Schema SUMmOnCondition.xsd


schema location:  C:\Documents and Settings\imsb\My Documents\SUMmOnConditionSchemas\1.0\SUMmOnCondition.xsd
targetNamespace:  http://summon.sf.net/SUMmOnCondition/1.0/
 
Elements 
SUMmOnCondition 


element SUMmOnCondition
diagram
namespace http://summon.sf.net/SUMmOnCondition/1.0/
children fragmentMasses modifiedResidue loss modify digestC digestN missCleaveC getMissCleaveC digestUnconstrained digestionStep digestionTolerance massTolerance startCharge endCharge centroiding normalization targetMs output nonInteractive
attributes
Name  Type  Use  Default  Fixed  Annotation
description  xs:string        
documentation 
Description of the content of condition file.
annotation
documentation 
This is the root element of a SUMmOn condition file.
source
<xs:element name="SUMmOnCondition">
  <xs:annotation>
    <xs:documentation>This is the root element of a SUMmOn condition file.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="fragmentMasses">
        <xs:annotation>
          <xs:documentation>The list of masses for the elemental units (e.g. amino acids in the case of a peptide) comprising the PTM under investigation. When using amino acid masses you should be carefull in setting the mass of the N/C terminal residues (i.e. remember to add one extra H or OH).           Use a new line for every mass and a 0 to indicate the site of attachement to the target peptide.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:simpleContent>
            <xs:extension base="xs:string">
              <xs:attribute name="type" type="xs:string" fixed="S">
                <xs:annotation>
                  <xs:documentation>For the moment this attribute must be set to "S".</xs:documentation>
                </xs:annotation>
              </xs:attribute>
            </xs:extension>
          </xs:simpleContent>
        </xs:complexType>
      </xs:element>
      <xs:element name="modifiedResidue">
        <xs:annotation>
          <xs:documentation>Information on the site of attachment of the PTM.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="residue" type="xs:string">
            <xs:annotation>
              <xs:documentation>Amino Acid residue from the target peptide to which the PTM is attached to.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="notTerminal" type="xs:boolean">
            <xs:annotation>
              <xs:documentation>Can the modified amino acid be at the termini of the target peptide. For instance attachment of SUMO to a Lysine residue hinders tryptic cleavage at that residue.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="loss" minOccurs="0" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>A global loss that is applied to every fragment in the target peptide ion series (e.g. loss of water or ammonia).</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="value" type="xs:double">
            <xs:annotation>
              <xs:documentation>Mass in Da of the global loss.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="modify">
        <xs:annotation>
          <xs:documentation>Modification to be applied to a specific amino acid from the target peptide.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="residue" type="xs:string">
            <xs:annotation>
              <xs:documentation>Modified residue.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="mass" type="xs:double">
            <xs:annotation>
              <xs:documentation>Mass of the modification in Da.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="static" type="xs:boolean">
            <xs:annotation>
              <xs:documentation>1=static, 0=variable</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:sequence>
        <xs:choice>
          <xs:sequence>
            <xs:element name="digestC" minOccurs="0" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Digestion C terminal of a residue.</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:attribute name="residue" type="xs:string">
                  <xs:annotation>
                    <xs:documentation>The residue after which the digestion takes place.</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="notResidue" type="xs:string">
                  <xs:annotation>
                    <xs:documentation>If this residue is C terminal of the "residue" the enzyme will not cleave (use X if you always want a cleavage).</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
            <xs:element name="digestN" minOccurs="0" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Digestion N terminal of a residue.</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:attribute name="residue" type="xs:string">
                  <xs:annotation>
                    <xs:documentation>The residue before which digestion takes place.</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="notResidue" type="xs:string">
                  <xs:annotation>
                    <xs:documentation>If this residue is N terminal of the "residue" the enzyme will not cleave (use X if you always want a cleavage).</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
            <xs:element name="missCleaveC" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Adds up to "value" missed cleavages after "residue".</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:attribute name="residue" type="xs:string"/>
                <xs:attribute name="value" type="xs:int"/>
              </xs:complexType>
            </xs:element>
            <xs:element name="getMissCleaveC" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Discards every target peptide that doesn't have exactly "value" missed cleavages at "residue". If residue is followed by "notResidue" it is counted both as a missed cleavage as well as a non missed cleavage.</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:attribute name="residue" type="xs:string"/>
                <xs:attribute name="notResidue" type="xs:string"/>
                <xs:attribute name="value" type="xs:int"/>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:element name="digestUnconstrained" minOccurs="0">
            <xs:annotation>
              <xs:documentation>Digest unconstrained.</xs:documentation>
            </xs:annotation>
            <xs:complexType>
              <xs:attribute name="residue" type="xs:string">
                <xs:annotation>
                  <xs:documentation>Only keep residues that contain this residue.</xs:documentation>
                </xs:annotation>
              </xs:attribute>
              <xs:attribute name="value" type="xs:int">
                <xs:annotation>
                  <xs:documentation>Maximal lenght of a target peptide.</xs:documentation>
                </xs:annotation>
              </xs:attribute>
            </xs:complexType>
          </xs:element>
        </xs:choice>
      </xs:sequence>
      <xs:element name="digestionStep" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Maximal number of proteins that will be digested at once when looking up the target peptides. This is only helpfull if you are using a big subDB.fasta and are running out of memory.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="value" type="xs:int"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="digestionTolerance">
        <xs:annotation>
          <xs:documentation>Tolerance (in Da) to be used when matching target peptide precursor ions.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="value" type="xs:int"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="massTolerance">
        <xs:annotation>
          <xs:documentation>Tolerance (in Da) to be used when matching fragment ions.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="value" type="xs:int"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="startCharge">
        <xs:annotation>
          <xs:documentation>The lower charge limit that SUMmOn will use when searching data for which the charge states have not been determined. The default value is 1.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="value" type="xs:int"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="endCharge">
        <xs:annotation>
          <xs:documentation>The upper charge limit that SUMmOn will use when searching data for which the charge states have not been determined. The maximal value is 9.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="value" type="xs:int"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="centroiding">
        <xs:annotation>
          <xs:documentation>If your mzXML file contains profile mode data you must use this element to specify how to centroid it.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="type" type="xs:int">
            <xs:annotation>
              <xs:documentation>0=No centroiding, 1=Mathematical Averaging, 2=Weighted Averaging</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="iterations" type="xs:int" use="optional">
            <xs:annotation>
              <xs:documentation>The number of times the centroiding algorithm will run through the data (e.g. 4 should be a reasonable number).</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="normalization">
        <xs:annotation>
          <xs:documentation>This for the moment should always set to "-2".</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="type" type="xs:int" default="-2"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="targetMs">
        <xs:annotation>
          <xs:documentation>The MS level SUMmOn will analyze (e.g. 2 -> MS/MS ; 3 -> MS/MS/MS).</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="level" type="xs:int"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="output">
        <xs:annotation>
          <xs:documentation>1 will allow for more detailed post-analysis interpretation, but create a bigger file than 0.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="type" type="xs:int" default="1"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="nonInteractive">
        <xs:annotation>
          <xs:documentation>When set to 1 SUMmOn will save the results without switching to interactive mode in the middle of the analysis.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="value" type="xs:int"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="description" type="xs:string">
      <xs:annotation>
        <xs:documentation>Description of the content of condition file.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/fragmentMasses
diagram
type extension of xs:string
attributes
Name  Type  Use  Default  Fixed  Annotation
type  xs:string      S  
documentation 
For the moment this attribute must be set to "S".
annotation
documentation 
The list of masses for the elemental units (e.g. amino acids in the case of a peptide) comprising the PTM under investigation. When using amino acid masses you should be carefull in setting the mass of the N/C terminal residues (i.e. remember to add one extra H or OH).           Use a new line for every mass and a 0 to indicate the site of attachement to the target peptide.
source
<xs:element name="fragmentMasses">
  <xs:annotation>
    <xs:documentation>The list of masses for the elemental units (e.g. amino acids in the case of a peptide) comprising the PTM under investigation. When using amino acid masses you should be carefull in setting the mass of the N/C terminal residues (i.e. remember to add one extra H or OH).           Use a new line for every mass and a 0 to indicate the site of attachement to the target peptide.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:simpleContent>
      <xs:extension base="xs:string">
        <xs:attribute name="type" type="xs:string" fixed="S">
          <xs:annotation>
            <xs:documentation>For the moment this attribute must be set to "S".</xs:documentation>
          </xs:annotation>
        </xs:attribute>
      </xs:extension>
    </xs:simpleContent>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/modifiedResidue
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
residue  xs:string        
documentation 
Amino Acid residue from the target peptide to which the PTM is attached to.
notTerminal  xs:boolean        
documentation 
Can the modified amino acid be at the termini of the target peptide. For instance attachment of SUMO to a Lysine residue hinders tryptic cleavage at that residue.
annotation
documentation 
Information on the site of attachment of the PTM.
source
<xs:element name="modifiedResidue">
  <xs:annotation>
    <xs:documentation>Information on the site of attachment of the PTM.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="residue" type="xs:string">
      <xs:annotation>
        <xs:documentation>Amino Acid residue from the target peptide to which the PTM is attached to.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="notTerminal" type="xs:boolean">
      <xs:annotation>
        <xs:documentation>Can the modified amino acid be at the termini of the target peptide. For instance attachment of SUMO to a Lysine residue hinders tryptic cleavage at that residue.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/loss
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
value  xs:double        
documentation 
Mass in Da of the global loss.
annotation
documentation 
A global loss that is applied to every fragment in the target peptide ion series (e.g. loss of water or ammonia).
source
<xs:element name="loss" minOccurs="0" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>A global loss that is applied to every fragment in the target peptide ion series (e.g. loss of water or ammonia).</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="value" type="xs:double">
      <xs:annotation>
        <xs:documentation>Mass in Da of the global loss.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/modify
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
residue  xs:string        
documentation 
Modified residue.
mass  xs:double        
documentation 
Mass of the modification in Da.
static  xs:boolean        
documentation 
1=static, 0=variable
annotation
documentation 
Modification to be applied to a specific amino acid from the target peptide.
source
<xs:element name="modify">
  <xs:annotation>
    <xs:documentation>Modification to be applied to a specific amino acid from the target peptide.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="residue" type="xs:string">
      <xs:annotation>
        <xs:documentation>Modified residue.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="mass" type="xs:double">
      <xs:annotation>
        <xs:documentation>Mass of the modification in Da.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="static" type="xs:boolean">
      <xs:annotation>
        <xs:documentation>1=static, 0=variable</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/digestC
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
residue  xs:string        
documentation 
The residue after which the digestion takes place.
notResidue  xs:string        
documentation 
If this residue is C terminal of the "residue" the enzyme will not cleave (use X if you always want a cleavage).
annotation
documentation 
Digestion C terminal of a residue.
source
<xs:element name="digestC" minOccurs="0" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Digestion C terminal of a residue.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="residue" type="xs:string">
      <xs:annotation>
        <xs:documentation>The residue after which the digestion takes place.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="notResidue" type="xs:string">
      <xs:annotation>
        <xs:documentation>If this residue is C terminal of the "residue" the enzyme will not cleave (use X if you always want a cleavage).</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/digestN
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
residue  xs:string        
documentation 
The residue before which digestion takes place.
notResidue  xs:string        
documentation 
If this residue is N terminal of the "residue" the enzyme will not cleave (use X if you always want a cleavage).
annotation
documentation 
Digestion N terminal of a residue.
source
<xs:element name="digestN" minOccurs="0" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Digestion N terminal of a residue.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="residue" type="xs:string">
      <xs:annotation>
        <xs:documentation>The residue before which digestion takes place.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="notResidue" type="xs:string">
      <xs:annotation>
        <xs:documentation>If this residue is N terminal of the "residue" the enzyme will not cleave (use X if you always want a cleavage).</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/missCleaveC
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
residue  xs:string        
value  xs:int        
annotation
documentation 
Adds up to "value" missed cleavages after "residue".
source
<xs:element name="missCleaveC" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Adds up to "value" missed cleavages after "residue".</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="residue" type="xs:string"/>
    <xs:attribute name="value" type="xs:int"/>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/getMissCleaveC
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
residue  xs:string        
notResidue  xs:string        
value  xs:int        
annotation
documentation 
Discards every target peptide that doesn't have exactly "value" missed cleavages at "residue". If residue is followed by "notResidue" it is counted both as a missed cleavage as well as a non missed cleavage.
source
<xs:element name="getMissCleaveC" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Discards every target peptide that doesn't have exactly "value" missed cleavages at "residue". If residue is followed by "notResidue" it is counted both as a missed cleavage as well as a non missed cleavage.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="residue" type="xs:string"/>
    <xs:attribute name="notResidue" type="xs:string"/>
    <xs:attribute name="value" type="xs:int"/>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/digestUnconstrained
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
residue  xs:string        
documentation 
Only keep residues that contain this residue.
value  xs:int        
documentation 
Maximal lenght of a target peptide.
annotation
documentation 
Digest unconstrained.
source
<xs:element name="digestUnconstrained" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Digest unconstrained.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="residue" type="xs:string">
      <xs:annotation>
        <xs:documentation>Only keep residues that contain this residue.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="value" type="xs:int">
      <xs:annotation>
        <xs:documentation>Maximal lenght of a target peptide.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/digestionStep
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
value  xs:int        
annotation
documentation 
Maximal number of proteins that will be digested at once when looking up the target peptides. This is only helpfull if you are using a big subDB.fasta and are running out of memory.
source
<xs:element name="digestionStep" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Maximal number of proteins that will be digested at once when looking up the target peptides. This is only helpfull if you are using a big subDB.fasta and are running out of memory.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="value" type="xs:int"/>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/digestionTolerance
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
value  xs:int        
annotation
documentation 
Tolerance (in Da) to be used when matching target peptide precursor ions.
source
<xs:element name="digestionTolerance">
  <xs:annotation>
    <xs:documentation>Tolerance (in Da) to be used when matching target peptide precursor ions.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="value" type="xs:int"/>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/massTolerance
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
value  xs:int        
annotation
documentation 
Tolerance (in Da) to be used when matching fragment ions.
source
<xs:element name="massTolerance">
  <xs:annotation>
    <xs:documentation>Tolerance (in Da) to be used when matching fragment ions.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="value" type="xs:int"/>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/startCharge
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
value  xs:int        
annotation
documentation 
The lower charge limit that SUMmOn will use when searching data for which the charge states have not been determined. The default value is 1.
source
<xs:element name="startCharge">
  <xs:annotation>
    <xs:documentation>The lower charge limit that SUMmOn will use when searching data for which the charge states have not been determined. The default value is 1.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="value" type="xs:int"/>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/endCharge
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
value  xs:int        
annotation
documentation 
The upper charge limit that SUMmOn will use when searching data for which the charge states have not been determined. The maximal value is 9.
source
<xs:element name="endCharge">
  <xs:annotation>
    <xs:documentation>The upper charge limit that SUMmOn will use when searching data for which the charge states have not been determined. The maximal value is 9.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="value" type="xs:int"/>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/centroiding
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
type  xs:int        
documentation 
0=No centroiding, 1=Mathematical Averaging, 2=Weighted Averaging
iterations  xs:int  optional      
documentation 
The number of times the centroiding algorithm will run through the data (e.g. 4 should be a reasonable number).
annotation
documentation 
If your mzXML file contains profile mode data you must use this element to specify how to centroid it.
source
<xs:element name="centroiding">
  <xs:annotation>
    <xs:documentation>If your mzXML file contains profile mode data you must use this element to specify how to centroid it.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="type" type="xs:int">
      <xs:annotation>
        <xs:documentation>0=No centroiding, 1=Mathematical Averaging, 2=Weighted Averaging</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="iterations" type="xs:int" use="optional">
      <xs:annotation>
        <xs:documentation>The number of times the centroiding algorithm will run through the data (e.g. 4 should be a reasonable number).</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/normalization
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
type  xs:int    -2    
annotation
documentation 
This for the moment should always set to "-2".
source
<xs:element name="normalization">
  <xs:annotation>
    <xs:documentation>This for the moment should always set to "-2".</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="type" type="xs:int" default="-2"/>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/targetMs
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
level  xs:int        
annotation
documentation 
The MS level SUMmOn will analyze (e.g. 2 -> MS/MS ; 3 -> MS/MS/MS).
source
<xs:element name="targetMs">
  <xs:annotation>
    <xs:documentation>The MS level SUMmOn will analyze (e.g. 2 -> MS/MS ; 3 -> MS/MS/MS).</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="level" type="xs:int"/>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/output
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
type  xs:int    1    
annotation
documentation 
1 will allow for more detailed post-analysis interpretation, but create a bigger file than 0.
source
<xs:element name="output">
  <xs:annotation>
    <xs:documentation>1 will allow for more detailed post-analysis interpretation, but create a bigger file than 0.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="type" type="xs:int" default="1"/>
  </xs:complexType>
</xs:element>

element SUMmOnCondition/nonInteractive
diagram
attributes
Name  Type  Use  Default  Fixed  Annotation
value  xs:int        
annotation
documentation 
When set to 1 SUMmOn will save the results without switching to interactive mode in the middle of the analysis.
source
<xs:element name="nonInteractive">
  <xs:annotation>
    <xs:documentation>When set to 1 SUMmOn will save the results without switching to interactive mode in the middle of the analysis.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="value" type="xs:int"/>
  </xs:complexType>
</xs:element>


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