Schema mzXML_idx_2.1.xsd


schema location:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/mzXML_idx_2.1.xsd
attribute form default:  unqualified
element form default:  qualified
targetNamespace:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
 
Elements 
mzXML 


schema location:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/mzXML_2.1.xsd
attribute form default:  unqualified
element form default:  qualified
targetNamespace:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
 
Elements  Simple types 
msRun  strictBase64Type 
operator 
scan 
software 


schema location:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/separations/separation_technique_1.0.xsd
attribute form default:  unqualified
element form default:  qualified
targetNamespace:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
 
Elements  Complex types 
separationTechnique  separationTechniqueType 


schema location:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/general_types_1.0.xsd
attribute form default:  unqualified
element form default:  qualified
targetNamespace:  http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
 
Complex types 
namevalueType 
ontologyEntryType 


element mzXML
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
content complex
children msRun index indexOffset sha1
annotation
documentation 
Comment describing your root element
source 
<xs:element name="mzXML">
  <xs:annotation>
    <xs:documentation>Comment describing your root element</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element ref="msRun"/>
      <xs:element name="index" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Index for non sequential data access</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="offset" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Offset of the element identified by name (index attribute) and id</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:simpleContent>
                  <xs:extension base="xs:long">
                    <xs:attribute name="id" type="xs:positiveInteger" use="required">
                      <xs:annotation>
                        <xs:documentation>This is a unique identifier for the elements of type "name" present in the index (e.g.: for an element of type scan, this will be the scan number)</xs:documentation>
                      </xs:annotation>
                    </xs:attribute>
                  </xs:extension>
                </xs:simpleContent>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="name" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>name of the element the index entries are pointing to (e.g: scan)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="indexOffset" type="xs:long" nillable="1">
        <xs:annotation>
          <xs:documentation>offset of the index element (if 0 no index present)</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="sha1" minOccurs="0">
        <xs:annotation>
          <xs:documentation>sha-1 sum for this file (from the beginning of the file up to (and including) the opening tag of sha1</xs:documentation>
        </xs:annotation>
        <xs:simpleType>
          <xs:restriction base="xs:string">
            <xs:length value="40"/>
          </xs:restriction>
        </xs:simpleType>
      </xs:element>
    </xs:sequence>
  </xs:complexType>
</xs:element>

element mzXML/index
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
isRef 0
content complex
children offset
attributes
Name  Type  Use  Default  Fixed  Annotation
name  xs:stringrequired      
documentation 
name of the element the index entries are pointing to (e.g: scan)
annotation
documentation 
Index for non sequential data access
source 
<xs:element name="index" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Index for non sequential data access</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="offset" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Offset of the element identified by name (index attribute) and id</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:simpleContent>
            <xs:extension base="xs:long">
              <xs:attribute name="id" type="xs:positiveInteger" use="required">
                <xs:annotation>
                  <xs:documentation>This is a unique identifier for the elements of type "name" present in the index (e.g.: for an element of type scan, this will be the scan number)</xs:documentation>
                </xs:annotation>
              </xs:attribute>
            </xs:extension>
          </xs:simpleContent>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="name" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>name of the element the index entries are pointing to (e.g: scan)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element mzXML/index/offset
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type extension of xs:long
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:positiveIntegerrequired      
documentation 
This is a unique identifier for the elements of type "name" present in the index (e.g.: for an element of type scan, this will be the scan number)
annotation
documentation 
Offset of the element identified by name (index attribute) and id
source 
<xs:element name="offset" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Offset of the element identified by name (index attribute) and id</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:simpleContent>
      <xs:extension base="xs:long">
        <xs:attribute name="id" type="xs:positiveInteger" use="required">
          <xs:annotation>
            <xs:documentation>This is a unique identifier for the elements of type "name" present in the index (e.g.: for an element of type scan, this will be the scan number)</xs:documentation>
          </xs:annotation>
        </xs:attribute>
      </xs:extension>
    </xs:simpleContent>
  </xs:complexType>
</xs:element>

element mzXML/indexOffset
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type xs:long
properties
isRef 0
content simple
nillable 1
annotation
documentation 
offset of the index element (if 0 no index present)
source 
<xs:element name="indexOffset" type="xs:long" nillable="1">
  <xs:annotation>
    <xs:documentation>offset of the index element (if 0 no index present)</xs:documentation>
  </xs:annotation>
</xs:element>

element mzXML/sha1
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type restriction of xs:string
properties
isRef 0
content simple
facets
length 40
annotation
documentation 
sha-1 sum for this file (from the beginning of the file up to (and including) the opening tag of sha1
source 
<xs:element name="sha1" minOccurs="0">
  <xs:annotation>
    <xs:documentation>sha-1 sum for this file (from the beginning of the file up to (and including) the opening tag of sha1</xs:documentation>
  </xs:annotation>
  <xs:simpleType>
    <xs:restriction base="xs:string">
      <xs:length value="40"/>
    </xs:restriction>
  </xs:simpleType>
</xs:element>

element msRun
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
content complex
children cff:parentFile cff:msInstrument cff:dataProcessing cff:separation cff:spotting scan cff:sha1
used by
element mzXML
attributes
Name  Type  Use  Default  Fixed  Annotation
scanCount  xs:positiveIntegeroptional      
documentation 
Total number of scans contained in the XML instance document. This number should be equal to the total number of scans in the original RAW data, unless some were not converted (e.g.: signal below threshold)..
startTime  xs:durationoptional      
documentation 
The time at which the run was started.
endTime  xs:durationoptional      
documentation 
The time at which the run was ended.
source 
<xs:element name="msRun">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="parentFile" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Path to all the ancestor files (up to the native acquisition file) used to generate the current XML instance document.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:simpleContent>
            <xs:extension base="xs:anySimpleType">
              <xs:attribute name="fileName" type="xs:anyURI" use="required">
                <xs:annotation>
                  <xs:documentation>Name of the parent file</xs:documentation>
                </xs:annotation>
              </xs:attribute>
              <xs:attribute name="fileType" use="required">
                <xs:annotation>
                  <xs:documentation>Was the parent file a native acquisition file? Or was it processed data?</xs:documentation>
                </xs:annotation>
                <xs:simpleType>
                  <xs:restriction base="xs:string">
                    <xs:enumeration value="RAWData"/>
                    <xs:enumeration value="processedData"/>
                  </xs:restriction>
                </xs:simpleType>
              </xs:attribute>
              <xs:attribute name="fileSha1" use="required">
                <xs:annotation>
                  <xs:documentation>sha-1 sum of the parent file</xs:documentation>
                </xs:annotation>
                <xs:simpleType>
                  <xs:restriction base="xs:string">
                    <xs:length value="40"/>
                  </xs:restriction>
                </xs:simpleType>
              </xs:attribute>
            </xs:extension>
          </xs:simpleContent>
        </xs:complexType>
        <xs:key name="parentFileKey">
          <xs:selector xpath="."/>
          <xs:field xpath="@fileSha1"/>
        </xs:key>
      </xs:element>
      <xs:element name="msInstrument" minOccurs="0">
        <xs:annotation>
          <xs:documentation>General information about the MS instrument.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="msManufacturer">
              <xs:complexType>
                <xs:complexContent>
                  <xs:extension base="cff:ontologyEntryType"/>
                </xs:complexContent>
              </xs:complexType>
            </xs:element>
            <xs:element name="msModel" type="cff:ontologyEntryType"/>
            <xs:element name="msIonisation" type="cff:ontologyEntryType"/>
            <xs:element name="msMassAnalyzer">
              <xs:complexType>
                <xs:complexContent>
                  <xs:extension base="cff:ontologyEntryType"/>
                </xs:complexContent>
              </xs:complexType>
            </xs:element>
            <xs:element name="msDetector" type="cff:ontologyEntryType"/>
            <xs:element ref="cff:software"/>
            <xs:element name="msResolution" type="cff:ontologyEntryType" minOccurs="0"/>
            <xs:element ref="cff:operator" minOccurs="0"/>
            <xs:sequence minOccurs="0" maxOccurs="unbounded">
              <xs:element name="nameValue" type="cff:namevalueType">
                <xs:annotation>
                  <xs:documentation>Any additional property of the instrument not included elsewhere in the instrument element.</xs:documentation>
                </xs:annotation>
              </xs:element>
              <xs:element name="comment" type="xs:string" minOccurs="0">
                <xs:annotation>
                  <xs:documentation>Additional comments.</xs:documentation>
                </xs:annotation>
              </xs:element>
            </xs:sequence>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="dataProcessing" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Description of any manipulation (from the first conversion to mzXML format until the creation of the current mzXML instance document) applied to the data.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element ref="cff:software">
              <xs:annotation>
                <xs:documentation>Software used to convert the data. If data has been processed (e.g. profile > centroid) by any additional progs these should be added too.</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:sequence minOccurs="0" maxOccurs="unbounded">
              <xs:element name="processingOperation" type="cff:namevalueType">
                <xs:annotation>
                  <xs:documentation>Any additional manipulation not included elsewhere in the dataProcessing element.</xs:documentation>
                </xs:annotation>
              </xs:element>
              <xs:element name="comment" type="xs:string" minOccurs="0">
                <xs:annotation>
                  <xs:documentation>Additional comments</xs:documentation>
                </xs:annotation>
              </xs:element>
            </xs:sequence>
          </xs:sequence>
          <xs:attribute name="intensityCutoff" type="xs:float" use="optional">
            <xs:annotation>
              <xs:documentation>Intensity threshold for including a peak in the XML output</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="centroided" type="xs:boolean" use="optional">
            <xs:annotation>
              <xs:documentation>Is the data centroided</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="deisotoped" type="xs:boolean" use="optional">
            <xs:annotation>
              <xs:documentation>Is the data deisotoped</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="chargeDeconvoluted" type="xs:boolean" use="optional">
            <xs:annotation>
              <xs:documentation>Has the charge state been deconvoluted</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="spotIntegration" type="xs:boolean" use="optional"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="separation" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Information about the separation technique, if any, used right before the acquisition.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element ref="cff:separationTechnique" maxOccurs="unbounded"/>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="spotting" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Acquisition independent properties of a MALDI experiment.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="plate" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Information about a MALDI plate.</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="plateManufacturer" type="cff:ontologyEntryType"/>
                  <xs:element name="plateModel" type="cff:ontologyEntryType"/>
                  <xs:element name="pattern" minOccurs="0">
                    <xs:complexType>
                      <xs:sequence>
                        <xs:element name="spottingPattern" type="cff:ontologyEntryType"/>
                        <xs:element name="orientation">
                          <xs:annotation>
                            <xs:documentation>Defines the orientation of the spotting pattern, with the IDs of the fist two consecutive spotted spots.</xs:documentation>
                          </xs:annotation>
                          <xs:complexType>
                            <xs:attribute name="firstSpotID" type="xs:string" use="required">
                              <xs:annotation>
                                <xs:documentation>ID of the first spot spotted using "spottingPattern". This ID must have been defined also in the spot element.</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="secondSpotID" type="xs:string" use="required">
                              <xs:annotation>
                                <xs:documentation>ID of the second spot spotted using "spottingPattern". This ID must have been defined also in the spot element.</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                          </xs:complexType>
                          <xs:keyref name="onlyValidFirstSpotID" refer="cff:spotKey">
                            <xs:selector xpath="."/>
                            <xs:field xpath="@spotID"/>
                          </xs:keyref>
                          <xs:keyref name="onlyValidSecondSpotID" refer="cff:spotKey">
                            <xs:selector xpath="."/>
                            <xs:field xpath="@spotID"/>
                          </xs:keyref>
                        </xs:element>
                      </xs:sequence>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="spot" maxOccurs="unbounded">
                    <xs:annotation>
                      <xs:documentation>Information about individual spots.</xs:documentation>
                    </xs:annotation>
                    <xs:complexType>
                      <xs:sequence>
                        <xs:element name="maldiMatrix" type="cff:ontologyEntryType"/>
                      </xs:sequence>
                      <xs:attribute name="spotID" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>Unique identifier for the spot.</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="spotXPosition" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>X cartesian position of the spot.</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="spotYPosition" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>Y cartesian position of the spot.</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="spotDiameter" type="xs:positiveInteger" use="optional"/>
                    </xs:complexType>
                    <xs:key name="spotKey">
                      <xs:selector xpath="."/>
                      <xs:field xpath="@spotID"/>
                    </xs:key>
                  </xs:element>
                </xs:sequence>
                <xs:attribute name="plateID" type="xs:positiveInteger" use="required">
                  <xs:annotation>
                    <xs:documentation>Unique identifier for the plate.</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="spotXCount" type="xs:positiveInteger" use="required"/>
                <xs:attribute name="spotYCount" type="xs:positiveInteger" use="required"/>
              </xs:complexType>
              <xs:key name="plateKey">
                <xs:selector xpath="."/>
                <xs:field xpath="@plateID"/>
              </xs:key>
            </xs:element>
            <xs:element name="robot" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Information about the robot, if any, used to spot the plates.</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="robotManufacturer" type="cff:ontologyEntryType"/>
                  <xs:element name="robotModel" type="cff:ontologyEntryType"/>
                </xs:sequence>
                <xs:attribute name="timePerSpot" type="xs:duration" use="required"/>
                <xs:attribute name="deadVolume" type="xs:nonNegativeInteger" use="optional">
                  <xs:annotation>
                    <xs:documentation>Dead volume in ul of the spotting robot.</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element ref="cff:scan" maxOccurs="unbounded"/>
      <xs:element name="sha1" minOccurs="0">
        <xs:annotation>
          <xs:documentation>sha-1 sum for this file (from the beginning of the file up to (and including) the opening tag of sha1</xs:documentation>
        </xs:annotation>
        <xs:simpleType>
          <xs:restriction base="xs:string">
            <xs:length value="40"/>
          </xs:restriction>
        </xs:simpleType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="scanCount" type="xs:positiveInteger" use="optional">
      <xs:annotation>
        <xs:documentation>Total number of scans contained in the XML instance document. This number should be equal to the total number of scans in the original RAW data, unless some were not converted (e.g.: signal below threshold)..</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="startTime" type="xs:duration" use="optional">
      <xs:annotation>
        <xs:documentation>The time at which the run was started.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="endTime" type="xs:duration" use="optional">
      <xs:annotation>
        <xs:documentation>The time at which the run was ended.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element msRun/parentFile
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type extension of xs:anySimpleType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
fileName  xs:anyURIrequired      
documentation 
Name of the parent file
fileType  required      
documentation 
Was the parent file a native acquisition file? Or was it processed data?
fileSha1  required      
documentation 
sha-1 sum of the parent file
identity constraints
  Name  Refer  Selector  Field(s)  
key  parentFileKey    .  @fileSha1  
annotation
documentation 
Path to all the ancestor files (up to the native acquisition file) used to generate the current XML instance document.
source 
<xs:element name="parentFile" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Path to all the ancestor files (up to the native acquisition file) used to generate the current XML instance document.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:simpleContent>
      <xs:extension base="xs:anySimpleType">
        <xs:attribute name="fileName" type="xs:anyURI" use="required">
          <xs:annotation>
            <xs:documentation>Name of the parent file</xs:documentation>
          </xs:annotation>
        </xs:attribute>
        <xs:attribute name="fileType" use="required">
          <xs:annotation>
            <xs:documentation>Was the parent file a native acquisition file? Or was it processed data?</xs:documentation>
          </xs:annotation>
          <xs:simpleType>
            <xs:restriction base="xs:string">
              <xs:enumeration value="RAWData"/>
              <xs:enumeration value="processedData"/>
            </xs:restriction>
          </xs:simpleType>
        </xs:attribute>
        <xs:attribute name="fileSha1" use="required">
          <xs:annotation>
            <xs:documentation>sha-1 sum of the parent file</xs:documentation>
          </xs:annotation>
          <xs:simpleType>
            <xs:restriction base="xs:string">
              <xs:length value="40"/>
            </xs:restriction>
          </xs:simpleType>
        </xs:attribute>
      </xs:extension>
    </xs:simpleContent>
  </xs:complexType>
  <xs:key name="parentFileKey">
    <xs:selector xpath="."/>
    <xs:field xpath="@fileSha1"/>
  </xs:key>
</xs:element>

element msRun/msInstrument
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
isRef 0
content complex
children cff:msManufacturer cff:msModel cff:msIonisation cff:msMassAnalyzer cff:msDetector software cff:msResolution operator cff:nameValue cff:comment
annotation
documentation 
General information about the MS instrument.
source 
<xs:element name="msInstrument" minOccurs="0">
  <xs:annotation>
    <xs:documentation>General information about the MS instrument.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="msManufacturer">
        <xs:complexType>
          <xs:complexContent>
            <xs:extension base="cff:ontologyEntryType"/>
          </xs:complexContent>
        </xs:complexType>
      </xs:element>
      <xs:element name="msModel" type="cff:ontologyEntryType"/>
      <xs:element name="msIonisation" type="cff:ontologyEntryType"/>
      <xs:element name="msMassAnalyzer">
        <xs:complexType>
          <xs:complexContent>
            <xs:extension base="cff:ontologyEntryType"/>
          </xs:complexContent>
        </xs:complexType>
      </xs:element>
      <xs:element name="msDetector" type="cff:ontologyEntryType"/>
      <xs:element ref="cff:software"/>
      <xs:element name="msResolution" type="cff:ontologyEntryType" minOccurs="0"/>
      <xs:element ref="cff:operator" minOccurs="0"/>
      <xs:sequence minOccurs="0" maxOccurs="unbounded">
        <xs:element name="nameValue" type="cff:namevalueType">
          <xs:annotation>
            <xs:documentation>Any additional property of the instrument not included elsewhere in the instrument element.</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="comment" type="xs:string" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Additional comments.</xs:documentation>
          </xs:annotation>
        </xs:element>
      </xs:sequence>
    </xs:sequence>
  </xs:complexType>
</xs:element>

element msRun/msInstrument/msManufacturer
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type extension of ontologyEntryType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
category  xs:stringrequired      
value  xs:stringrequired      
source 
<xs:element name="msManufacturer">
  <xs:complexType>
    <xs:complexContent>
      <xs:extension base="cff:ontologyEntryType"/>
    </xs:complexContent>
  </xs:complexType>
</xs:element>

element msRun/msInstrument/msModel
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type ontologyEntryType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
category  xs:stringrequired      
value  xs:stringrequired      
source 
<xs:element name="msModel" type="cff:ontologyEntryType"/>

element msRun/msInstrument/msIonisation
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type ontologyEntryType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
category  xs:stringrequired      
value  xs:stringrequired      
source 
<xs:element name="msIonisation" type="cff:ontologyEntryType"/>

element msRun/msInstrument/msMassAnalyzer
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type extension of ontologyEntryType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
category  xs:stringrequired      
value  xs:stringrequired      
source 
<xs:element name="msMassAnalyzer">
  <xs:complexType>
    <xs:complexContent>
      <xs:extension base="cff:ontologyEntryType"/>
    </xs:complexContent>
  </xs:complexType>
</xs:element>

element msRun/msInstrument/msDetector
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type ontologyEntryType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
category  xs:stringrequired      
value  xs:stringrequired      
source 
<xs:element name="msDetector" type="cff:ontologyEntryType"/>

element msRun/msInstrument/msResolution
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type ontologyEntryType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
category  xs:stringrequired      
value  xs:stringrequired      
source 
<xs:element name="msResolution" type="cff:ontologyEntryType" minOccurs="0"/>

element msRun/msInstrument/nameValue
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type namevalueType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
name  xs:stringoptional      
value  xs:anySimpleTypeoptional      
type  xs:anySimpleTypeoptional      
annotation
documentation 
Any additional property of the instrument not included elsewhere in the instrument element.
source 
<xs:element name="nameValue" type="cff:namevalueType">
  <xs:annotation>
    <xs:documentation>Any additional property of the instrument not included elsewhere in the instrument element.</xs:documentation>
  </xs:annotation>
</xs:element>

element msRun/msInstrument/comment
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type xs:string
properties
isRef 0
content simple
annotation
documentation 
Additional comments.
source 
<xs:element name="comment" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Additional comments.</xs:documentation>
  </xs:annotation>
</xs:element>

element msRun/dataProcessing
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
isRef 0
content complex
children software cff:processingOperation cff:comment
attributes
Name  Type  Use  Default  Fixed  Annotation
intensityCutoff  xs:floatoptional      
documentation 
Intensity threshold for including a peak in the XML output
centroided  xs:booleanoptional      
documentation 
Is the data centroided
deisotoped  xs:booleanoptional      
documentation 
Is the data deisotoped
chargeDeconvoluted  xs:booleanoptional      
documentation 
Has the charge state been deconvoluted
spotIntegration  xs:booleanoptional      
annotation
documentation 
Description of any manipulation (from the first conversion to mzXML format until the creation of the current mzXML instance document) applied to the data.
source 
<xs:element name="dataProcessing" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Description of any manipulation (from the first conversion to mzXML format until the creation of the current mzXML instance document) applied to the data.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element ref="cff:software">
        <xs:annotation>
          <xs:documentation>Software used to convert the data. If data has been processed (e.g. profile > centroid) by any additional progs these should be added too.</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:sequence minOccurs="0" maxOccurs="unbounded">
        <xs:element name="processingOperation" type="cff:namevalueType">
          <xs:annotation>
            <xs:documentation>Any additional manipulation not included elsewhere in the dataProcessing element.</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="comment" type="xs:string" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Additional comments</xs:documentation>
          </xs:annotation>
        </xs:element>
      </xs:sequence>
    </xs:sequence>
    <xs:attribute name="intensityCutoff" type="xs:float" use="optional">
      <xs:annotation>
        <xs:documentation>Intensity threshold for including a peak in the XML output</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="centroided" type="xs:boolean" use="optional">
      <xs:annotation>
        <xs:documentation>Is the data centroided</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="deisotoped" type="xs:boolean" use="optional">
      <xs:annotation>
        <xs:documentation>Is the data deisotoped</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="chargeDeconvoluted" type="xs:boolean" use="optional">
      <xs:annotation>
        <xs:documentation>Has the charge state been deconvoluted</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="spotIntegration" type="xs:boolean" use="optional"/>
  </xs:complexType>
</xs:element>

element msRun/dataProcessing/processingOperation
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type namevalueType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
name  xs:stringoptional      
value  xs:anySimpleTypeoptional      
type  xs:anySimpleTypeoptional      
annotation
documentation 
Any additional manipulation not included elsewhere in the dataProcessing element.
source 
<xs:element name="processingOperation" type="cff:namevalueType">
  <xs:annotation>
    <xs:documentation>Any additional manipulation not included elsewhere in the dataProcessing element.</xs:documentation>
  </xs:annotation>
</xs:element>

element msRun/dataProcessing/comment
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type xs:string
properties
isRef 0
content simple
annotation
documentation 
Additional comments
source 
<xs:element name="comment" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Additional comments</xs:documentation>
  </xs:annotation>
</xs:element>

element msRun/separation
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
isRef 0
content complex
children separationTechnique
annotation
documentation 
Information about the separation technique, if any, used right before the acquisition.
source 
<xs:element name="separation" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Information about the separation technique, if any, used right before the acquisition.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element ref="cff:separationTechnique" maxOccurs="unbounded"/>
    </xs:sequence>
  </xs:complexType>
</xs:element>

element msRun/spotting
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
isRef 0
content complex
children cff:plate cff:robot
annotation
documentation 
Acquisition independent properties of a MALDI experiment.
source 
<xs:element name="spotting" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Acquisition independent properties of a MALDI experiment.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="plate" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Information about a MALDI plate.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="plateManufacturer" type="cff:ontologyEntryType"/>
            <xs:element name="plateModel" type="cff:ontologyEntryType"/>
            <xs:element name="pattern" minOccurs="0">
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="spottingPattern" type="cff:ontologyEntryType"/>
                  <xs:element name="orientation">
                    <xs:annotation>
                      <xs:documentation>Defines the orientation of the spotting pattern, with the IDs of the fist two consecutive spotted spots.</xs:documentation>
                    </xs:annotation>
                    <xs:complexType>
                      <xs:attribute name="firstSpotID" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>ID of the first spot spotted using "spottingPattern". This ID must have been defined also in the spot element.</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="secondSpotID" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>ID of the second spot spotted using "spottingPattern". This ID must have been defined also in the spot element.</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                    </xs:complexType>
                    <xs:keyref name="onlyValidFirstSpotID" refer="cff:spotKey">
                      <xs:selector xpath="."/>
                      <xs:field xpath="@spotID"/>
                    </xs:keyref>
                    <xs:keyref name="onlyValidSecondSpotID" refer="cff:spotKey">
                      <xs:selector xpath="."/>
                      <xs:field xpath="@spotID"/>
                    </xs:keyref>
                  </xs:element>
                </xs:sequence>
              </xs:complexType>
            </xs:element>
            <xs:element name="spot" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Information about individual spots.</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="maldiMatrix" type="cff:ontologyEntryType"/>
                </xs:sequence>
                <xs:attribute name="spotID" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>Unique identifier for the spot.</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="spotXPosition" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>X cartesian position of the spot.</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="spotYPosition" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>Y cartesian position of the spot.</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="spotDiameter" type="xs:positiveInteger" use="optional"/>
              </xs:complexType>
              <xs:key name="spotKey">
                <xs:selector xpath="."/>
                <xs:field xpath="@spotID"/>
              </xs:key>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="plateID" type="xs:positiveInteger" use="required">
            <xs:annotation>
              <xs:documentation>Unique identifier for the plate.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="spotXCount" type="xs:positiveInteger" use="required"/>
          <xs:attribute name="spotYCount" type="xs:positiveInteger" use="required"/>
        </xs:complexType>
        <xs:key name="plateKey">
          <xs:selector xpath="."/>
          <xs:field xpath="@plateID"/>
        </xs:key>
      </xs:element>
      <xs:element name="robot" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Information about the robot, if any, used to spot the plates.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="robotManufacturer" type="cff:ontologyEntryType"/>
            <xs:element name="robotModel" type="cff:ontologyEntryType"/>
          </xs:sequence>
          <xs:attribute name="timePerSpot" type="xs:duration" use="required"/>
          <xs:attribute name="deadVolume" type="xs:nonNegativeInteger" use="optional">
            <xs:annotation>
              <xs:documentation>Dead volume in ul of the spotting robot.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
  </xs:complexType>
</xs:element>

element msRun/spotting/plate
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
isRef 0
content complex
children cff:plateManufacturer cff:plateModel cff:pattern cff:spot
attributes
Name  Type  Use  Default  Fixed  Annotation
plateID  xs:positiveIntegerrequired      
documentation 
Unique identifier for the plate.
spotXCount  xs:positiveIntegerrequired      
spotYCount  xs:positiveIntegerrequired      
identity constraints
  Name  Refer  Selector  Field(s)  
key  plateKey    .  @plateID  
annotation
documentation 
Information about a MALDI plate.
source 
<xs:element name="plate" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Information about a MALDI plate.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="plateManufacturer" type="cff:ontologyEntryType"/>
      <xs:element name="plateModel" type="cff:ontologyEntryType"/>
      <xs:element name="pattern" minOccurs="0">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="spottingPattern" type="cff:ontologyEntryType"/>
            <xs:element name="orientation">
              <xs:annotation>
                <xs:documentation>Defines the orientation of the spotting pattern, with the IDs of the fist two consecutive spotted spots.</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:attribute name="firstSpotID" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>ID of the first spot spotted using "spottingPattern". This ID must have been defined also in the spot element.</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="secondSpotID" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>ID of the second spot spotted using "spottingPattern". This ID must have been defined also in the spot element.</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
              <xs:keyref name="onlyValidFirstSpotID" refer="cff:spotKey">
                <xs:selector xpath="."/>
                <xs:field xpath="@spotID"/>
              </xs:keyref>
              <xs:keyref name="onlyValidSecondSpotID" refer="cff:spotKey">
                <xs:selector xpath="."/>
                <xs:field xpath="@spotID"/>
              </xs:keyref>
            </xs:element>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="spot" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Information about individual spots.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="maldiMatrix" type="cff:ontologyEntryType"/>
          </xs:sequence>
          <xs:attribute name="spotID" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Unique identifier for the spot.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="spotXPosition" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>X cartesian position of the spot.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="spotYPosition" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Y cartesian position of the spot.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="spotDiameter" type="xs:positiveInteger" use="optional"/>
        </xs:complexType>
        <xs:key name="spotKey">
          <xs:selector xpath="."/>
          <xs:field xpath="@spotID"/>
        </xs:key>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="plateID" type="xs:positiveInteger" use="required">
      <xs:annotation>
        <xs:documentation>Unique identifier for the plate.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="spotXCount" type="xs:positiveInteger" use="required"/>
    <xs:attribute name="spotYCount" type="xs:positiveInteger" use="required"/>
  </xs:complexType>
  <xs:key name="plateKey">
    <xs:selector xpath="."/>
    <xs:field xpath="@plateID"/>
  </xs:key>
</xs:element>

element msRun/spotting/plate/plateManufacturer
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type ontologyEntryType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
category  xs:stringrequired      
value  xs:stringrequired      
source 
<xs:element name="plateManufacturer" type="cff:ontologyEntryType"/>

element msRun/spotting/plate/plateModel
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type ontologyEntryType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
category  xs:stringrequired      
value  xs:stringrequired      
source 
<xs:element name="plateModel" type="cff:ontologyEntryType"/>

element msRun/spotting/plate/pattern
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
isRef 0
content complex
children cff:spottingPattern cff:orientation
source 
<xs:element name="pattern" minOccurs="0">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="spottingPattern" type="cff:ontologyEntryType"/>
      <xs:element name="orientation">
        <xs:annotation>
          <xs:documentation>Defines the orientation of the spotting pattern, with the IDs of the fist two consecutive spotted spots.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="firstSpotID" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>ID of the first spot spotted using "spottingPattern". This ID must have been defined also in the spot element.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="secondSpotID" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>ID of the second spot spotted using "spottingPattern". This ID must have been defined also in the spot element.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
        <xs:keyref name="onlyValidFirstSpotID" refer="cff:spotKey">
          <xs:selector xpath="."/>
          <xs:field xpath="@spotID"/>
        </xs:keyref>
        <xs:keyref name="onlyValidSecondSpotID" refer="cff:spotKey">
          <xs:selector xpath="."/>
          <xs:field xpath="@spotID"/>
        </xs:keyref>
      </xs:element>
    </xs:sequence>
  </xs:complexType>
</xs:element>

element msRun/spotting/plate/pattern/spottingPattern
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type ontologyEntryType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
category  xs:stringrequired      
value  xs:stringrequired      
source 
<xs:element name="spottingPattern" type="cff:ontologyEntryType"/>

element msRun/spotting/plate/pattern/orientation
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
firstSpotID  xs:stringrequired      
documentation 
ID of the first spot spotted using "spottingPattern". This ID must have been defined also in the spot element.
secondSpotID  xs:stringrequired      
documentation 
ID of the second spot spotted using "spottingPattern". This ID must have been defined also in the spot element.
identity constraints
  Name  Refer  Selector  Field(s)  
keyref  onlyValidFirstSpotID  cff:spotKey  .  @spotID  
keyref  onlyValidSecondSpotID  cff:spotKey  .  @spotID  
annotation
documentation 
Defines the orientation of the spotting pattern, with the IDs of the fist two consecutive spotted spots.
source 
<xs:element name="orientation">
  <xs:annotation>
    <xs:documentation>Defines the orientation of the spotting pattern, with the IDs of the fist two consecutive spotted spots.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="firstSpotID" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>ID of the first spot spotted using "spottingPattern". This ID must have been defined also in the spot element.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="secondSpotID" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>ID of the second spot spotted using "spottingPattern". This ID must have been defined also in the spot element.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
  <xs:keyref name="onlyValidFirstSpotID" refer="cff:spotKey">
    <xs:selector xpath="."/>
    <xs:field xpath="@spotID"/>
  </xs:keyref>
  <xs:keyref name="onlyValidSecondSpotID" refer="cff:spotKey">
    <xs:selector xpath="."/>
    <xs:field xpath="@spotID"/>
  </xs:keyref>
</xs:element>

element msRun/spotting/plate/spot
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
isRef 0
content complex
children cff:maldiMatrix
attributes
Name  Type  Use  Default  Fixed  Annotation
spotID  xs:stringrequired      
documentation 
Unique identifier for the spot.
spotXPosition  xs:stringrequired      
documentation 
X cartesian position of the spot.
spotYPosition  xs:stringrequired      
documentation 
Y cartesian position of the spot.
spotDiameter  xs:positiveIntegeroptional      
identity constraints
  Name  Refer  Selector  Field(s)  
key  spotKey    .  @spotID  
annotation
documentation 
Information about individual spots.
source 
<xs:element name="spot" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Information about individual spots.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="maldiMatrix" type="cff:ontologyEntryType"/>
    </xs:sequence>
    <xs:attribute name="spotID" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Unique identifier for the spot.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="spotXPosition" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>X cartesian position of the spot.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="spotYPosition" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Y cartesian position of the spot.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="spotDiameter" type="xs:positiveInteger" use="optional"/>
  </xs:complexType>
  <xs:key name="spotKey">
    <xs:selector xpath="."/>
    <xs:field xpath="@spotID"/>
  </xs:key>
</xs:element>

element msRun/spotting/plate/spot/maldiMatrix
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type ontologyEntryType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
category  xs:stringrequired      
value  xs:stringrequired      
source 
<xs:element name="maldiMatrix" type="cff:ontologyEntryType"/>

element msRun/spotting/robot
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
isRef 0
content complex
children cff:robotManufacturer cff:robotModel
attributes
Name  Type  Use  Default  Fixed  Annotation
timePerSpot  xs:durationrequired      
deadVolume  xs:nonNegativeIntegeroptional      
documentation 
Dead volume in ul of the spotting robot.
annotation
documentation 
Information about the robot, if any, used to spot the plates.
source 
<xs:element name="robot" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Information about the robot, if any, used to spot the plates.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="robotManufacturer" type="cff:ontologyEntryType"/>
      <xs:element name="robotModel" type="cff:ontologyEntryType"/>
    </xs:sequence>
    <xs:attribute name="timePerSpot" type="xs:duration" use="required"/>
    <xs:attribute name="deadVolume" type="xs:nonNegativeInteger" use="optional">
      <xs:annotation>
        <xs:documentation>Dead volume in ul of the spotting robot.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element msRun/spotting/robot/robotManufacturer
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type ontologyEntryType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
category  xs:stringrequired      
value  xs:stringrequired      
source 
<xs:element name="robotManufacturer" type="cff:ontologyEntryType"/>

element msRun/spotting/robot/robotModel
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type ontologyEntryType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
category  xs:stringrequired      
value  xs:stringrequired      
source 
<xs:element name="robotModel" type="cff:ontologyEntryType"/>

element msRun/sha1
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type restriction of xs:string
properties
isRef 0
content simple
facets
length 40
annotation
documentation 
sha-1 sum for this file (from the beginning of the file up to (and including) the opening tag of sha1
source 
<xs:element name="sha1" minOccurs="0">
  <xs:annotation>
    <xs:documentation>sha-1 sum for this file (from the beginning of the file up to (and including) the opening tag of sha1</xs:documentation>
  </xs:annotation>
  <xs:simpleType>
    <xs:restriction base="xs:string">
      <xs:length value="40"/>
    </xs:restriction>
  </xs:simpleType>
</xs:element>

element operator
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type extension of xs:anySimpleType
properties
content complex
used by
element msRun/msInstrument
attributes
Name  Type  Use  Default  Fixed  Annotation
first  xs:stringrequired      
documentation 
First name
last  xs:stringrequired      
documentation 
Last name
phone  xs:stringoptional      
documentation 
Phone number
email  optional      
documentation 
email address
URI  xs:anyURIoptional      
documentation 
Uniform Resource Identifier
annotation
documentation 
Contact information for the person responsible for the instrument.
source 
<xs:element name="operator">
  <xs:annotation>
    <xs:documentation>Contact information for the person responsible for the instrument.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:simpleContent>
      <xs:extension base="xs:anySimpleType">
        <xs:attribute name="first" type="xs:string" use="required">
          <xs:annotation>
            <xs:documentation>First name</xs:documentation>
          </xs:annotation>
        </xs:attribute>
        <xs:attribute name="last" type="xs:string" use="required">
          <xs:annotation>
            <xs:documentation>Last name</xs:documentation>
          </xs:annotation>
        </xs:attribute>
        <xs:attribute name="phone" type="xs:string" use="optional">
          <xs:annotation>
            <xs:documentation>Phone number</xs:documentation>
          </xs:annotation>
        </xs:attribute>
        <xs:attribute name="email" use="optional">
          <xs:annotation>
            <xs:documentation>email address</xs:documentation>
          </xs:annotation>
          <xs:simpleType>
            <xs:restriction base="xs:string">
              <xs:pattern value="(.)*[@](.)*\.(.)*"/>
            </xs:restriction>
          </xs:simpleType>
        </xs:attribute>
        <xs:attribute name="URI" type="xs:anyURI" use="optional">
          <xs:annotation>
            <xs:documentation>Uniform Resource Identifier</xs:documentation>
          </xs:annotation>
        </xs:attribute>
      </xs:extension>
    </xs:simpleContent>
  </xs:complexType>
</xs:element>

element scan
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
content complex
children cff:scanOrigin cff:precursorMz cff:maldi cff:peaks cff:nameValue cff:comment scan
used by
elements msRun scan
attributes
Name  Type  Use  Default  Fixed  Annotation
num  xs:positiveIntegerrequired      
documentation 
Scan number
msLevel  xs:positiveIntegerrequired      
documentation 
1: MS
2: MS/MS
...
peaksCount  xs:nonNegativeIntegerrequired      
documentation 
Total number of m/z-intensity pairs in the scan
polarity  optional      
documentation 
+: positive
-: negative
any
scanType  optional      
centroided  xs:booleanoptional      
documentation 
This only maters if centroided attribute of dataProcessing element is 0 or absent.
This attribute should be used only if some scans were processed and others not. If all scans were processed, than the corresponding attribute form the dataProcessing element should be used instead.
deisotoped  xs:booleanoptional      
documentation 
This only maters if deisotoped attribute of dataProcessing element is 0 or absent.
This attribute should be used only if some scans were processed and others not. If all scans were processed, than the corresponding attribute form the dataProcessing element should be used instead.
chargeDeconvoluted  xs:booleanoptional  0    
documentation 
This only maters if chargeDeconvoluted attribute of dataProcessing element is 0 or absent.
This attribute should be used only if some scans were processed and others not. If all scans were processed, than the corresponding attribute form the dataProcessing element should be used instead.
retentionTime  xs:durationoptional      
documentation 
Retention time of the scan
ionisationEnergy  xs:floatoptional      
collisionEnergy  xs:floatoptional      
documentation 
Collision energy used to fragment the parent ion.
cidGasPressure  xs:floatoptional      
startMz  xs:floatoptional      
documentation 
Setted low m/z boundary (this is the instrumetal setting)
endMz  xs:floatoptional      
documentation 
Setted high m/z boundary (this is the instrumetal setting)
lowMz  xs:floatoptional      
documentation 
Observed low m/z (this is what the actual data looks like)
highMz  xs:floatoptional      
documentation 
Observed high m/z (this is what the actual data looks like)
basePeakMz  xs:floatoptional      
documentation 
m/z of the base peak (most intense peak)
basePeakIntensity  xs:floatoptional      
documentation 
Intensity of the base peak (most intense peak)
totIonCurrent  xs:floatoptional      
documentation 
Total ion current (total intensity in the scan)
annotation
documentation 
The actual MS data is here
source 
<xs:element name="scan">
  <xs:annotation>
    <xs:documentation>The actual MS data is here</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="scanOrigin" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:attribute name="parentFileID" use="required">
            <xs:simpleType>
              <xs:restriction base="xs:string">
                <xs:length value="40"/>
              </xs:restriction>
            </xs:simpleType>
          </xs:attribute>
          <xs:attribute name="num" type="xs:nonNegativeInteger" use="required"/>
        </xs:complexType>
        <xs:keyref name="onlyValidParentFileID" refer="cff:parentFileKey">
          <xs:selector xpath="."/>
          <xs:field xpath="@parentFileID"/>
        </xs:keyref>
      </xs:element>
      <xs:element name="precursorMz" minOccurs="0" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Information about the precursor ion.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:simpleContent>
            <xs:extension base="xs:float">
              <xs:attribute name="precursorScanNum" type="xs:positiveInteger" use="optional">
                <xs:annotation>
                  <xs:documentation>This is a unique identifier in case more than one precusor  were selected to generate the MS/MS spectra</xs:documentation>
                </xs:annotation>
              </xs:attribute>
              <xs:attribute name="precursorIntensity" type="xs:float" use="required">
                <xs:annotation>
                  <xs:documentation>This is the Intensity of the parent Ion. It is required in case of future exporting to pkl format. This should be the intensity as measured by the instrument prior to any data elaboration</xs:documentation>
                </xs:annotation>
              </xs:attribute>
              <xs:attribute name="precursorCharge" type="xs:positiveInteger" use="optional">
                <xs:annotation>
                  <xs:documentation>If the charge state of the precursor is know, than it should be stored here.</xs:documentation>
                </xs:annotation>
              </xs:attribute>
              <xs:attribute name="windowWideness" type="xs:float" use="optional">
                <xs:annotation>
                  <xs:documentation>This is the total wideness of the precursor mass selection window. </xs:documentation>
                </xs:annotation>
              </xs:attribute>
            </xs:extension>
          </xs:simpleContent>
        </xs:complexType>
      </xs:element>
      <xs:element name="maldi" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Acquisition dependent properties of a MALDI experiment.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="plateID" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Unique plate ID. This ID must have been defined also in the plate element.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="spotID" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Unique spot ID. This ID must have been defined also in the spot element.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="laserShootCount" type="xs:positiveInteger" use="optional">
            <xs:annotation>
              <xs:documentation>Number of times the laser was fired to generate this scan.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="laserFrequency" type="xs:duration" use="optional">
            <xs:annotation>
              <xs:documentation>Frequency of the laser.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="laserIntensity" type="xs:positiveInteger" use="optional">
            <xs:annotation>
              <xs:documentation>Intensity of laser.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="collisionGas" type="xs:boolean" use="optional"/>
        </xs:complexType>
        <xs:keyref name="onlyValidPlateID" refer="cff:plateKey">
          <xs:selector xpath="."/>
          <xs:field xpath="@plateID"/>
        </xs:keyref>
        <xs:keyref name="onlyValidSpotID" refer="cff:spotKey">
          <xs:selector xpath="."/>
          <xs:field xpath="@spotID"/>
        </xs:keyref>
      </xs:element>
      <xs:element name="peaks" nillable="1">
        <xs:annotation>
          <xs:documentation>This is the actual data encoded using base64. Byte order must be network. The order of the pairs must be m/z – intensity.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:simpleContent>
            <xs:extension base="cff:strictBase64Type">
              <xs:attribute name="precision" use="required">
                <xs:annotation>
                  <xs:documentation>nr of bits used by each component</xs:documentation>
                </xs:annotation>
                <xs:simpleType>
                  <xs:restriction base="xs:positiveInteger">
                    <xs:enumeration value="32"/>
                    <xs:enumeration value="64"/>
                  </xs:restriction>
                </xs:simpleType>
              </xs:attribute>
              <xs:attribute name="byteOrder" type="xs:string" use="required" fixed="network">
                <xs:annotation>
                  <xs:documentation>Byte order of the encoded binary information (must be network).</xs:documentation>
                </xs:annotation>
              </xs:attribute>
              <xs:attribute name="pairOrder" type="xs:string" use="required" fixed="m/z-int">
                <xs:annotation>
                  <xs:documentation>Order of the m/z intensity pairs (must be m/z-int).</xs:documentation>
                </xs:annotation>
              </xs:attribute>
            </xs:extension>
          </xs:simpleContent>
        </xs:complexType>
      </xs:element>
      <xs:sequence minOccurs="0" maxOccurs="unbounded">
        <xs:element name="nameValue" type="cff:namevalueType">
          <xs:annotation>
            <xs:documentation>This is reserved for describing properties of the scan not elsewhere included in the schema</xs:documentation>
          </xs:annotation>
        </xs:element>
        <xs:element name="comment" type="xs:string" minOccurs="0">
          <xs:annotation>
            <xs:documentation>Additional comments</xs:documentation>
          </xs:annotation>
        </xs:element>
      </xs:sequence>
      <xs:element ref="cff:scan" minOccurs="0" maxOccurs="unbounded"/>
    </xs:sequence>
    <xs:attribute name="num" type="xs:positiveInteger" use="required">
      <xs:annotation>
        <xs:documentation>Scan number</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="msLevel" type="xs:positiveInteger" use="required">
      <xs:annotation>
        <xs:documentation>1: MS
2: MS/MS
...</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="peaksCount" type="xs:nonNegativeInteger" use="required">
      <xs:annotation>
        <xs:documentation>Total number of m/z-intensity pairs in the scan</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="polarity" use="optional">
      <xs:annotation>
        <xs:documentation>+: positive
-: negative
any</xs:documentation>
      </xs:annotation>
      <xs:simpleType>
        <xs:restriction base="xs:string">
          <xs:enumeration value="+"/>
          <xs:enumeration value="-"/>
          <xs:enumeration value="any"/>
        </xs:restriction>
      </xs:simpleType>
    </xs:attribute>
    <xs:attribute name="scanType" use="optional">
      <xs:simpleType>
        <xs:restriction base="xs:string">
          <xs:enumeration value="Full"/>
          <xs:enumeration value="zoom"/>
          <xs:enumeration value="SIM"/>
          <xs:enumeration value="SRM"/>
          <xs:enumeration value="CRM"/>
          <xs:enumeration value="Q1"/>
          <xs:enumeration value="Q3"/>
        </xs:restriction>
      </xs:simpleType>
    </xs:attribute>
    <xs:attribute name="centroided" type="xs:boolean" use="optional">
      <xs:annotation>
        <xs:documentation>This only maters if centroided attribute of dataProcessing element is 0 or absent.
This attribute should be used only if some scans were processed and others not. If all scans were processed, than the corresponding attribute form the dataProcessing element should be used instead.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="deisotoped" type="xs:boolean" use="optional">
      <xs:annotation>
        <xs:documentation>This only maters if deisotoped attribute of dataProcessing element is 0 or absent.
This attribute should be used only if some scans were processed and others not. If all scans were processed, than the corresponding attribute form the dataProcessing element should be used instead.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="chargeDeconvoluted" type="xs:boolean" use="optional" default="0">
      <xs:annotation>
        <xs:documentation>This only maters if chargeDeconvoluted attribute of dataProcessing element is 0 or absent.
This attribute should be used only if some scans were processed and others not. If all scans were processed, than the corresponding attribute form the dataProcessing element should be used instead.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="retentionTime" type="xs:duration" use="optional">
      <xs:annotation>
        <xs:documentation>Retention time of the scan</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="ionisationEnergy" type="xs:float" use="optional"/>
    <xs:attribute name="collisionEnergy" type="xs:float" use="optional">
      <xs:annotation>
        <xs:documentation>Collision energy used to fragment the parent ion.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="cidGasPressure" type="xs:float" use="optional"/>
    <xs:attribute name="startMz" type="xs:float" use="optional">
      <xs:annotation>
        <xs:documentation>Setted low m/z boundary (this is the instrumetal setting)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="endMz" type="xs:float" use="optional">
      <xs:annotation>
        <xs:documentation>Setted high m/z boundary (this is the instrumetal setting)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="lowMz" type="xs:float" use="optional">
      <xs:annotation>
        <xs:documentation>Observed low m/z (this is what the actual data looks like)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="highMz" type="xs:float" use="optional">
      <xs:annotation>
        <xs:documentation>Observed high m/z (this is what the actual data looks like)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="basePeakMz" type="xs:float" use="optional">
      <xs:annotation>
        <xs:documentation>m/z of the base peak (most intense peak)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="basePeakIntensity" type="xs:float" use="optional">
      <xs:annotation>
        <xs:documentation>Intensity of the base peak (most intense peak)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="totIonCurrent" type="xs:float" use="optional">
      <xs:annotation>
        <xs:documentation>Total ion current (total intensity in the scan)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element scan/scanOrigin
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
parentFileID  required      
num  xs:nonNegativeIntegerrequired      
identity constraints
  Name  Refer  Selector  Field(s)  
keyref  onlyValidParentFileID  cff:parentFileKey  .  @parentFileID  
source 
<xs:element name="scanOrigin" minOccurs="0" maxOccurs="unbounded">
  <xs:complexType>
    <xs:attribute name="parentFileID" use="required">
      <xs:simpleType>
        <xs:restriction base="xs:string">
          <xs:length value="40"/>
        </xs:restriction>
      </xs:simpleType>
    </xs:attribute>
    <xs:attribute name="num" type="xs:nonNegativeInteger" use="required"/>
  </xs:complexType>
  <xs:keyref name="onlyValidParentFileID" refer="cff:parentFileKey">
    <xs:selector xpath="."/>
    <xs:field xpath="@parentFileID"/>
  </xs:keyref>
</xs:element>

element scan/precursorMz
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type extension of xs:float
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
precursorScanNum  xs:positiveIntegeroptional      
documentation 
This is a unique identifier in case more than one precusor  were selected to generate the MS/MS spectra
precursorIntensity  xs:floatrequired      
documentation 
This is the Intensity of the parent Ion. It is required in case of future exporting to pkl format. This should be the intensity as measured by the instrument prior to any data elaboration
precursorCharge  xs:positiveIntegeroptional      
documentation 
If the charge state of the precursor is know, than it should be stored here.
windowWideness  xs:floatoptional      
documentation 
This is the total wideness of the precursor mass selection window.
annotation
documentation 
Information about the precursor ion.
source 
<xs:element name="precursorMz" minOccurs="0" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Information about the precursor ion.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:simpleContent>
      <xs:extension base="xs:float">
        <xs:attribute name="precursorScanNum" type="xs:positiveInteger" use="optional">
          <xs:annotation>
            <xs:documentation>This is a unique identifier in case more than one precusor  were selected to generate the MS/MS spectra</xs:documentation>
          </xs:annotation>
        </xs:attribute>
        <xs:attribute name="precursorIntensity" type="xs:float" use="required">
          <xs:annotation>
            <xs:documentation>This is the Intensity of the parent Ion. It is required in case of future exporting to pkl format. This should be the intensity as measured by the instrument prior to any data elaboration</xs:documentation>
          </xs:annotation>
        </xs:attribute>
        <xs:attribute name="precursorCharge" type="xs:positiveInteger" use="optional">
          <xs:annotation>
            <xs:documentation>If the charge state of the precursor is know, than it should be stored here.</xs:documentation>
          </xs:annotation>
        </xs:attribute>
        <xs:attribute name="windowWideness" type="xs:float" use="optional">
          <xs:annotation>
            <xs:documentation>This is the total wideness of the precursor mass selection window. </xs:documentation>
          </xs:annotation>
        </xs:attribute>
      </xs:extension>
    </xs:simpleContent>
  </xs:complexType>
</xs:element>

element scan/maldi
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
plateID  xs:stringrequired      
documentation 
Unique plate ID. This ID must have been defined also in the plate element.
spotID  xs:stringrequired      
documentation 
Unique spot ID. This ID must have been defined also in the spot element.
laserShootCount  xs:positiveIntegeroptional      
documentation 
Number of times the laser was fired to generate this scan.
laserFrequency  xs:durationoptional      
documentation 
Frequency of the laser.
laserIntensity  xs:positiveIntegeroptional      
documentation 
Intensity of laser.
collisionGas  xs:booleanoptional      
identity constraints
  Name  Refer  Selector  Field(s)  
keyref  onlyValidPlateID  cff:plateKey  .  @plateID  
keyref  onlyValidSpotID  cff:spotKey  .  @spotID  
annotation
documentation 
Acquisition dependent properties of a MALDI experiment.
source 
<xs:element name="maldi" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Acquisition dependent properties of a MALDI experiment.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="plateID" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Unique plate ID. This ID must have been defined also in the plate element.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="spotID" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Unique spot ID. This ID must have been defined also in the spot element.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="laserShootCount" type="xs:positiveInteger" use="optional">
      <xs:annotation>
        <xs:documentation>Number of times the laser was fired to generate this scan.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="laserFrequency" type="xs:duration" use="optional">
      <xs:annotation>
        <xs:documentation>Frequency of the laser.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="laserIntensity" type="xs:positiveInteger" use="optional">
      <xs:annotation>
        <xs:documentation>Intensity of laser.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="collisionGas" type="xs:boolean" use="optional"/>
  </xs:complexType>
  <xs:keyref name="onlyValidPlateID" refer="cff:plateKey">
    <xs:selector xpath="."/>
    <xs:field xpath="@plateID"/>
  </xs:keyref>
  <xs:keyref name="onlyValidSpotID" refer="cff:spotKey">
    <xs:selector xpath="."/>
    <xs:field xpath="@spotID"/>
  </xs:keyref>
</xs:element>

element scan/peaks
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type extension of strictBase64Type
properties
isRef 0
content complex
nillable 1
facets
pattern ([A-Za-z0-9/\+=])*
attributes
Name  Type  Use  Default  Fixed  Annotation
precision  required      
documentation 
nr of bits used by each component
byteOrder  xs:stringrequired    network  
documentation 
Byte order of the encoded binary information (must be network).
pairOrder  xs:stringrequired    m/z-int  
documentation 
Order of the m/z intensity pairs (must be m/z-int).
annotation
documentation 
This is the actual data encoded using base64. Byte order must be network. The order of the pairs must be m/z – intensity.
source 
<xs:element name="peaks" nillable="1">
  <xs:annotation>
    <xs:documentation>This is the actual data encoded using base64. Byte order must be network. The order of the pairs must be m/z – intensity.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:simpleContent>
      <xs:extension base="cff:strictBase64Type">
        <xs:attribute name="precision" use="required">
          <xs:annotation>
            <xs:documentation>nr of bits used by each component</xs:documentation>
          </xs:annotation>
          <xs:simpleType>
            <xs:restriction base="xs:positiveInteger">
              <xs:enumeration value="32"/>
              <xs:enumeration value="64"/>
            </xs:restriction>
          </xs:simpleType>
        </xs:attribute>
        <xs:attribute name="byteOrder" type="xs:string" use="required" fixed="network">
          <xs:annotation>
            <xs:documentation>Byte order of the encoded binary information (must be network).</xs:documentation>
          </xs:annotation>
        </xs:attribute>
        <xs:attribute name="pairOrder" type="xs:string" use="required" fixed="m/z-int">
          <xs:annotation>
            <xs:documentation>Order of the m/z intensity pairs (must be m/z-int).</xs:documentation>
          </xs:annotation>
        </xs:attribute>
      </xs:extension>
    </xs:simpleContent>
  </xs:complexType>
</xs:element>

element scan/nameValue
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type namevalueType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
name  xs:stringoptional      
value  xs:anySimpleTypeoptional      
type  xs:anySimpleTypeoptional      
annotation
documentation 
This is reserved for describing properties of the scan not elsewhere included in the schema
source 
<xs:element name="nameValue" type="cff:namevalueType">
  <xs:annotation>
    <xs:documentation>This is reserved for describing properties of the scan not elsewhere included in the schema</xs:documentation>
  </xs:annotation>
</xs:element>

element scan/comment
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type xs:string
properties
isRef 0
content simple
annotation
documentation 
Additional comments
source 
<xs:element name="comment" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Additional comments</xs:documentation>
  </xs:annotation>
</xs:element>

element software
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type extension of xs:anySimpleType
properties
content complex
used by
elements msRun/dataProcessing msRun/msInstrument
attributes
Name  Type  Use  Default  Fixed  Annotation
type  required      
documentation 
acquisition: acquisition software running the MS (instrument section)
conversion: RAW data to XML converter utility (dataProcessing section)
processing: any form of data processing software not included by the two previous definitions (dataProcessing section)
name  xs:stringrequired      
documentation 
Name of the acquisition software
version  xs:stringrequired      
documentation 
Version of the acquisition software. Legal patterns are n.m(a or b)
completionTime  xs:dateTimeoptional      
documentation 
Time of completion of the dataProcessing operation
annotation
documentation 
Software identifier
source 
<xs:element name="software">
  <xs:annotation>
    <xs:documentation>Software identifier</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:simpleContent>
      <xs:extension base="xs:anySimpleType">
        <xs:attribute name="type" use="required">
          <xs:annotation>
            <xs:documentation>acquisition: acquisition software running the MS (instrument section)
conversion: RAW data to XML converter utility (dataProcessing section)
processing: any form of data processing software not included by the two previous definitions (dataProcessing section)</xs:documentation>
          </xs:annotation>
          <xs:simpleType>
            <xs:restriction base="xs:string">
              <xs:enumeration value="acquisition"/>
              <xs:enumeration value="conversion"/>
              <xs:enumeration value="processing"/>
            </xs:restriction>
          </xs:simpleType>
        </xs:attribute>
        <xs:attribute name="name" type="xs:string" use="required">
          <xs:annotation>
            <xs:documentation>Name of the acquisition software</xs:documentation>
          </xs:annotation>
        </xs:attribute>
        <xs:attribute name="version" type="xs:string" use="required">
          <xs:annotation>
            <xs:documentation>Version of the acquisition software. Legal patterns are n.m(a or b)</xs:documentation>
          </xs:annotation>
        </xs:attribute>
        <xs:attribute name="completionTime" type="xs:dateTime" use="optional">
          <xs:annotation>
            <xs:documentation>Time of completion of the dataProcessing operation</xs:documentation>
          </xs:annotation>
        </xs:attribute>
      </xs:extension>
    </xs:simpleContent>
  </xs:complexType>
</xs:element>

simpleType strictBase64Type
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type restriction of xs:base64Binary
used by
element scan/peaks
facets
pattern ([A-Za-z0-9/\+=])*
source 
<xs:simpleType name="strictBase64Type">
  <xs:restriction base="xs:base64Binary">
    <xs:pattern value="([A-Za-z0-9/\+=])*"/>
  </xs:restriction>
</xs:simpleType>

element separationTechnique
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type separationTechniqueType
properties
content complex
abstract true
used by
element msRun/separation
annotation
documentation 
Since this schema is only for MS data, the actual implementation of this element is left to another schema. See "Implementing variable content containers using an abstract element and element substitution" (http://www.xfront.com/VariableContentContainers.pdf).
source 
<xs:element name="separationTechnique" type="separationTechniqueType" abstract="true">
  <xs:annotation>
    <xs:documentation>Since this schema is only for MS data, the actual implementation of this element is left to another schema. See "Implementing variable content containers using an abstract element and element substitution" (http://www.xfront.com/VariableContentContainers.pdf).</xs:documentation>
  </xs:annotation>
</xs:element>

complexType separationTechniqueType
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
used by
element separationTechnique
source 
<xs:complexType name="separationTechniqueType"/>

complexType namevalueType
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
type extension of xs:anySimpleType
properties
base xs:anySimpleType
used by
elements msRun/msInstrument/nameValue scan/nameValue msRun/dataProcessing/processingOperation
attributes
Name  Type  Use  Default  Fixed  Annotation
name  xs:stringoptional      
value  xs:anySimpleTypeoptional      
type  xs:anySimpleTypeoptional      
source 
<xs:complexType name="namevalueType">
  <xs:simpleContent>
    <xs:extension base="xs:anySimpleType">
      <xs:attribute name="name" type="xs:string" use="optional"/>
      <xs:attribute name="value" type="xs:anySimpleType" use="optional"/>
      <xs:attribute name="type" type="xs:anySimpleType" use="optional"/>
    </xs:extension>
  </xs:simpleContent>
</xs:complexType>

complexType ontologyEntryType
diagram
namespace http://sashimi.sourceforge.net/schema_revision/mzXML_2.1
used by
elements msRun/spotting/plate/spot/maldiMatrix msRun/msInstrument/msDetector msRun/msInstrument/msIonisation msRun/msInstrument/msManufacturer msRun/msInstrument/msMassAnalyzer msRun/msInstrument/msModel msRun/msInstrument/msResolution msRun/spotting/plate/plateManufacturer msRun/spotting/plate/plateModel msRun/spotting/robot/robotManufacturer msRun/spotting/robot/robotModel msRun/spotting/plate/pattern/spottingPattern
attributes
Name  Type  Use  Default  Fixed  Annotation
category  xs:stringrequired      
value  xs:stringrequired      
source 
<xs:complexType name="ontologyEntryType">
  <xs:attribute name="category" type="xs:string" use="required"/>
  <xs:attribute name="value" type="xs:string" use="required"/>
</xs:complexType>


XML Schema documentation generated with XMLSpy Schema Editor http://www.altova.com/xmlspy