Element <indexedmzML>

Definition:

Container element for mzML which allows the addition of an index.

Type:

Attributes:

none

Subelements:

Subelement Name	min	max	Definition
dx:mzML	1	1	-
indexList	1	1	List of indices.
indexListOffset	1	1	File pointer offset (in bytes) of the 'indexList' element.
fileChecksum	1	1	SHA-1 checksum from beginning of file to end of 'fileChecksum' open tag.

Example Context:

<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">
  <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.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="1.18.2" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
      <cv id="UO" fullName="Unit Ontology" version="04:03:2009" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
    </cvList>
    <fileDescription>
  ...
</indexedmzML>

Element <dx:mzML>

This element is defined in another xsd document.

Element <indexList>

Definition:

List of indices.

Type:

dx:IndexListType

Attributes:

Attribute Name	Data Type	Use	Definition
count	xs:nonNegativeInteger	required	Number of indices in this list.

Subelements:

Subelement Name	min	max	Definition
index	1	unlim	Index element containing one or more offsets for random data access for the entity described in the 'name' attribute.

Example Context:

<indexList count="2">
  <index name="spectrum">
    <offset idRef="controllerType=0 controllerNumber=1 scan=1">4363</offset>
    <offset idRef="controllerType=0 controllerNumber=1 scan=2">326365</offset>
    <offset idRef="controllerType=0 controllerNumber=1 scan=3">646528</offset>
    <offset idRef="controllerType=0 controllerNumber=1 scan=4">659047</offset>
    <offset idRef="controllerType=0 controllerNumber=1 scan=5">679908</offset>
  ...
</indexList>

Element <indexListOffset>

Definition:	File pointer offset (in bytes) of the 'indexList' element.
Type:	xs:long
Attributes:	none
Subelements:	none
Example Context:	<indexListOffset>5098921</indexListOffset>

Element <fileChecksum>

Definition:	SHA-1 checksum from beginning of file to end of 'fileChecksum' open tag.
Type:	xs:string
Attributes:	none
Subelements:	none
Example Context:	<fileChecksum>0dbebfb99075881afa2002177d37e4d6215fdced</fileChecksum>

Element <index>

Definition:

Index element containing one or more offsets for random data access for the entity described in the 'name' attribute.

Type:

dx:IndexType

Attributes:

Attribute Name	Data Type	Use	Definition
name	xs:string	required	The name of the entity the index entries are pointing to.

Subelements:

Subelement Name	min	max	Definition
offset	1	unlim	File pointer offset (in bytes) of the element identified by the 'id' attribute.

Example Context:

<index name="spectrum">
  <offset idRef="controllerType=0 controllerNumber=1 scan=1">4363</offset>
  <offset idRef="controllerType=0 controllerNumber=1 scan=2">326365</offset>
  <offset idRef="controllerType=0 controllerNumber=1 scan=3">646528</offset>
  <offset idRef="controllerType=0 controllerNumber=1 scan=4">659047</offset>
  <offset idRef="controllerType=0 controllerNumber=1 scan=5">679908</offset>
  <offset idRef="controllerType=0 controllerNumber=1 scan=6">698062</offset>
  ...
</index>

Element <offset>

Definition:

File pointer offset (in bytes) of the element identified by the 'id' attribute.

Type:

dx:OffsetType

Attributes:

Attribute Name	Data Type	Use	Definition
idRef	xs:string	required	Reference to the 'id' attribute of the indexed element.
scanTime	xs:double	optional	In the case of a spectrum representing a single scan, this attribute may be used to reference it by the time at which the scan was acquired (a.k.a. scan time or retention time).
spotID	xs:string	optional	The identifier for the spot from which this spectrum was derived, if a MALDI or similar run.

Subelements:

none

Example Context:

<offset idRef="controllerType=0 controllerNumber=1 scan=10">1297508</offset>