Element <mzML>

Definition:

This is the root element for the Proteomics Standards Initiative (PSI) mzML schema, which is intended to capture the use of a mass spectrometer, the data generated, and the initial processing of that data (to the level of the peak list).

Attributes:

Attribute Name	Data Type	Use	Definition
accession	xs:string	optional	An optional accession number for the mzML document.
id	xs:string	optional	An optional id for the mzML document. It is recommended to use LSIDs when possible.
version	xs:string	required	The version of this mzML document.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvList	1	1	Container for one or more controlled vocabulary definitions.
fileDescription	1	1	Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is stored here.
referenceableParamGroupList	0	1	Container for a list of referenceableParamGroups
sampleList	0	1	List and descriptions of samples.
instrumentConfigurationList	1	1	List and descriptions of instrument configurations.
softwareList	1	1	List and descriptions of software used to acquire and/or process the data in this mzML file.
dataProcessingList	1	1	List and descriptions of data processing applied to this data.
acquisitionSettingsList	0	1	List with the descriptions of the acquisition settings applied prior to the start of data acquisition.
run	1	1	A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument.

Graphical Context:

Example Context:

<mzML xmlns="http://psi.hupo.org/schema_revision/mzML_1.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/schema_revision/mzML_1.0.0 mzML1.0.0.xsd" id="urn:lsid:psidev.info:mzML.instanceDocuments.tiny.pwiz" version="1.0">
  <cvList count="2">
    <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="2.0.2" URI="http://psidev.sourceforge.net/ms/xml/mzdata/psi-ms.2.0.2.obo"/>
    <cv id="UO" fullName="Unit Ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
  </cvList>
  ...
</mzML>

Notes and Constraints:

The <mzML> element and all content below may occur by itself in an XML document, but is also designed to be wrapped in the mzML indexing schema in order to facilitate random access within the file with appropriate reader software.

Element <cvList>

Definition:

Container for one or more controlled vocabulary definitions.

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	The number of CV definitionsin this mzML file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cv	1	unbounded	Information about an ontology or CV source and a short 'lookup' tag to refer to.

Graphical Context:

Example Context:

<cvList count="2">
  <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="2.0.2" URI="http://psidev.sourceforge.net/ms/xml/mzdata/psi-ms.2.0.2.obo"/>
  <cv id="UO" fullName="Unit Ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
</cvList>

Notes and Constraints:

One of the <cv> elements in this list MUST be the PSI MS controlled vocabulary. All <cvParam> elements in the document MUST refer to one of the <cv> elements in this list.

Element <fileDescription>

Definition:

Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is stored here.

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
fileContent	1	1	This summarizes the different types of spectra that can be expected in the file. This is expected to aid processing software in skipping files that do not contain appropriate spectrum types for it.
sourceFileList	0	1	List and descriptions of the source files this mzML document was generated or derived from
contact	0	unbounded	Structure allowing the use of a controlled (cvParam) or uncontrolled vocabulary (userParam), or a reference to a predefined set of these in this mzML file (paramGroupRef).

Graphical Context:

Example Context:

<fileDescription>
  <fileContent>
    <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
  </fileContent>
  <sourceFileList count="2">
  ...
</fileDescription>

Element <referenceableParamGroupList>

Definition:

Container for a list of referenceableParamGroups

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	The number of ParamGroups defined in this mzML file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
referenceableParamGroup	1	unbounded	A collection of CVParam and UserParam elements that can be referenced from elsewhere in this mzML document by using the 'paramGroupRef' element in that location to reference the 'id' attribute value of this element.

Graphical Context:

Example Context:

<referenceableParamGroupList count="2">
  <referenceableParamGroup id="CommonMS1SpectrumParams">
    <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
    <cvParam cvRef="MS" accession="MS:1000498" name="full scan" value=""/>
  </referenceableParamGroup>
  ...
</referenceableParamGroupList>

Element <sampleList>

Definition:

List and descriptions of samples.

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	The number of Samples defined in this mzML file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
sample	1	unbounded	Expansible description of the sample used to generate the dataset, named in sampleName.

Graphical Context:

Example Context:

<sampleList count="1">
  <sample id="sample1" name="Sample1">
  </sample>
</sampleList>

Element <instrumentConfigurationList>

Definition:

List and descriptions of instrument configurations.

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	The number of instrument configurations present in this list.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
instrumentConfiguration	1	unbounded	Description of a particular hardware configuration of a mass spectrometer. Each configuration MUST have one (and only one) of the three different components used for an analysis. For hybrid instruments, such as an LTQ-FT, there MUST be one configuration for each permutation of the components that is used in the document. For software configuration, use a ReferenceableParamGroup element.

Example Context:

<instrumentConfigurationList count="1">
  <instrumentConfiguration id="LCQDeca">
    <cvParam cvRef="MS" accession="MS:1000554" name="LCQ Deca" value=""/>
    <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="23433"/>
    <componentList count="3">
  ...
</instrumentConfigurationList>

Element <softwareList>

Definition:

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

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	The number of softwares defined in this mzML file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
software	1	unbounded	A piece of software.

Graphical Context:

Example Context:

<softwareList count="3">
  <software id="Bioworks">
    <softwareParam cvRef="MS" accession="MS:1000533" name="Bioworks" version="3.3.1 sp1"/>
  </software>
  <software id="pwiz">
  ...
</softwareList>

Element <dataProcessingList>

Definition:

List and descriptions of data processing applied to this data.

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	The number of DataProcessingTypes in this mzML file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
dataProcessing	1	unbounded	Description of the way in which a particular software was used.

Graphical Context:

Example Context:

<dataProcessingList count="2">
  <dataProcessing id="XcaliburProcessing" softwareRef="Xcalibur">
    <processingMethod order="1">
      <cvParam cvRef="MS" accession="MS:1000033" name="deisotoping" value="false"/>
      <cvParam cvRef="MS" accession="MS:1000034" name="charge deconvolution" value="false"/>
  ...
</dataProcessingList>

Element <acquisitionSettingsList>

Definition:

List with the descriptions of the acquisition settings applied prior to the start of data acquisition.

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	The number of AcquisitionType elements in this list.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
acquisitionSettings	1	unbounded	Description of the acquisition settings of the instrument prior to the start of the run.

Graphical Context:

Example Context:

<acquisitionSettingsList count="1">
  <acquisitionSettings id="as1" instrumentConfigurationRef="LCQDeca">
    <sourceFileRefList count="1">
      <sourceFileRef ref="sf_parameters"/>
    </sourceFileRefList>
  ...
</acquisitionSettingsList>

Element <run>

Definition:

A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument.

Attributes:

Attribute Name	Data Type	Use	Definition
defaultInstrumentConfigurationRef	xs:IDREF	required	This attribute MUST reference the 'id' of the default instrument configuration. If a scan does not reference an instrument configuration, it implicitly refers to this configuration.
id	xs:ID	required	A unique identifier for this run.
sampleRef	xs:IDREF	optional	This attribute MUST reference the 'id' of the appropriate sample.
startTimeStamp	xs:dateTime	optional	The optional start timestamp of the run, in UT.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
referenceableParamGroupRef	0	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	0	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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
sourceFileRefList	0	1	Container for a list of source file references.
spectrumList	1	1	All mass spectra and the acquisitions underlying them are described and attached here. Subsidiary data arrays are also both described and attached here.
chromatogramList	0	1	All chromatograms for thsi run.

Graphical Context:

Example Context:

<run id="Exp01" defaultInstrumentConfigurationRef="LCQDeca" sampleRef="sample1" startTimeStamp="2007-06-27T15:23:45.00035">
  <sourceFileRefList count="1">
    <sourceFileRef ref="sf1"/>
  </sourceFileRefList>
  <spectrumList count="3">
  ...
</run>

Element <cv>

Definition:

Information about an ontology or CV source and a short 'lookup' tag to refer to.

Attributes:

Attribute Name	Data Type	Use	Definition
URI	xs:anyURI	required	The URI for the resource.
fullName	xs:string	required	The usual name for the resource (e.g. The PSI-MS Controlled Vocabulary).
id	xs:ID	required	The short label to be used as a reference tag with which to refer to this particular Controlled Vocabulary source description (e.g., from the cvLabel attribute, in CVParamType elements).
version	xs:string	optional	The version of the CV from which the referred-to terms are drawn.

Subelements:

none

Example Context:

<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="2.0.2" URI="http://psidev.sourceforge.net/ms/xml/mzdata/psi-ms.2.0.2.obo"/>

Element <fileContent>

Definition:

This summarizes the different types of spectra that can be expected in the file. This is expected to aid processing software in skipping files that do not contain appropriate spectrum types for it.

Attributes:

none

Subelements:

Subelement Name	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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

Example Context:

<fileContent>
  <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
</fileContent>

cvParam Mapping Rules:

MUST supply a *child* term of MS:1000524 (data file content) one or more times
  e.g.: MS:1000235 (total ion current chromatogram)
  e.g.: MS:1000579 (MS1 spectrum)
  e.g.: MS:1000580 (MSn spectrum)
  e.g.: MS:1000581 (CRM spectrum)
  e.g.: MS:1000582 (SIM spectrum)
  e.g.: MS:1000583 (SRM spectrum)
  e.g.: MS:1000620 (PDA spectrum)
  e.g.: MS:1000627 (selected ion current chromatogram)
  e.g.: MS:1000628 (basepeak chromatogram)

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>

Element <sourceFileList>

Definition:

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

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	Number of source files used in generating the instance document.

Subelements:

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

Example Context:

<sourceFileList count="2">
  <sourceFile id="sf1" name="tiny1.RAW" location="file:///F:/data/Exp01">
    <cvParam cvRef="MS" accession="MS:1000563" name="Xcalibur RAW file" value=""/>
    <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="71be39fb2700ab2f3c8b2234b91274968b6899b1"/>
  </sourceFile>
  ...
</sourceFileList>

Element <contact>

Definition:

Structure allowing the use of a controlled (cvParam) or uncontrolled vocabulary (userParam), or a reference to a predefined set of these in this mzML file (paramGroupRef).

Attributes:

none

Subelements:

Subelement Name	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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

Example Context:

<contact>
  <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="William Pennington"/>
  <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Higglesworth University, 12 Higglesworth Avenue, 12045, HI, USA"/>
  <cvParam cvRef="MS" accession="MS:1000588" name="contact URL" value="http://www.higglesworth.edu/"/>
  <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="wpennington@higglesworth.edu"/>
  ...
</contact>

cvParam Mapping Rules:

MUST supply a *child* term of MS:1000585 (contact person 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)

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="William Pennington"/>
<cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Higglesworth University, 12 Higglesworth Avenue, 12045, HI, USA"/>
<cvParam cvRef="MS" accession="MS:1000588" name="contact URL" value="http://www.higglesworth.edu/"/>
<cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="wpennington@higglesworth.edu"/>

Element <referenceableParamGroup>

Definition:

A collection of CVParam and UserParam elements that can be referenced from elsewhere in this mzML document by using the 'paramGroupRef' element in that location to reference the 'id' attribute value of this element.

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	The identifier with which to reference this ReferenceableParamGroup.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	0	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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:

<referenceableParamGroup id="CommonMS1SpectrumParams">
  <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
  <cvParam cvRef="MS" accession="MS:1000498" name="full scan" value=""/>
</referenceableParamGroup>

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
<cvParam cvRef="MS" accession="MS:1000498" name="full scan" value=""/>

Element <sample>

Definition:

Expansible description of the sample used to generate the dataset, named in sampleName.

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	A unique identifier across the samples with which to reference this sample description.
name	xs:string	optional	An optional name for the sample description, mostly intended as a quick mnemonic.

Subelements:

Subelement Name	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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

Example Context:

<sample id="sample1" name="Sample1">
</sample>

cvParam Mapping Rules:

MAY supply a *child* term of GO:0005575 (cellular_component) one or more times
MAY supply a *child* term of BTO:0000000 (brenda source tissue ontology) one or more times
MAY supply a *child* term of PATO:0001241 (quality of an object) one or more times
MAY supply a *child* term of MS:1000548 (sample attribute) one or more times
  e.g.: MS:1000001 (sample number)
  e.g.: MS:1000004 (sample mass)
  e.g.: MS:1000005 (sample volume)
  e.g.: MS:1000006 (sample concentration)
  e.g.: MS:1000053 (sample batch)

Element <instrumentConfiguration>

Definition:

Description of a particular hardware configuration of a mass spectrometer. Each configuration MUST have one (and only one) of the three different components used for an analysis. For hybrid instruments, such as an LTQ-FT, there MUST be one configuration for each permutation of the components that is used in the document. For software configuration, use a ReferenceableParamGroup element.

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	An identifier for this instrument configuration.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
referenceableParamGroupRef	0	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	0	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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
componentList	1	1	List with the different components used in the mass spectrometer. At least one source, one mass analyzer and one detector need to be specified.
softwareRef	0	1	Reference to a previously defined software element

Example Context:

<instrumentConfiguration id="LCQDeca">
  <cvParam cvRef="MS" accession="MS:1000554" name="LCQ Deca" value=""/>
  <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="23433"/>
  <componentList count="3">
    <source order="1">
  ...
</instrumentConfiguration>

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000554" name="LCQ Deca" value=""/>
<cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="23433"/>

Element <software>

Definition:

A piece of software.

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	An identifier for this software that is unique across all SoftwareTypes.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
softwareParam	1	1	A description of the software, based on CV information and a software version.

Example Context:

<software id="Bioworks">
  <softwareParam cvRef="MS" accession="MS:1000533" name="Bioworks" version="3.3.1 sp1"/>
</software>

Element <dataProcessing>

Definition:

Description of the way in which a particular software was used.

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	A unique identifier for this data processing that is unique across all DataProcessingTypes.
softwareRef	xs:IDREF	required	This attribute MUST reference the 'id' of the appropriate SoftwareType.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
processingMethod	1	unbounded	Description of the default peak processing method. This element describes the base method used in the generation of a particular mzML file. Variable methods should be described in the appropriate acquisition section - if no acquisition-specific details are found, then this information serves as the default.

Example Context:

<dataProcessing id="XcaliburProcessing" softwareRef="Xcalibur">
  <processingMethod order="1">
    <cvParam cvRef="MS" accession="MS:1000033" name="deisotoping" value="false"/>
    <cvParam cvRef="MS" accession="MS:1000034" name="charge deconvolution" value="false"/>
    <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value="true"/>
  ...
</dataProcessing>

Element <acquisitionSettings>

Definition:

Description of the acquisition settings of the instrument prior to the start of the run.

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	A unique identifier for this acquisition setting.
instrumentConfigurationRef	xs:IDREF	required	This attribute MUST reference the 'id' of the appropriate instrument configuration.

Subelements:

Subelement Name	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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
sourceFileRefList	1	Container for a list of source file references.
targetList	1	Target list (or 'inclusion list') configured prior to the run.

Example Context:

<acquisitionSettings id="as1" instrumentConfigurationRef="LCQDeca">
  <sourceFileRefList count="1">
    <sourceFileRef ref="sf_parameters"/>
  </sourceFileRefList>
  <targetList count="2">
  ...
</acquisitionSettings>

Element <referenceableParamGroupRef>

Definition:

A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.

Attributes:

Attribute Name	Data Type	Use	Definition
ref	xs:IDREF	required	Reference to the id attribute in a referenceableParamGroup.

Subelements:

none

Example Context:

<referenceableParamGroupRef ref="CommonMS1SpectrumParams"/>

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000016" name="scan time" value="5.8905" unitCvRef="MS" unitAccession="MS:1000038" unitName="minute"/>
<cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="+ c NSI Full ms [ 400.00-1800.00]"/>
<cvParam cvRef="MS" accession="MS:1000616" name="preset scan configuration" value="3"/>

Element <cvParam>

Definition:

This element holds additional data or annotation. Only controlled values are allowed here.

Attributes:

Attribute Name	Data Type	Use	Definition
accession	xs:string	required	The accession number of the referred-to term in the named resource (e.g.: MS:000012).
cvRef	xs:IDREF	required	A reference to the CV 'id' attribute as defined in the cvList in this mzML file.
name	xs:string	required	The actual name for the parameter, from the referred-to controlled vocabulary. This should be the preferred name associated with the specified accession number.
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; may be absent if not appropriate, or a numeric or symbolic value, or may itself be CV (legal values for a parameter should be enumerated and defined in the ontology).

Subelements:

none

Example Context:

<cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>

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

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="example" value="spectrum with no data (no BinaryDataArrayList)"/>

Element <sourceFileRefList>

Definition:

Container for a list of source file references.

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	This number of source files referenced in this list.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
sourceFileRef	0	unbounded	Reference to a previously defined sourceFile.

Graphical Context:

Example Context:

<sourceFileRefList count="1">
  <sourceFileRef ref="sf_parameters"/>
</sourceFileRefList>

Element <spectrumList>

Definition:

All mass spectra and the acquisitions underlying them are described and attached here. Subsidiary data arrays are also both described and attached here.

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	The number of spectra defined in this mzML file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
spectrum	0	unbounded	The structure that captures the generation of a peak list (including the underlying acquisitions)

Graphical Context:

Example Context:

<spectrumList count="3">
  <spectrum index="0" id="S19" nativeID="19" defaultArrayLength="15">
    <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
    <spectrumDescription>
  ...
</spectrumList>

Element <chromatogramList>

Definition:

All chromatograms for thsi run.

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	The number of chromatograms defined in this mzML file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
chromatogram	1	unbounded	A single chromatogram.

Graphical Context:

Example Context:

<chromatogramList count="2">
  <chromatogram index="0" id="tic" nativeID="tic native" defaultArrayLength="15" dataProcessingRef="XcaliburProcessing">
    <cvParam cvRef="MS" accession="MS:1000235" name="total ion current chromatogram" value=""/>
    <binaryDataArrayList count="2">
      <binaryDataArray encodedLength="160" dataProcessingRef="pwizconversion">
  ...
</chromatogramList>

Element <sourceFile>

Definition:

Description of the source file, including location and type.

Attributes:

Attribute Name	Data Type	Use	Definition
id	xs:ID	required	An identifier for this file.
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	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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

Example Context:

<sourceFile id="sf1" name="tiny1.RAW" location="file:///F:/data/Exp01">
  <cvParam cvRef="MS" accession="MS:1000563" name="Xcalibur RAW file" value=""/>
  <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="71be39fb2700ab2f3c8b2234b91274968b6899b1"/>
</sourceFile>

cvParam Mapping Rules:

MUST 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)
MUST supply a *child* term of MS:1000560 (source file type) one or more times
  e.g.: MS:1000526 (MassLynx raw format)
  e.g.: MS:1000562 (wiff file)
  e.g.: MS:1000563 (Xcalibur RAW file)
  e.g.: MS:1000564 (mzData file)
  e.g.: MS:1000565 (pkl file)
  e.g.: MS:1000566 (mzXML file)
  e.g.: MS:1000567 (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)

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000563" name="Xcalibur RAW file" value=""/>
<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="71be39fb2700ab2f3c8b2234b91274968b6899b1"/>

Element <componentList>

Definition:

List with the different components used in the mass spectrometer. At least one source, one mass analyzer and one detector need to be specified.

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	The number of components in this list.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
source	1	1	A source component.
analyzer	1	1	A mass analyzer (or mass filter) component.
detector	1	1	A detector component.

Example Context:

<componentList count="3">
  <source order="1">
    <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/>
  </source>
  <analyzer order="2">
  ...
</componentList>

Element <softwareRef>

Definition:

Reference to a previously defined software element

Attributes:

Attribute Name	Data Type	Use	Definition
ref	xs:IDREF	required	This attribute MUST be used to reference the 'id' attribute of a software element.

Subelements:

none

Example Context:

<softwareRef ref="Xcalibur"/>

Element <softwareParam>

Definition:

A description of the software, based on CV information and a software version.

Attributes:

Attribute Name	Data Type	Use	Definition
accession	xs:string	required	The accession number for this CV term.
cvRef	xs:IDREF	required	A reference to the CV 'id' attribute as defined in the cvList in this mzML file.
name	xs:string	required	The preferred name in the CV for the accession number of this CV term.
version	xs:string	required	The software version.

Subelements:

none

Example Context:

<softwareParam cvRef="MS" accession="MS:1000533" name="Bioworks" version="3.3.1 sp1"/>

Element <processingMethod>

Definition:

Description of the default peak processing method. This element describes the base method used in the generation of a particular mzML file. Variable methods should be described in the appropriate acquisition section - if no acquisition-specific details are found, then this information serves as the default.

Attributes:

Attribute Name	Data Type	Use	Definition
order	xs:nonNegativeInteger	required	This attributes allows a series of consecutive steps to be placed in the correct order.

Subelements:

Subelement Name	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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

Example Context:

<processingMethod order="1">
  <cvParam cvRef="MS" accession="MS:1000033" name="deisotoping" value="false"/>
  <cvParam cvRef="MS" accession="MS:1000034" name="charge deconvolution" value="false"/>
  <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value="true"/>
</processingMethod>
  ...
</processingMethod>

cvParam Mapping Rules:

MUST supply a *child* term of MS:1000543 (data processing action) one or more times
  e.g.: MS:1000033 (deisotoping)
  e.g.: MS:1000034 (charge deconvolution)
  e.g.: MS:1000035 (peak picking)
  e.g.: MS:1000592 (smoothing)
  e.g.: MS:1000593 (baseline reduction)
  e.g.: MS:1000594 (low intensity data point removal)
MUST supply a *child* term of MS:1000530 (file format conversion) one or more times
  e.g.: MS:1000544 (Conversion to mzML)
  e.g.: MS:1000545 (Conversion to mzXML)
  e.g.: MS:1000546 (Conversion to mzData)

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000033" name="deisotoping" value="false"/>
<cvParam cvRef="MS" accession="MS:1000034" name="charge deconvolution" value="false"/>
<cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value="true"/>
<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>

Element <targetList>

Definition:

Target list (or 'inclusion list') configured prior to the run.

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	The number of TargetType elements in this list.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
target	1	unbounded	Structure allowing the use of a controlled (cvParam) or uncontrolled vocabulary (userParam), or a reference to a predefined set of these in this mzML file (paramGroupRef).

Example Context:

<targetList count="2">
  <target>
    <cvParam cvRef="MS" accession="MS:1000040" name="m/z" value="1000"/>
  </target>
  <target>
  ...
</targetList>

Element <sourceFileRef>

Definition:

Reference to a previously defined sourceFile.

Attributes:

Attribute Name	Data Type	Use	Definition
ref	xs:IDREF	required	This attribute MUST reference the 'id' of the appropriate sourceFile.

Subelements:

none

Example Context:

<sourceFileRef ref="sf_parameters"/>

Element <spectrum>

Definition:

The structure that captures the generation of a peak list (including the underlying acquisitions)

Attributes:

Attribute Name	Data Type	Use	Definition
dataProcessingRef	xs:IDREF	optional	This attribute can optionally reference the 'id' of the appropriate dataProcessing.
defaultArrayLength	xs:int	required	Default length of binary data arrays contained in this element.
id	xs:ID	required	A unique identifier for this spectrum. It should be expected that external files may use this identifier together with the mzML filename or accession to reference a particular spectrum.
index	xs:nonNegativeInteger	required	The zero-based, consecutive index of the spectrum in the SpectrumList.
nativeID	xs:string	required	The native identifier for the spectrum, used by the acquisition software.
sourceFileRef	xs:IDREF	optional	This attribute can optionally reference the 'id' of the appropriate sourceFile.
spotID	xs:string	optional	The identifier for the spot from which this spectrum was derived, if a MALDI or similar run.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
referenceableParamGroupRef	0	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	0	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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
spectrumDescription	1	1	Description of the parameters for the mass spectrometer for a given acquisition (or list of acquisitions).
binaryDataArrayList	0	1	List of binary data arrays.

Graphical Context:

Example Context:

<spectrum index="0" id="S19" nativeID="19" defaultArrayLength="15">
  <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
  <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
  <spectrumDescription>
    <cvParam cvRef="MS" accession="MS:1000127" name="centroid mass spectrum" value=""/>
  ...
</spectrum>

cvParam Mapping Rules:

MUST supply a *child* term of MS:1000559 (spectrum type) only once
  e.g.: MS:1000579 (MS1 spectrum)
  e.g.: MS:1000580 (MSn spectrum)
  e.g.: MS:1000581 (CRM spectrum)
  e.g.: MS:1000582 (SIM spectrum)
  e.g.: MS:1000583 (SRM spectrum)
  e.g.: MS:1000620 (PDA spectrum)
  e.g.: MS:1000627 (selected ion current chromatogram)

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>

Notes and Constraints:

id's MUST be unique within a file. They may be LSIDs or simply the scan number. scanNumbers MUST be unique within a file and MUST be monotonically increasing throughout the file, although not necessarily sequentially. If a scan yields no peaks, it should still be reported, but with a defaultArrayLength of 0 and no <binaryDataArrayList> element.

Element <chromatogram>

Definition:

A single chromatogram.

Attributes:

Attribute Name	Data Type	Use	Definition
dataProcessingRef	xs:IDREF	optional	This attribute can optionally reference the 'id' of the appropriate dataProcessing.
defaultArrayLength	xs:int	required	Default length of binary data arrays contained in this element.
id	xs:ID	required	A unique identifier for this chromatogram.
index	xs:nonNegativeInteger	required	The zero-based index for this chromatogram in the chromatogram list.
nativeID	xs:string	required	The native identifier for the spectrum, used by the acquisition software.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
referenceableParamGroupRef	0	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	0	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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
binaryDataArrayList	1	1	List of binary data arrays.

Example Context:

<chromatogram index="0" id="tic" nativeID="tic native" defaultArrayLength="15" dataProcessingRef="XcaliburProcessing">
  <cvParam cvRef="MS" accession="MS:1000235" name="total ion current chromatogram" value=""/>
  <binaryDataArrayList count="2">
    <binaryDataArray encodedLength="160" dataProcessingRef="pwizconversion">
      <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
  ...
</chromatogram>

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000235" name="total ion current chromatogram" value=""/>

Element <source>

Definition:

A source component.

Attributes:

Attribute Name	Data Type	Use	Definition
order	xs:int	required	This attribute MUST be used to indicate the order in which the components are encountered from source to detector (e.g., in a Q-TOF, the quadrupole would have the lower order number, and the TOF the higher number of the two).

Subelements:

Subelement Name	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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

Example Context:

<source order="1">
  <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/>
</source>

cvParam Mapping Rules:

MUST 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:1000552 (maldi spot identifier)
MUST supply a *child* term of MS:1000008 (ionization type) one or more times
  e.g.: MS:1000070 (atmospheric pressure chemical ionization)
  e.g.: MS:1000071 (chemical ionization)
  e.g.: MS:1000074 (fast atom bombardment ionization)
  e.g.: MS:1000075 (matrix-assisted laser desorption ionization)
  e.g.: MS:1000227 (multiphoton ionization)
  e.g.: MS:1000239 (atmospheric pressure matrix-assisted laser desorption ionization)
  e.g.: MS:1000255 (flowing afterglow)
  e.g.: MS:1000257 (field desorption)
  e.g.: MS:1000258 (field ionization)
  e.g.: MS:1000259 (glow discharge ionization)
  et al.
MUST supply a *child* term of MS:1000007 (inlet type) one or more times
  e.g.: MS:1000055 (continuous flow fast atom bombardment)
  e.g.: MS:1000056 (direct inlet)
  e.g.: MS:1000058 (flow injection analysis)
  e.g.: MS:1000059 (inductively coupled plasma)
  e.g.: MS:1000060 (infusion)
  e.g.: MS:1000061 (jet separator)
  e.g.: MS:1000062 (membrane separator)
  e.g.: MS:1000063 (moving belt)
  e.g.: MS:1000064 (moving wire)
  e.g.: MS:1000065 (open split)
  et al.

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/>

Element <analyzer>

Definition:

A mass analyzer (or mass filter) component.

Attributes:

Attribute Name	Data Type	Use	Definition
order	xs:int	required	This attribute MUST be used to indicate the order in which the components are encountered from source to detector (e.g., in a Q-TOF, the quadrupole would have the lower order number, and the TOF the higher number of the two).

Subelements:

Subelement Name	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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

Example Context:

<analyzer order="2">
  <cvParam cvRef="MS" accession="MS:1000082" name="quadrupole ion trap" value=""/>
</analyzer>

cvParam Mapping Rules:

MUST supply a *child* term of MS:1000012 (resolution measurement method) one or more times
  e.g.: MS:1000085 (baseline)
  e.g.: MS:1000086 (full width at half-maximum)
  e.g.: MS:1000087 (ten percent valley)
MUST supply a *child* term of MS:1000480 (mass analyzer attribute) one or more times
  e.g.: MS:1000014 (accuracy)
  e.g.: MS:1000022 (TOF Total Path Length)
  e.g.: MS:1000024 (final MS exponent)
  e.g.: MS:1000025 (magnetic field strength)
  e.g.: MS:1000105 (reflectron off)
  e.g.: MS:1000106 (reflectron on)
MUST supply a *child* term of MS:1000443 (mass analyzer type) one or more times
  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.

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000082" name="quadrupole ion trap" value=""/>

Element <detector>

Definition:

A detector component.

Attributes:

Attribute Name	Data Type	Use	Definition
order	xs:int	required	This attribute MUST be used to indicate the order in which the components are encountered from source to detector (e.g., in a Q-TOF, the quadrupole would have the lower order number, and the TOF the higher number of the two).

Subelements:

Subelement Name	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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

Example Context:

<detector order="3">
  <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/>
</detector>

cvParam Mapping Rules:

MUST supply a *child* term of MS:1000026 (detector type) only once
  e.g.: MS:1000107 (channeltron)
  e.g.: MS:1000108 (conversion dynode electron multiplier)
  e.g.: MS:1000109 (conversion dynode photomultiplier)
  e.g.: MS:1000110 (daly detector)
  e.g.: MS:1000111 (electron multiplier tube)
  e.g.: MS:1000112 (faraday cup)
  e.g.: MS:1000113 (focal plane array)
  e.g.: MS:1000114 (microchannel plate detector)
  e.g.: MS:1000115 (multi-collector)
  e.g.: MS:1000116 (photomultiplier)
  et al.
MUST supply a *child* term of MS:1000481 (detector attribute) only once
  e.g.: MS:1000028 (detector resolution)
  e.g.: MS:1000029 (sampling frequency)
MUST supply a *child* term of MS:1000027 (detector acquisition mode) only once
  e.g.: MS:1000117 (analog-digital converter)
  e.g.: MS:1000118 (pulse counting)
  e.g.: MS:1000119 (time-digital converter)
  e.g.: MS:1000120 (transient recorder)

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/>

Element <target>

Definition:

Structure allowing the use of a controlled (cvParam) or uncontrolled vocabulary (userParam), or a reference to a predefined set of these in this mzML file (paramGroupRef).

Attributes:

none

Subelements:

Subelement Name	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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

Example Context:

<target>
  <cvParam cvRef="MS" accession="MS:1000040" name="m/z" value="1000"/>
</target>

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000040" name="m/z" value="1000"/>

Element <spectrumDescription>

Definition:

Description of the parameters for the mass spectrometer for a given acquisition (or list of acquisitions).

Attributes:

none

Subelements:

Subelement Name	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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
acquisitionList	1	List and descriptions of acquisitions .
precursorList	1	List and descriptions of precursors to the spectrum currently being described.
scan	1	The instrument's 'run time' parameters; common to the whole of this spectrum.

Graphical Context:

Example Context:

<spectrumDescription>
  <cvParam cvRef="MS" accession="MS:1000127" name="centroid mass spectrum" value=""/>
  <cvParam cvRef="MS" accession="MS:1000528" name="lowest m/z value" value="400.39"/>
  <cvParam cvRef="MS" accession="MS:1000527" name="highest m/z value" value="1795.56"/>
  <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="445.347"/>
  ...
</spectrumDescription>

cvParam Mapping Rules:

MUST supply a *child* term of MS:1000525 (spectrum representation) only once
  e.g.: MS:1000127 (centroid mass spectrum)
  e.g.: MS:1000128 (profile mass spectrum)
MUST supply a *child* term of MS:1000499 (spectrum attribute) one or more times
  e.g.: MS:1000285 (total ion current)
  e.g.: MS:1000504 (base peak m/z)
  e.g.: MS:1000505 (base peak intensity)
  e.g.: MS:1000527 (highest m/z value)
  e.g.: MS:1000528 (lowest m/z value)
  e.g.: MS:1000618 (highest wavelength value)
  e.g.: MS:1000619 (lowest wavelength value)

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000127" name="centroid mass spectrum" value=""/>
<cvParam cvRef="MS" accession="MS:1000528" name="lowest m/z value" value="400.39"/>
<cvParam cvRef="MS" accession="MS:1000527" name="highest m/z value" value="1795.56"/>
<cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="445.347"/>
<cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="120053"/>
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="16675500"/>

Element <binaryDataArrayList>

Definition:

List of binary data arrays.

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	The number of binary data arrays defined in this list.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
binaryDataArray	2	unbounded	The structure into which encoded binary data goes. Byte ordering is always little endian (Intel style). Computers using a different endian style MUST convert to/from little endian when writing/reading mzML

Example Context:

<binaryDataArrayList count="2">
  <binaryDataArray encodedLength="160" dataProcessingRef="XcaliburProcessing">
    <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
    <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
    <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value=""/>
  ...
</binaryDataArrayList>

Element <acquisitionList>

Definition:

List and descriptions of acquisitions .

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	the number of acquisitions defined in this mzML file.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
referenceableParamGroupRef	0	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	0	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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
acquisition	1	unbounded	Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile.

Graphical Context:

Example Context:

cvParam Mapping Rules:

MUST supply a *child* term of MS:1000570 (spectra combination) one or more times
  e.g.: MS:1000571 (sum of spectra)
  e.g.: MS:1000573 (median of spectra)
  e.g.: MS:1000575 (mean of spectra)

Element <precursorList>

Definition:

List and descriptions of precursors to the spectrum currently being described.

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	The number of precursors in this list.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
precursor	1	unbounded	The method of precursor ion selection and activation

Graphical Context:

Example Context:

<precursorList count="1">
  <precursor spectrumRef="S19">
    <selectedIonList count="1">
      <selectedIon>
        <cvParam cvRef="MS" accession="MS:1000040" name="m/z" value="445.34"/>
  ...
</precursorList>

Element <scan>

Definition:

The instrument's 'run time' parameters; common to the whole of this spectrum.

Attributes:

Attribute Name	Data Type	Use	Definition
instrumentConfigurationRef	xs:IDREF	optional	This attribute MUST reference the 'id' attribute of the appropriate instrument configuration.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
referenceableParamGroupRef	0	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	0	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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
scanWindowList	1	1	Container for a list of select windows.

Graphical Context:

Example Context:

<scan instrumentConfigurationRef="LCQDeca">
  <referenceableParamGroupRef ref="CommonMS1SpectrumParams"/>
  <cvParam cvRef="MS" accession="MS:1000016" name="scan time" value="5.8905" unitCvRef="MS" unitAccession="MS:1000038" unitName="minute"/>
  <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="+ c NSI Full ms [ 400.00-1800.00]"/>
  <cvParam cvRef="MS" accession="MS:1000616" name="preset scan configuration" value="3"/>
  ...
</scan>

cvParam Mapping Rules:

MUST supply a *child* term of MS:1000465 (scan polarity) only once
  e.g.: MS:1000129 (negative scan)
  e.g.: MS:1000130 (positive scan)
MUST supply a *child* term of MS:1000503 (scan attribute) one or more times
  e.g.: MS:1000011 (mass resolution)
  e.g.: MS:1000015 (scan rate)
  e.g.: MS:1000016 (scan time)
  e.g.: MS:1000023 (isolation width)
  e.g.: MS:1000511 (ms level)
  e.g.: MS:1000512 (filter string)
  e.g.: MS:1000616 (preset scan configuration)
MUST supply a *child* term of MS:1000018 (scan direction) only once
  e.g.: MS:1000092 (decreasing m/z scan)
  e.g.: MS:1000093 (increasing m/z scan)
MUST supply a *child* term of MS:1000019 (scan law) only once
  e.g.: MS:1000094 (exponential)
  e.g.: MS:1000095 (linear)
  e.g.: MS:1000096 (quadratic)
MUST supply a *child* term of MS:1000020 (scanning method) only once
  e.g.: MS:1000100 (precursor ion scan)
  e.g.: MS:1000101 (product ion scan)
  e.g.: MS:1000205 (selected ion monitoring)
  e.g.: MS:1000206 (selected reaction monitoring)
  e.g.: MS:1000244 (consecutive reaction monitoring)
  e.g.: MS:1000323 (constant neutral loss scan)
  e.g.: MS:1000324 (constant neutral gain scan)
  e.g.: MS:1000497 (zoom scan)
  e.g.: MS:1000498 (full scan)

Element <binaryDataArray>

Definition:

The structure into which encoded binary data goes. Byte ordering is always little endian (Intel style). Computers using a different endian style MUST convert to/from little endian when writing/reading mzML

Attributes:

Attribute Name	Data Type	Use	Definition
arrayLength	xs:nonNegativeInteger	optional	This optional attribute may override the 'defaultArrayLength' defined in SpectrumType. The two default arrays (m/z and intensity) should NEVER use this override option, and should therefore adhere to the 'defaultArrayLength' defined in SpectrumType. Parsing software can thus safely choose to ignore arrays of lengths different from the one defined in the 'defaultArrayLength' SpectrumType element.
dataProcessingRef	xs:IDREF	optional	This optional attribute may reference the 'id' attribute of the appropriate dataProcessing.
encodedLength	xs:nonNegativeInteger	required	The encoded length of the binary data array.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
referenceableParamGroupRef	0	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	0	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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
binary	1	1	The actual base64 encoded binary data.

Graphical Context:

Example Context:

<binaryDataArray encodedLength="160" dataProcessingRef="XcaliburProcessing">
  <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
  <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
  <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value=""/>
  <binary>AAAAAAAAAAAAAAAAAADwPwAAAAAAAABAAAAAAAAACEAAAAAAAA...</binary>
  ...
</binaryDataArray>

cvParam Mapping Rules:

MUST supply a *child* term of MS:1000572 (binary data compression type) only once
  e.g.: MS:1000574 (zlib compression)
  e.g.: MS:1000576 (no compression)
MUST supply a *child* term of MS:1000513 (binary data array) only once
  e.g.: MS:1000514 (m/z array)
  e.g.: MS:1000515 (intensity array)
  e.g.: MS:1000516 (charge array)
  e.g.: MS:1000517 (signal to noise array)
  e.g.: MS:1000595 (time array)
  e.g.: MS:1000617 (wavelength array)
MUST supply a *child* term of MS:1000518 (binary data type) only once
  e.g.: MS:1000519 (32-bit integer)
  e.g.: MS:1000520 (16-bit float)
  e.g.: MS:1000521 (32-bit float)
  e.g.: MS:1000522 (64-bit integer)
  e.g.: MS:1000523 (64-bit float)

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value=""/>
<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value=""/>
<cvParam cvRef="MS" accession="MS:1000595" name="time array" value=""/>

Notes and Constraints:

The arrayLength attribute need only be specified if it is different from the defaultArrayLength specified in the <spectrum> element.

Element <acquisition>

Definition:

Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile.

Attributes:

Attribute Name	Data Type	Use	Definition
externalNativeID	xs:string	optional	For acquisitions that are external to this document which can be referenced by nativeID, this string MUST correspond to the 'nativeID' attribute of a spectrum in the external document indicated by 'sourceFileRef'.
externalSpectrumID	xs:string	optional	For acquisitions that are external to this document which cannot be referenced by nativeID, this string MUST correspond to the 'id' attribute of a spectrum in the external document indicated by 'sourceFileRef'.
number	xs:int	required	A number for this acquisition.
sourceFileRef	xs:IDREF	optional	For acquisitions that are external to this document, this attribute MUST reference the 'id' attribute of a sourceFile representing that external document.
spectrumRef	xs:IDREF	optional	For acquisitions that are local to this document, this attribute MUST reference the 'id' attribute of the appropriate spectrum.

Subelements:

Subelement Name	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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

Example Context:

cvParam Mapping Rules:

MAY supply a *child* term of MS:1000503 (scan attribute) one or more times
  e.g.: MS:1000011 (mass resolution)
  e.g.: MS:1000015 (scan rate)
  e.g.: MS:1000016 (scan time)
  e.g.: MS:1000023 (isolation width)
  e.g.: MS:1000511 (ms level)
  e.g.: MS:1000512 (filter string)
  e.g.: MS:1000616 (preset scan configuration)

Element <precursor>

Definition:

The method of precursor ion selection and activation

Attributes:

Attribute Name	Data Type	Use	Definition
externalNativeID	xs:string	optional	For precursor spectra that are external to this document which can be referenced by nativeID, this string MUST correspond to the 'nativeID' attribute of a spectrum in the external document indicated by 'sourceFileRef'.
externalSpectrumID	xs:string	optional	For precursor spectra that are external to this document which cannot be referenced by nativeID, this string MUST correspond to the 'id' attribute of a spectrum in the external document indicated by 'sourceFileRef'.
sourceFileRef	xs:IDREF	optional	For precursor spectra that are external to this document, this attribute MUST reference the 'id' attribute of a sourceFile representing that external document.
spectrumRef	xs:IDREF	optional	Reference to the id attribute of the spectrum from which the precursor was selected.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
isolationWindow	0	1	This element captures the isolation (or 'selection') window configured to isolate one or more precursors.
selectedIonList	1	1	This list of precursor ions that were selected.
activation	1	1	The type and energy level used for activation.

Example Context:

<precursor spectrumRef="S19">
  <selectedIonList count="1">
    <selectedIon>
      <cvParam cvRef="MS" accession="MS:1000040" name="m/z" value="445.34"/>
      <cvParam cvRef="MS" accession="MS:1000042" name="intensity" value="120053"/>
  ...
</precursor>

Element <scanWindowList>

Definition:

Container for a list of select windows.

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:int	required	The number of selection windows defined in this list.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
scanWindow	1	unbounded	Definition of a selection window.

Example Context:

<scanWindowList count="1">
  <scanWindow>
    <cvParam cvRef="MS" accession="MS:1000501" name="scan m/z lower limit" value="400"/>
    <cvParam cvRef="MS" accession="MS:1000500" name="scan m/z upper limit" value="1800"/>
  </scanWindow>
  ...
</scanWindowList>

Element <binary>

Definition:	The actual base64 encoded binary data.
Attributes:	none
Subelements:	none
Example Context:

Element <isolationWindow>

Definition:

This element captures the isolation (or 'selection') window configured to isolate one or more precursors.

Attributes:

none

Subelements:

Subelement Name	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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

Example Context:

Element <selectedIonList>

Definition:

This list of precursor ions that were selected.

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	The number of selected precursor ions defined in this list.

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
selectedIon	1	unbounded	Structure allowing the use of a controlled (cvParam) or uncontrolled vocabulary (userParam), or a reference to a predefined set of these in this mzML file (paramGroupRef).

Example Context:

<selectedIonList count="1">
  <selectedIon>
    <cvParam cvRef="MS" accession="MS:1000040" name="m/z" value="445.34"/>
    <cvParam cvRef="MS" accession="MS:1000042" name="intensity" value="120053"/>
    <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
  ...
</selectedIonList>

Element <activation>

Definition:

The type and energy level used for activation.

Attributes:

none

Subelements:

Subelement Name	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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

Example Context:

<activation>
  <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
  <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="35" unitCvRef="MS" unitAccession="MS:1000137" unitName="electron volt"/>
</activation>

cvParam Mapping Rules:

MUST supply a *child* term of MS:1000456 (precursor activation) one or more times
  e.g.: MS:1000045 (collision energy)
  e.g.: MS:1000133 (collision-induced dissociation)
  e.g.: MS:1000134 (plasma desorption)
  e.g.: MS:1000135 (post-source decay)
  e.g.: MS:1000136 (surface-induced dissociation)
  e.g.: MS:1000242 (blackbody infrared radiative dissociation)
  e.g.: MS:1000245 (charge stripping)
  e.g.: MS:1000246 (delayed extraction)
  e.g.: MS:1000250 (electron capture dissociation)
  e.g.: MS:1000262 (infrared multiphoton dissociation)
  et al.

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
<cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="35" unitCvRef="MS" unitAccession="MS:1000137" unitName="electron volt"/>

Element <scanWindow>

Definition:

Definition of a selection window.

Attributes:

none

Subelements:

Subelement Name	minOccurs	maxOccurs	Definition
cvParam	2	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.

Example Context:

<scanWindow>
  <cvParam cvRef="MS" accession="MS:1000501" name="scan m/z lower limit" value="400"/>
  <cvParam cvRef="MS" accession="MS:1000500" name="scan m/z upper limit" value="1800"/>
</scanWindow>

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000501" name="scan m/z lower limit" value="400"/>
<cvParam cvRef="MS" accession="MS:1000500" name="scan m/z upper limit" value="1800"/>

Element <selectedIon>

Definition:

Structure allowing the use of a controlled (cvParam) or uncontrolled vocabulary (userParam), or a reference to a predefined set of these in this mzML file (paramGroupRef).

Attributes:

none

Subelements:

Subelement Name	maxOccurs	Definition
referenceableParamGroupRef	unbounded	A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
cvParam	unbounded	This element holds additional data or annotation. Only controlled values are allowed here.
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

Example Context:

<selectedIon>
  <cvParam cvRef="MS" accession="MS:1000040" name="m/z" value="445.34"/>
  <cvParam cvRef="MS" accession="MS:1000042" name="intensity" value="120053"/>
  <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>
</selectedIon>
  ...
</selectedIon>

Example cvParams:

<cvParam cvRef="MS" accession="MS:1000040" name="m/z" value="445.34"/>
<cvParam cvRef="MS" accession="MS:1000042" name="intensity" value="120053"/>
<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>