accession="MS:1000893" name="peptide group label" value="G1"/>
  <cvParam cvRef="MS" accession="MS:1000863" name="predicted isoelectric point" value="5.22"/>
  <cvParam cvRef="MS" accession="MS:1001117" name="theoretical mass" value="1189.22" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton"/>
  <userParam name="isomerization potential" value="0.583" type="xsd:float"/> <!-- Additional information may be added as a userParams if it is not possible and not appropriate to encode the information as a cvParam -->
  <ProteinRef ref="Q12149"/>
  ...
</Peptide>

cvParam Mapping Rules:

Path /TraML/CompoundList/Peptide
MAY supply term MS:1000863 (predicted isoelectric point) only once
MAY supply term MS:1000893 (peptide group label) only once
MAY supply term MS:1001117 (theoretical mass) only once
MAY supply a *child* term of MS:1000890 (peptide labeling state) one or more times
  e.g.: MS:1000891 (heavy labeled peptide)
  e.g.: MS:1000892 (unlabeled peptide)

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000891" name="heavy labeled peptide"/>
<cvParam cvRef="MS" accession="MS:1000893" name="peptide group label" value="G1"/>
<cvParam cvRef="MS" accession="MS:1000863" name="predicted isoelectric point" value="5.22"/>
<cvParam cvRef="MS" accession="MS:1001117" name="theoretical mass" value="1189.22" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton"/>

Element <Compound>

Definition:

Chemical compound other than a peptide for which one or more transitions

Type:

CompoundType

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	Identifier for the compound to be used for referencing within a document

Subelements:

Subelement Name	maxOccurs	Definition
cvParam	unbounded	Controlled vocabulary term adding information to the parent term
userParam	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead
RetentionTimeList	unbounded	List of retention time information entries

Example Context:

<Compound id="glyoxylate">
  <cvParam cvRef="MS" accession="MS:1001117" name="theoretical mass" value="423.39" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton"/>
  <cvParam cvRef="MS" accession="MS:1000866" name="molecular formula" value="C2HO3"/>
  <cvParam cvRef="MS" accession="MS:1000868" name="SMILES string" value="[CH](=[O])[C](=[O])[O-]"/>
  <RetentionTimeList>
    <RetentionTime>
      <cvParam cvRef="MS" accession="MS:1000896" name="normalized retention time" value="22.34" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
  ...
</Compound>

cvParam Mapping Rules:

Path /TraML/CompoundList/Compound
MAY supply term MS:1000863 (predicted isoelectric point) only once
MAY supply a *child* term of MS:1000864 (chemical compound formula) one or more times
  e.g.: MS:1000865 (empirical formula)
  e.g.: MS:1000866 (molecular formula)
  e.g.: MS:1000867 (structural formula)
  e.g.: MS:1000868 (SMILES string)
MAY supply term MS:1001117 (theoretical mass) only once

Example cvParams:

<cvParam cvRef="MS" accession="MS:1001117" name="theoretical mass" value="423.39" unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton"/>
<cvParam cvRef="MS" accession="MS:1000866" name="molecular formula" value="C2HO3"/>
<cvParam cvRef="MS" accession="MS:1000868" name="SMILES string" value="[CH](=[O])[C](=[O])[O-]"/>

Element <Transition>

Definition:

Information about a single transition for a peptide or other compound

Type:

TransitionType

Attributes:

Attribute Name	Data Type	Use	Definition
compoundRef	xs:IDREF	optional	Reference to a compound for this transition
id	xs:string	required	String label for this transition
peptideRef	xs:IDREF	optional	Reference to a peptide which this transition is intended to identify

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Precursor	1	1	Precursor (Q1) of the transition or target
IntermediateProduct	0	unbounded	Intermediate product ion information of the transition when using MS3 or above
Product	1	1	Product (Q3) of the transition
RetentionTime	0	1	Information about predicted or calibrated retention time
Prediction	0	1	Information about a prediction for a suitable transition using some software
cvParam	0	unbounded	Controlled vocabulary term adding information to the parent term
userParam	0	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Example Context:

<Transition id="ADTHFLLNIYDQLR-M1-T2" peptideRef="ADTHFLLNIYDQLR-M1">
  <Precursor>
    <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="1.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="1.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
  </Precursor>
  ...
</Transition>

Element <TargetIncludeList>

Definition:

List of precursor m/z targets to include

Type:

TargetIncludeListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Target	1	unbounded	A peptide or compound that is to be included or excluded from a target list of precursor m/z values.

Example Context:

<TargetIncludeList>
  <Target id="PEPTIDEC2+" peptideRef="PEPTIDEC">
    <Precursor>
      <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
      <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
    </Precursor>
    <RetentionTime softwareRef="Skyline0.5">
  ...
</TargetIncludeList>

Element <TargetExcludeList>

Definition:

List of precursor m/z targets to exclude

Type:

TargetExcludeListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Target	1	unbounded	A peptide or compound that is to be included or excluded from a target list of precursor m/z values.

Example Context:

<TargetExcludeList>
  <Target id="PEPTIDEM3+" peptideRef="PEPTIDEM">
    <Precursor>
      <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="698.3443" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
      <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="3"/>
    </Precursor>
  </Target>
  ...
</TargetExcludeList>

Element <Sequence>

Definition:	Amino acid sequence of the protein
Type:	SequenceType
Attributes:	none
Subelements:	none
Example Context:	<Sequence>MSTEMETKAEDVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDNGKEELISNSSDALDKI</Sequence>

Element <ProteinRef>

Definition:

Reference to a protein which this peptide is intended to identify

Type:

ProteinRefType

Attributes:

Attribute Name	Data Type	Use	Definition
ref	xs:IDREF	optional	Reference to a protein which this peptide is intended to identify

Subelements:

none

Example Context:

<ProteinRef ref="ENSP00000332698"/>

A molecule modification specification. If n modifications are present on the peptide, there should be n instances of the modification element. If multiple modifications are provided as cvParams, it is assumed the modification is ambiguous, i.e. one modification or the other. If no cvParams are provided it is assumed that the delta has not been matched to a known modification.

Type:

ModificationType

Attributes:

Attribute Name	Data Type	Use	Definition
averageMassDelta	xs:double	optional	Atomic mass delta when considering the natural distribution of isotopes in Daltons.
location	xs:int	required	Location of the modification within the peptide sequence, counted from the N-terminus, starting at position 1. Specific modifications to the N-terminus should be given the location 0. Modification to the C-terminus should be given as peptide length + 1.
monoisotopicMassDelta	xs:double	optional	Atomic mass delta when assuming only the most common isotope of elements in Daltons.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	0	unbounded	Controlled vocabulary term adding information to the parent term
userParam	0	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Example Context:

<Modification location="1" monoisotopicMassDelta="15.994919">
  <cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/>
</Modification>

cvParam Mapping Rules:

Path /TraML/CompoundList/Peptide/Modification
MAY supply a *child* term of UNIMOD:0 (unimod root node) one or more times

Example cvParams:

<cvParam cvRef="UNIMOD" accession="UNIMOD:29" name="SMA"/>
<cvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/>

Element <RetentionTimeList>

Definition:

List of retention time information entries

Type:

RetentionTimeListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
RetentionTime	1	unbounded	Information about predicted or calibrated retention time

Example Context:

<RetentionTimeList>
  <RetentionTime softwareRef="SSRCalc3.0">
    <cvParam cvRef="MS" accession="MS:1000897" name="predicted retention time" value="44.07" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
  </RetentionTime>
  <RetentionTime>
    <cvParam cvRef="MS" accession="MS:1000896" name="normalized retention time" value="38.43" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
    <cvParam cvRef="MS" accession="MS:1000902" name="H-PINS retention time normalization standard"/>
  ...
</RetentionTimeList>

Element <Evidence>

Definition:

Information about empirical mass spectrometer observations of the peptide

Type:

EvidenceType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	Controlled vocabulary term adding information to the parent term
userParam	0	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Example Context:

<Evidence>
  <cvParam cvRef="MS" accession="MS:1001100" name="confident peptide" value="6"/>
</Evidence>

cvParam Mapping Rules:

Path /TraML/CompoundList/Peptide/Evidence
MAY supply term MS:1001100 (confident peptide) only once

Example cvParams:

<cvParam cvRef="MS" accession="MS:1001100" name="confident peptide" value="6"/>

Element <Precursor>

Definition:

Precursor (Q1) of the transition or target

Type:

PrecursorType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	0	unbounded	Controlled vocabulary term adding information to the parent term
userParam	0	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Example Context:

<Precursor>
  <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
  <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="1.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
  <cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="1.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
  <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
</Precursor>

cvParam Mapping Rules:

Path /TraML/TargetExcludeList/Target/Precursor
MAY supply term MS:1000828 (isolation window lower offset) only once
MAY supply term MS:1000829 (isolation window upper offset) only once

Path /TraML/TransitionList/Transition/Precursor
MAY supply term MS:1000828 (isolation window lower offset) only once
MAY supply term MS:1000829 (isolation window upper offset) only once
MUST supply term MS:1000827 (isolation window target m/z) only once
MAY supply term MS:1000041 (charge state) only once

Path /TraML/TargetList/TargetIncludeList/Target/Precursor
MUST supply term MS:1000827 (isolation window target m/z) only once
MAY supply term MS:1000041 (charge state) only once

Path /TraML/TargetList/TargetExcludeList/Target/Precursor
MUST supply term MS:1000827 (isolation window target m/z) only once
MAY supply term MS:1000041 (charge state) only once

Path /TraML/TargetIncludeList/Target/Precursor
MAY supply term MS:1000828 (isolation window lower offset) only once
MAY supply term MS:1000829 (isolation window upper offset) only once

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
<cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="1.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="1.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>

Element <IntermediateProduct>

Definition:

Intermediate product ion information of the transition when using MS3 or above

Type:

IntermediateProductType

Attributes:

none

Subelements:

Subelement Name	maxOccurs	Definition
cvParam	unbounded	Controlled vocabulary term adding information to the parent term
userParam	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead
InterpretationList	1	List of possible interprations of fragment ions for a transition
ConfigurationList	1	List of insutrument configurations used in the validation or optimization of the transitions

Example Context:

<IntermediateProduct>
  <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="1040.57" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
  <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>
  <InterpretationList>
    <Interpretation>
      <cvParam cvRef="MS" accession="MS:1000926" name="product interpretation rank" value="1"/>
      <cvParam cvRef="MS" accession="MS:1001220" name="frag: y ion"/>
  ...
</IntermediateProduct>

cvParam Mapping Rules:

Path /TraML/TransitionList/Transition/IntermediateProduct
MAY supply term MS:1000828 (isolation window lower offset) only once
MAY supply term MS:1000829 (isolation window upper offset) only once
MUST supply term MS:1000827 (isolation window target m/z) only once
MAY supply term MS:1000041 (charge state) only once

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="1040.57" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>

Element <Product>

Definition:

Product (Q3) of the transition

Type:

ProductType

Attributes:

none

Subelements:

Subelement Name	maxOccurs	Definition
cvParam	unbounded	Controlled vocabulary term adding information to the parent term
userParam	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead
InterpretationList	1	List of possible interprations of fragment ions for a transition
ConfigurationList	1	List of insutrument configurations used in the validation or optimization of the transitions

Example Context:

<Product>
  <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="1040.57" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
  <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>
  <InterpretationList>
    <Interpretation>
      <cvParam cvRef="MS" accession="MS:1000926" name="product interpretation rank" value="1"/>
      <cvParam cvRef="MS" accession="MS:1001220" name="frag: y ion"/>
  ...
</Product>

cvParam Mapping Rules:

Path /TraML/TransitionList/Transition/Product
MAY supply term MS:1000828 (isolation window lower offset) only once
MAY supply term MS:1000829 (isolation window upper offset) only once
MUST supply term MS:1000827 (isolation window target m/z) only once
MAY supply term MS:1000041 (charge state) only once

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="1040.57" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>

Element <RetentionTime>

Definition:

Information about predicted or calibrated retention time

Type:

RetentionTimeType

Attributes:

Attribute Name	Data Type	Use	Definition
softwareRef	xs:IDREF	optional	Software used to determine the retention time

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	1	unbounded	Controlled vocabulary term adding information to the parent term
userParam	0	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Example Context:

<RetentionTime softwareRef="Skyline0.5">
  <cvParam cvRef="MS" accession="MS:1000895" name="local retention time" value="40.02" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
  <cvParam cvRef="MS" accession="MS:1000916" name="retention time window lower offset" value="3.0" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
  <cvParam cvRef="MS" accession="MS:1000917" name="retention time window upper offset" value="3.0" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
</RetentionTime>

cvParam Mapping Rules:

Path /TraML/TransitionList/Transition/RetentionTime/RetentionTime
MAY supply a *child* term of MS:1000915 (retention time window attribute) one or more times
  e.g.: MS:1000916 (retention time window lower offset)
  e.g.: MS:1000917 (retention time window upper offset)
  e.g.: MS:1001907 (retention time window width)
MAY supply a *child* term of MS:1000901 (retention time normalization standard) only once
  e.g.: MS:1000902 (H-PINS retention time normalization standard)
MUST supply term MS:1000895 (local retention time) only once

Path /TraML/TargetList/Target/RetentionTime/RetentionTime
MAY supply a *child* term of MS:1000915 (retention time window attribute) one or more times
  e.g.: MS:1000916 (retention time window lower offset)
  e.g.: MS:1000917 (retention time window upper offset)
  e.g.: MS:1001907 (retention time window width)
MAY supply a *child* term of MS:1000901 (retention time normalization standard) only once
  e.g.: MS:1000902 (H-PINS retention time normalization standard)
MUST supply term MS:1000895 (local retention time) only once

Path /TraML/CompoundList/Peptide/RetentionTimeList/RetentionTime
MAY supply a *child* term of MS:1000915 (retention time window attribute) one or more times
  e.g.: MS:1000916 (retention time window lower offset)
  e.g.: MS:1000917 (retention time window upper offset)
  e.g.: MS:1001907 (retention time window width)
MAY supply a *child* term of MS:1000901 (retention time normalization standard) only once
  e.g.: MS:1000902 (H-PINS retention time normalization standard)
MAY supply a *child* term of MS:1000894 (retention time) one or more times
  e.g.: MS:1000895 (local retention time)
  e.g.: MS:1000896 (normalized retention time)
  e.g.: MS:1000897 (predicted retention time)
  e.g.: MS:1000916 (retention time window lower offset)
  e.g.: MS:1000917 (retention time window upper offset)
  e.g.: MS:1001907 (retention time window width)

Path /TraML/CompoundList/Compound/RetentionTimeList/RetentionTime
MAY supply a *child* term of MS:1000915 (retention time window attribute) one or more times
  e.g.: MS:1000916 (retention time window lower offset)
  e.g.: MS:1000917 (retention time window upper offset)
  e.g.: MS:1001907 (retention time window width)
MAY supply a *child* term of MS:1000901 (retention time normalization standard) only once
  e.g.: MS:1000902 (H-PINS retention time normalization standard)
MAY supply a *child* term of MS:1000894 (retention time) one or more times
  e.g.: MS:1000895 (local retention time)
  e.g.: MS:1000896 (normalized retention time)
  e.g.: MS:1000897 (predicted retention time)
  e.g.: MS:1000916 (retention time window lower offset)
  e.g.: MS:1000917 (retention time window upper offset)
  e.g.: MS:1001907 (retention time window width)

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000897" name="predicted retention time" value="44.07" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
<cvParam cvRef="MS" accession="MS:1000896" name="normalized retention time" value="38.43" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
<cvParam cvRef="MS" accession="MS:1000902" name="H-PINS retention time normalization standard"/>
<cvParam cvRef="MS" accession="MS:1000895" name="local retention time" value="40.02" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
<cvParam cvRef="MS" accession="MS:1000916" name="retention time window lower offset" value="3.0" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
<cvParam cvRef="MS" accession="MS:1000917" name="retention time window upper offset" value="3.0" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>

Element <Prediction>

Definition:

Information about a prediction for a suitable transition using some software

Type:

PredictionType

Attributes:

Attribute Name	Data Type	Use	Definition
contactRef	xs:IDREF	optional	Reference to a contact person that generated this prediction
softwareRef	xs:IDREF	required	Reference to a software package from which this prediction is derived

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	0	unbounded	Controlled vocabulary term adding information to the parent term
userParam	0	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Example Context:

<Prediction softwareRef="MaRiMba" contactRef="CS">
  <cvParam cvRef="MS" accession="MS:1000912" name="transition purported from an MS/MS spectrum on a different, specified instrument"/>
  <cvParam cvRef="MS" accession="MS:1000291" name="linear ion trap"/>
  <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="10000" unitCvRef="MS" unitAccession="MS:1000905" unitName="percent of base peak times 100"/>
  <cvParam cvRef="MS" accession="MS:1000906" name="peak intensity rank" value="1"/>
  <cvParam cvRef="MS" accession="MS:1000907" name="peak targeting suitability rank" value="1"/>
</Prediction>

cvParam Mapping Rules:

Path /TraML/TransitionList/Transition/Prediction
MAY supply term MS:1000042 (peak intensity) only once
MAY supply a *child* term of MS:1000909 (transition validation method) only once
  e.g.: MS:1000910 (transition optimized on specified instrument)
  e.g.: MS:1000911 (transition validated with an MS/MS spectrum on specified instrument)
  e.g.: MS:1000912 (transition purported from an MS/MS spectrum on a different, specified instrument)
  e.g.: MS:1000913 (transition predicted by informatic analysis)
MAY supply term MS:1000443 (mass analyzer type) or any of its children only once
  e.g.: MS:1000078 (axial ejection linear ion trap)
  e.g.: MS:1000079 (fourier transform ion cyclotron resonance mass spectrometer)
  e.g.: MS:1000080 (magnetic sector)
  e.g.: MS:1000081 (quadrupole)
  e.g.: MS:1000082 (quadrupole ion trap)
  e.g.: MS:1000083 (radial ejection linear ion trap)
  e.g.: MS:1000084 (time-of-flight)
  e.g.: MS:1000254 (electrostatic energy analyzer)
  e.g.: MS:1000284 (stored waveform inverse fourier transform)
  e.g.: MS:1000288 (cyclotron)
  et al.
MAY supply term MS:1000906 (peak intensity rank) only once
MAY supply term MS:1000907 (peak targeting suitability rank) only once
MAY supply term MS:1000031 (instrument model) or any of its children only once
  e.g.: MS:1000139 (4000 QTRAP)
  e.g.: MS:1000140 (4700 Proteomics Analyzer)
  e.g.: MS:1000141 (apex IV)
  e.g.: MS:1000142 (apex Q)
  e.g.: MS:1000143 (API 150EX)
  e.g.: MS:1000144 (API 150EX Prep)
  e.g.: MS:1000145 (API 2000)
  e.g.: MS:1000146 (API 3000)
  e.g.: MS:1000147 (API 4000)
  e.g.: MS:1000148 (autoflex II)
  et al.

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000912" name="transition purported from an MS/MS spectrum on a different, specified instrument"/>
<cvParam cvRef="MS" accession="MS:1000291" name="linear ion trap"/>
<cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="10000" unitCvRef="MS" unitAccession="MS:1000905" unitName="percent of base peak times 100"/>
<cvParam cvRef="MS" accession="MS:1000906" name="peak intensity rank" value="1"/>
<cvParam cvRef="MS" accession="MS:1000907" name="peak targeting suitability rank" value="1"/>

Element <Target>

Definition:

A peptide or compound that is to be included or excluded from a target list of precursor m/z values.

Type:

TargetType

Attributes:

Attribute Name	Data Type	Use	Definition
compoundRef	xs:IDREF	optional	Reference to a compound for which this target is the trigger
id	xs:string	required	String label for this target
peptideRef	xs:IDREF	optional	Reference to a peptide for which this target is the trigger

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Precursor	1	1	Precursor (Q1) of the transition or target
RetentionTime	0	1	Information about predicted or calibrated retention time
ConfigurationList	0	1	List of insutrument configurations used in the validation or optimization of the transitions
cvParam	0	unbounded	Controlled vocabulary term adding information to the parent term
userParam	0	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Example Context:

<Target id="PEPTIDEC2+" peptideRef="PEPTIDEC">
  <Precursor>
    <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
    <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
  </Precursor>
  <RetentionTime softwareRef="Skyline0.5">
    <cvParam cvRef="MS" accession="MS:1000895" name="local retention time" value="27.44" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
  ...
</Target>

Element <InterpretationList>

Definition:

List of possible interprations of fragment ions for a transition

Type:

InterpretationListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Interpretation	1	unbounded	A possible interpretation of the product ion for a transition

Example Context:

<InterpretationList>
  <Interpretation>
      <cvParam cvRef="MS" accession="MS:1000926" name="product interpretation rank" value="1"/>
      <cvParam cvRef="MS" accession="MS:1001220" name="frag: y ion"/>
      <cvParam cvRef="MS" accession="MS:1000903" name="product ion series ordinal" value="8"/>
      <cvParam cvRef="MS" accession="MS:1000904" name="product ion m/z delta" value="0.03" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
  </Interpretation>
  ...
</InterpretationList>

Element <ConfigurationList>

Definition:

List of insutrument configurations used in the validation or optimization of the transitions

Type:

ConfigurationListType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
Configuration	1	unbounded	Instrument configuration used in the testing, validation or optimization of the transitions

Example Context:

<ConfigurationList>
  <Configuration instrumentRef="QTRAP" contactRef="CS">
    <cvParam cvRef="MS" accession="MS:1000502" name="dwell time" value="0.12" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
    <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="26" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
    <cvParam cvRef="MS" accession="MS:1000875" name="declustering potential" value="64" unitCvRef="UO" unitAccession="UO:0000218" unitName="volt"/>
    <cvParam cvRef="MS" accession="MS:1000419" name="collision gas" value="argon"/>
    <cvParam cvRef="MS" accession="MS:1000869" name="collision gas pressure" value="12" unitCvRef="UO" unitAccession="UO:0000110" unitName="pascal"/>
  ...
</ConfigurationList>

Element <Interpretation>

Definition:

A possible interpretation of the product ion for a transition

Type:

InterpretationType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	0	unbounded	Controlled vocabulary term adding information to the parent term
userParam	0	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Example Context:

<Interpretation>
      <cvParam cvRef="MS" accession="MS:1000926" name="product interpretation rank" value="2"/>
      <cvParam cvRef="MS" accession="MS:1001222" name="frag: b ion - H2O"/>
      <cvParam cvRef="MS" accession="MS:1000903" name="product ion series ordinal" value="9"/>
      <cvParam cvRef="MS" accession="MS:1000904" name="product ion m/z delta" value="-0.43" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
</Interpretation>

cvParam Mapping Rules:

Path /TraML/TransitionList/Transition/IntermediateProduct/InterpretationList/Interpretation
MUST supply a *child* term of MS:1001221 (fragmentation information) one or more times
  e.g.: MS:1000903 (product ion series ordinal)
  e.g.: MS:1000904 (product ion m/z delta)
  e.g.: MS:1000926 (product interpretation rank)
  e.g.: MS:1001220 (frag: y ion)
  e.g.: MS:1001222 (frag: b ion - H2O)
  e.g.: MS:1001223 (frag: y ion - H2O)
  e.g.: MS:1001224 (frag: b ion)
  e.g.: MS:1001225 (product ion m/z)
  e.g.: MS:1001226 (product ion intensity)
  e.g.: MS:1001227 (product ion m/z error)
  et al.
MAY supply term MS:1000904 (product ion m/z delta) only once
MUST supply term MS:1000926 (product interpretation rank) only once
MUST supply term MS:1000903 (product ion series ordinal) only once

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000926" name="product interpretation rank" value="1"/>
<cvParam cvRef="MS" accession="MS:1001220" name="frag: y ion"/>
<cvParam cvRef="MS" accession="MS:1000903" name="product ion series ordinal" value="8"/>
<cvParam cvRef="MS" accession="MS:1000904" name="product ion m/z delta" value="0.03" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="MS" accession="MS:1001222" name="frag: b ion - H2O"/>

Element <Configuration>

Definition:

Instrument configuration used in the testing, validation or optimization of the transitions

Type:

ConfigurationType

Attributes:

Attribute Name	Data Type	Use	Definition
contactRef	xs:IDREF	optional	Reference to a contact person originating this information
instrumentRef	xs:IDREF	required	Reference to an instrument for which this configuration information is appropriate

Subelements:

Subelement Name	maxOccurs	Definition
cvParam	unbounded	Controlled vocabulary term adding information to the parent term
userParam	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead
ValidationStatus	unbounded	Information about the state of validation of a transition on a given instrument model

Example Context:

<Configuration instrumentRef="QTRAP" contactRef="CS">
  <cvParam cvRef="MS" accession="MS:1000502" name="dwell time" value="0.12" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
  <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="26" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
  <cvParam cvRef="MS" accession="MS:1000875" name="declustering potential" value="64" unitCvRef="UO" unitAccession="UO:0000218" unitName="volt"/>
  <cvParam cvRef="MS" accession="MS:1000419" name="collision gas" value="argon"/>
  <cvParam cvRef="MS" accession="MS:1000869" name="collision gas pressure" value="12" unitCvRef="UO" unitAccession="UO:0000110" unitName="pascal"/>
  <cvParam cvRef="MS" accession="MS:1000876" name="cone voltage" value="1200" unitCvRef="UO" unitAccession="UO:0000218" unitName="volt"/>
  ...
</Configuration>

cvParam Mapping Rules:

Path /TraML/TargetList/TargetIncludeList/Target/ConfigurationList/Configuration
MAY supply a *child* term of MS:1000482 (source attribute) one or more times
  e.g.: MS:1000392 (ionization efficiency)
  e.g.: MS:1000486 (source potential)
  e.g.: MS:1000843 (wavelength)
  e.g.: MS:1000844 (focus diameter x)
  e.g.: MS:1000845 (focus diameter y)
  e.g.: MS:1000846 (pulse energy)
  e.g.: MS:1000847 (pulse duration)
  e.g.: MS:1000848 (attenuation)
  e.g.: MS:1000849 (impact angle)
  e.g.: MS:1000850 (gas laser)
  et al.
MAY supply a *child* term of MS:1000510 (precursor activation attribute) one or more times
  e.g.: MS:1000045 (collision energy)
  e.g.: MS:1000138 (percent collision energy)
  e.g.: MS:1000245 (charge stripping)
  e.g.: MS:1000412 (buffer gas)
  e.g.: MS:1000419 (collision gas)
  e.g.: MS:1000509 (activation energy)
  e.g.: MS:1000869 (collision gas pressure)
MAY supply term MS:1000502 (dwell time) only once

Path /TraML/TransitionList/Transition/Product/ConfigurationList/Configuration
MAY supply a *child* term of MS:1000482 (source attribute) one or more times
  e.g.: MS:1000392 (ionization efficiency)
  e.g.: MS:1000486 (source potential)
  e.g.: MS:1000843 (wavelength)
  e.g.: MS:1000844 (focus diameter x)
  e.g.: MS:1000845 (focus diameter y)
  e.g.: MS:1000846 (pulse energy)
  e.g.: MS:1000847 (pulse duration)
  e.g.: MS:1000848 (attenuation)
  e.g.: MS:1000849 (impact angle)
  e.g.: MS:1000850 (gas laser)
  et al.
MAY supply a *child* term of MS:1000510 (precursor activation attribute) one or more times
  e.g.: MS:1000045 (collision energy)
  e.g.: MS:1000138 (percent collision energy)
  e.g.: MS:1000245 (charge stripping)
  e.g.: MS:1000412 (buffer gas)
  e.g.: MS:1000419 (collision gas)
  e.g.: MS:1000509 (activation energy)
  e.g.: MS:1000869 (collision gas pressure)
MAY supply term MS:1000502 (dwell time) only once

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000502" name="dwell time" value="0.12" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
<cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="26" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/>
<cvParam cvRef="MS" accession="MS:1000875" name="declustering potential" value="64" unitCvRef="UO" unitAccession="UO:0000218" unitName="volt"/>
<cvParam cvRef="MS" accession="MS:1000419" name="collision gas" value="argon"/>
<cvParam cvRef="MS" accession="MS:1000869" name="collision gas pressure" value="12" unitCvRef="UO" unitAccession="UO:0000110" unitName="pascal"/>
<cvParam cvRef="MS" accession="MS:1000876" name="cone voltage" value="1200" unitCvRef="UO" unitAccession="UO:0000218" unitName="volt"/>
<cvParam cvRef="MS" accession="MS:1000880" name="interchannel delay" value="0.01" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/>
<cvParam cvRef="MS" accession="MS:1000877" name="tube lens voltage" value="23" unitCvRef="UO" unitAccession="UO:0000218" unitName="volt"/>

Element <ValidationStatus>

Definition:

Information about the state of validation of a transition on a given instrument model

Type:

ValidationStatusType

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	0	unbounded	Controlled vocabulary term adding information to the parent term
userParam	0	unbounded	Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead

Example Context:

<ValidationStatus>
        <cvParam cvRef="MS" accession="MS:1000910" name="transition optimized on specified instrument"/>
        <cvParam cvRef="MS" accession="MS:1000139" name="4000 QTRAP"/>
        <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="4072" unitCvRef="MS" unitAccession="MS:1000905" unitName="percent of base peak times 100"/>
        <cvParam cvRef="MS" accession="MS:1000906" name="peak intensity rank" value="2"/>
        <cvParam cvRef="MS" accession="MS:1000907" name="peak targeting suitability rank" value="1"/>
</ValidationStatus>

cvParam Mapping Rules:

Path /TraML/TransitionList/Transition/ConfigurationList/Configuration/ValidationStatus
MAY supply term MS:1000042 (peak intensity) only once
MAY supply a *child* term of MS:1000909 (transition validation method) only once
  e.g.: MS:1000910 (transition optimized on specified instrument)
  e.g.: MS:1000911 (transition validated with an MS/MS spectrum on specified instrument)
  e.g.: MS:1000912 (transition purported from an MS/MS spectrum on a different, specified instrument)
  e.g.: MS:1000913 (transition predicted by informatic analysis)
MAY supply term MS:1000906 (peak intensity rank) only once
MAY supply term MS:1000907 (peak targeting suitability rank) only once
MAY supply term MS:1000031 (instrument model) or any of its children only once
  e.g.: MS:1000139 (4000 QTRAP)
  e.g.: MS:1000140 (4700 Proteomics Analyzer)
  e.g.: MS:1000141 (apex IV)
  e.g.: MS:1000142 (apex Q)
  e.g.: MS:1000143 (API 150EX)
  e.g.: MS:1000144 (API 150EX Prep)
  e.g.: MS:1000145 (API 2000)
  e.g.: MS:1000146 (API 3000)
  e.g.: MS:1000147 (API 4000)
  e.g.: MS:1000148 (autoflex II)
  et al.

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000910" name="transition optimized on specified instrument"/>
<cvParam cvRef="MS" accession="MS:1000139" name="4000 QTRAP"/>
<cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="4072" unitCvRef="MS" unitAccession="MS:1000905" unitName="percent of base peak times 100"/>
<cvParam cvRef="MS" accession="MS:1000906" name="peak intensity rank" value="2"/>
<cvParam cvRef="MS" accession="MS:1000907" name="peak targeting suitability rank" value="1"/>

Notes and Constraints:

If the "peak intensity" cvParam is used, its absolute units is not important. However, it MUST be proportional to other fragment ions from the same precursor. Ideally it will also be proportional to the intensities for other peptide ions from the same protein.

Element <TraML>

Element <cvList>

Element <SourceFileList>

Element <ContactList>

Element <PublicationList>

Element <InstrumentList>

Element <SoftwareList>

Element <ProteinList>

Element <CompoundList>

Element <TransitionList>

Element <TargetList>

Element <cv>

Element <SourceFile>

Element <Contact>

Element <Publication>

Element <Instrument>

Element <Software>

Element <Protein>

Element <cvParam>

Element <userParam>

Element <Peptide>

Element <Compound>

Element <Transition>

Element <TargetIncludeList>

Element <TargetExcludeList>

Element <Sequence>

Element <ProteinRef>

Element <Modification>

Element <RetentionTimeList>

Element <Evidence>

Element <Precursor>

Element <IntermediateProduct>

Element <Product>

Element <RetentionTime>

Element <Prediction>

Element <Target>

Element <InterpretationList>

Element <ConfigurationList>

Element <Interpretation>

Element <Configuration>

Element <ValidationStatus>