Schema pepXML_v18.xsd


schema location:  http://localhost/pepXML_v18.xsd
attribute form default: 
element form default:  qualified
targetNamespace:  http://regis-web.systemsbiology.net/pepXML
 
Elements  Complex types  Simple types 
asapratio_contribution  nameValueType  aa_symbolType 
asapratio_lc_heavypeak  engineType 
asapratio_lc_lightpeak  massType 
asapratio_peptide_data  model_dis_type 
asapratio_result  positiveInt 
asapratio_summary  term_symbolType 
asapratio_timestamp 
database_refresh_timestamp 
interact_summary 
libra_result 
libra_summary 
msms_pipeline_analysis 
peptideprophet_result 
peptideprophet_summary 
xpressratio_result 
xpressratio_summary 
xpressratio_timestamp 


element asapratio_contribution
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
content complex
children asapratio_lc_lightpeak asapratio_lc_heavypeak
used by
element asapratio_peptide_data
attributes
Name  Type  Use  Default  Fixed  Annotation
ratio  xs:floatrequired      
error  xs:floatrequired      
charge  xs:nonNegativeIntegerrequired      
use  xs:unsignedByterequired      
source
<xs:element name="asapratio_contribution">
  <xs:complexType>
    <xs:sequence>
      <xs:element ref="asapratio_lc_lightpeak"/>
      <xs:element ref="asapratio_lc_heavypeak"/>
    </xs:sequence>
    <xs:attribute name="ratio" type="xs:float" use="required"/>
    <xs:attribute name="error" type="xs:float" use="required"/>
    <xs:attribute name="charge" type="xs:nonNegativeInteger" use="required"/>
    <xs:attribute name="use" type="xs:unsignedByte" use="required"/>
  </xs:complexType>
</xs:element>

element asapratio_lc_heavypeak
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
content complex
used by
element asapratio_contribution
attributes
Name  Type  Use  Default  Fixed  Annotation
status  xs:byterequired      
left_valley  xs:intrequired      
right_valley  xs:intrequired      
background  xs:floatrequired      
area  xs:floatrequired      
area_error  xs:floatrequired      
time  xs:floatrequired      
time_width  xs:floatrequired      
is_heavy  xs:stringrequired      
source
<xs:element name="asapratio_lc_heavypeak">
  <xs:complexType>
    <xs:attribute name="status" type="xs:byte" use="required"/>
    <xs:attribute name="left_valley" type="xs:int" use="required"/>
    <xs:attribute name="right_valley" type="xs:int" use="required"/>
    <xs:attribute name="background" type="xs:float" use="required"/>
    <xs:attribute name="area" type="xs:float" use="required"/>
    <xs:attribute name="area_error" type="xs:float" use="required"/>
    <xs:attribute name="time" type="xs:float" use="required"/>
    <xs:attribute name="time_width" type="xs:float" use="required"/>
    <xs:attribute name="is_heavy" type="xs:string" use="required"/>
  </xs:complexType>
</xs:element>

element asapratio_lc_lightpeak
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
content complex
used by
element asapratio_contribution
attributes
Name  Type  Use  Default  Fixed  Annotation
status  xs:byterequired      
left_valley  xs:intrequired      
right_valley  xs:intrequired      
background  xs:floatrequired      
area  xs:floatrequired      
area_error  xs:floatrequired      
time  xs:floatrequired      
time_width  xs:floatrequired      
is_heavy  xs:stringrequired      
source
<xs:element name="asapratio_lc_lightpeak">
  <xs:complexType>
    <xs:attribute name="status" type="xs:byte" use="required"/>
    <xs:attribute name="left_valley" type="xs:int" use="required"/>
    <xs:attribute name="right_valley" type="xs:int" use="required"/>
    <xs:attribute name="background" type="xs:float" use="required"/>
    <xs:attribute name="area" type="xs:float" use="required"/>
    <xs:attribute name="area_error" type="xs:float" use="required"/>
    <xs:attribute name="time" type="xs:float" use="required"/>
    <xs:attribute name="time_width" type="xs:float" use="required"/>
    <xs:attribute name="is_heavy" type="xs:string" use="required"/>
  </xs:complexType>
</xs:element>

element asapratio_peptide_data
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
content complex
children asapratio_contribution
used by
element asapratio_result
attributes
Name  Type  Use  Default  Fixed  Annotation
status  xs:byterequired      
cidIndex  xs:intrequired      
light_mass  xs:floatrequired      
heavy_mass  xs:floatrequired      
area_flag  xs:unsignedIntrequired      
source
<xs:element name="asapratio_peptide_data">
  <xs:complexType>
    <xs:sequence>
      <xs:element ref="asapratio_contribution" maxOccurs="unbounded"/>
    </xs:sequence>
    <xs:attribute name="status" type="xs:byte" use="required"/>
    <xs:attribute name="cidIndex" type="xs:int" use="required"/>
    <xs:attribute name="light_mass" type="xs:float" use="required"/>
    <xs:attribute name="heavy_mass" type="xs:float" use="required"/>
    <xs:attribute name="area_flag" type="xs:unsignedInt" use="required"/>
  </xs:complexType>
</xs:element>

element asapratio_result
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
content complex
children asapratio_peptide_data
attributes
Name  Type  Use  Default  Fixed  Annotation
mean  xs:floatrequired      
error  xs:floatrequired      
heavy2light_mean  xs:floatrequired      
heavy2light_error  xs:floatrequired      
annotation
documentation 
ASAPRatio quantitation results for search hit
source
<xs:element name="asapratio_result">
  <xs:annotation>
    <xs:documentation>ASAPRatio quantitation results for search hit</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element ref="asapratio_peptide_data"/>
    </xs:sequence>
    <xs:attribute name="mean" type="xs:float" use="required"/>
    <xs:attribute name="error" type="xs:float" use="required"/>
    <xs:attribute name="heavy2light_mean" type="xs:float" use="required"/>
    <xs:attribute name="heavy2light_error" type="xs:float" use="required"/>
  </xs:complexType>
</xs:element>

element asapratio_summary
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
version  xs:stringrequired      
author  xs:stringrequired      
elution  xs:integerrequired      
documentation 
Elution order of light vs heavy labeled peptide
labeled_residues  xs:stringrequired      
documentation 
Aminoacids and termini that are differentially labeled for quantitaiton
area_flag  xs:nonNegativeIntegerrequired      
static_quant  xs:stringrequired      
documentation 
Y if dataset is all light or heavy labeled, N if dataset is mixed heavy and light labeled
annotation
documentation 
Quantitation
source
<xs:element name="asapratio_summary">
  <xs:annotation>
    <xs:documentation>Quantitation</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="version" type="xs:string" use="required"/>
    <xs:attribute name="author" type="xs:string" use="required"/>
    <xs:attribute name="elution" type="xs:integer" use="required">
      <xs:annotation>
        <xs:documentation>Elution order of light vs heavy labeled peptide</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="labeled_residues" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Aminoacids and termini that are differentially labeled for quantitaiton</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="area_flag" type="xs:nonNegativeInteger" use="required"/>
    <xs:attribute name="static_quant" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Y if dataset is all light or heavy labeled, N if dataset is mixed heavy and light labeled</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element asapratio_timestamp
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
quant_label_masses  xs:string      
static_quant_label  xs:string      
source
<xs:element name="asapratio_timestamp">
  <xs:complexType>
    <xs:attribute name="quant_label_masses" type="xs:string"/>
    <xs:attribute name="static_quant_label" type="xs:string"/>
  </xs:complexType>
</xs:element>

element database_refresh_timestamp
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
database  xs:stringrequired      
min_num_enz_term  xs:nonNegativeInteger      
documentation 
minimum number of termini compaitble with enzyme used (should correspond with search enzyme constraint)
source
<xs:element name="database_refresh_timestamp">
  <xs:complexType>
    <xs:attribute name="database" type="xs:string" use="required"/>
    <xs:attribute name="min_num_enz_term" type="xs:nonNegativeInteger">
      <xs:annotation>
        <xs:documentation>minimum number of termini compaitble with enzyme used (should correspond with search enzyme constraint)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element interact_summary
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
content complex
children inputfile
attributes
Name  Type  Use  Default  Fixed  Annotation
filename  xs:stringrequired      
documentation 
Self reference
directory  xs:stringrequired      
documentation 
Directory of self
annotation
documentation 
Combined datasets
source
<xs:element name="interact_summary">
  <xs:annotation>
    <xs:documentation>Combined datasets</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="inputfile" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Input file</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="name" type="xs:string" use="required"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="filename" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Self reference</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="directory" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Directory of self</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element interact_summary/inputfile
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
name  xs:stringrequired      
annotation
documentation 
Input file
source
<xs:element name="inputfile" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Input file</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="name" type="xs:string" use="required"/>
  </xs:complexType>
</xs:element>

element libra_result
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
content complex
children intensity
attributes
Name  Type  Use  Default  Fixed  Annotation
is_rejected  xs:booleanoptional  0    
documentation 
whether or not to reject this ratio as valid
identity constraints
  Name  Refer  Selector  Field(s)  
unique  libra_result_channel_index    .  @channel  
annotation
documentation 
libra quantitation for search hit
source
<xs:element name="libra_result">
  <xs:annotation>
    <xs:documentation>libra quantitation for search hit</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="intensity" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>integrated mass intensity</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="channel" type="positiveInt" use="required">
            <xs:annotation>
              <xs:documentation>mass channel number</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="target_mass" type="xs:float" use="required">
            <xs:annotation>
              <xs:documentation>mass of channel</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="absolute" type="xs:float" use="required">
            <xs:annotation>
              <xs:documentation>absolute integrated intensity</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="normalized" type="xs:float" use="required">
            <xs:annotation>
              <xs:documentation>normalized integrated intensity (normalization channel stored in libra_summary)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="reject" type="xs:boolean" use="optional" default="0">
            <xs:annotation>
              <xs:documentation>whether or not to reject this ratio as valid</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="is_rejected" type="xs:boolean" use="optional" default="0">
      <xs:annotation>
        <xs:documentation>whether or not to reject this ratio as valid</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
  <xs:unique name="libra_result_channel_index">
    <xs:annotation>
      <xs:documentation>channel number must be unique</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="."/>
    <xs:field xpath="@channel"/>
  </xs:unique>
</xs:element>

element libra_result/intensity
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
channel  positiveIntrequired      
documentation 
mass channel number
target_mass  xs:floatrequired      
documentation 
mass of channel
absolute  xs:floatrequired      
documentation 
absolute integrated intensity
normalized  xs:floatrequired      
documentation 
normalized integrated intensity (normalization channel stored in libra_summary)
reject  xs:booleanoptional  0    
documentation 
whether or not to reject this ratio as valid
annotation
documentation 
integrated mass intensity
source
<xs:element name="intensity" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>integrated mass intensity</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="channel" type="positiveInt" use="required">
      <xs:annotation>
        <xs:documentation>mass channel number</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="target_mass" type="xs:float" use="required">
      <xs:annotation>
        <xs:documentation>mass of channel</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="absolute" type="xs:float" use="required">
      <xs:annotation>
        <xs:documentation>absolute integrated intensity</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="normalized" type="xs:float" use="required">
      <xs:annotation>
        <xs:documentation>normalized integrated intensity (normalization channel stored in libra_summary)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="reject" type="xs:boolean" use="optional" default="0">
      <xs:annotation>
        <xs:documentation>whether or not to reject this ratio as valid</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element libra_summary
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
content complex
children fragment_masses isotopic_contributions
attributes
Name  Type  Use  Default  Fixed  Annotation
mass_tolerance  xs:floatrequired      
documentation 
channel mass width
centroiding_preference  xs:intrequired      
normalization  xs:intrequired      
documentation 
channel used as denominator for normalized integrated intensities (0 means use channel with strongest absolute integrated intensity)
output_type  xs:intrequired      
channel_code  xs:string      
documentation 
concatenated channel masses (used as signature for defined channel masses)
identity constraints
  Name  Refer  Selector  Field(s)  
key  libra_channel_index    ./pepx:fragment_masses  @channel  
keyref  libra_contr_channel_index_ref  libra_channel_index  ./pepx:isotopic_contributions/pepx:contributing_channel  @channel  
keyref  libra_aff_channel_index_ref  libra_channel_index  ./pepx:isotopic_contributions/pepx:contributing_channel/pepx:affected_channel  @channel  
annotation
documentation 
summary info for libra quantitation analysis
source
<xs:element name="libra_summary">
  <xs:annotation>
    <xs:documentation>summary info for libra quantitation analysis</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="fragment_masses" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>quantitation channel</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="channel" type="positiveInt" use="required">
            <xs:annotation>
              <xs:documentation>channel number</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="mz" type="xs:float" use="required">
            <xs:annotation>
              <xs:documentation>channel mass</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="offset" type="xs:float">
            <xs:annotation>
              <xs:documentation>mass offset from mz value</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="isotopic_contributions" minOccurs="0">
        <xs:annotation>
          <xs:documentation>isotopic contributions from one channel to others</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="contributing_channel" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>channel donor</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="affected_channel" maxOccurs="unbounded">
                    <xs:annotation>
                      <xs:documentation>channel recipient</xs:documentation>
                    </xs:annotation>
                    <xs:complexType>
                      <xs:attribute name="channel" type="positiveInt" use="required">
                        <xs:annotation>
                          <xs:documentation>channel number</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="correction" type="xs:float" use="required">
                        <xs:annotation>
                          <xs:documentation>fraction of affected channel due to contributing</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                    </xs:complexType>
                  </xs:element>
                </xs:sequence>
                <xs:attribute name="channel" type="positiveInt" use="required">
                  <xs:annotation>
                    <xs:documentation>channel number</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="mass_tolerance" type="xs:float" use="required">
      <xs:annotation>
        <xs:documentation>channel mass width</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="centroiding_preference" type="xs:int" use="required"/>
    <xs:attribute name="normalization" type="xs:int" use="required">
      <xs:annotation>
        <xs:documentation>channel used as denominator for normalized integrated intensities (0 means use channel with strongest absolute integrated intensity)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="output_type" type="xs:int" use="required"/>
    <xs:attribute name="channel_code" type="xs:string">
      <xs:annotation>
        <xs:documentation>concatenated channel masses (used as signature for defined channel masses)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
  <xs:key name="libra_channel_index">
    <xs:selector xpath="./pepx:fragment_masses"/>
    <xs:field xpath="@channel"/>
  </xs:key>
  <xs:keyref name="libra_contr_channel_index_ref" refer="libra_channel_index">
    <xs:annotation>
      <xs:documentation>contributing channel numbers must correspond with defined channels</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="./pepx:isotopic_contributions/pepx:contributing_channel"/>
    <xs:field xpath="@channel"/>
  </xs:keyref>
  <xs:keyref name="libra_aff_channel_index_ref" refer="libra_channel_index">
    <xs:annotation>
      <xs:documentation>contributing channel numbers must correspond with defined channels</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="./pepx:isotopic_contributions/pepx:contributing_channel/pepx:affected_channel"/>
    <xs:field xpath="@channel"/>
  </xs:keyref>
</xs:element>

element libra_summary/fragment_masses
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
channel  positiveIntrequired      
documentation 
channel number
mz  xs:floatrequired      
documentation 
channel mass
offset  xs:float      
documentation 
mass offset from mz value
annotation
documentation 
quantitation channel
source
<xs:element name="fragment_masses" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>quantitation channel</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="channel" type="positiveInt" use="required">
      <xs:annotation>
        <xs:documentation>channel number</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="mz" type="xs:float" use="required">
      <xs:annotation>
        <xs:documentation>channel mass</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="offset" type="xs:float">
      <xs:annotation>
        <xs:documentation>mass offset from mz value</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element libra_summary/isotopic_contributions
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
children contributing_channel
annotation
documentation 
isotopic contributions from one channel to others
source
<xs:element name="isotopic_contributions" minOccurs="0">
  <xs:annotation>
    <xs:documentation>isotopic contributions from one channel to others</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="contributing_channel" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>channel donor</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="affected_channel" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>channel recipient</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:attribute name="channel" type="positiveInt" use="required">
                  <xs:annotation>
                    <xs:documentation>channel number</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="correction" type="xs:float" use="required">
                  <xs:annotation>
                    <xs:documentation>fraction of affected channel due to contributing</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="channel" type="positiveInt" use="required">
            <xs:annotation>
              <xs:documentation>channel number</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
  </xs:complexType>
</xs:element>

element libra_summary/isotopic_contributions/contributing_channel
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
children affected_channel
attributes
Name  Type  Use  Default  Fixed  Annotation
channel  positiveIntrequired      
documentation 
channel number
annotation
documentation 
channel donor
source
<xs:element name="contributing_channel" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>channel donor</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="affected_channel" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>channel recipient</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="channel" type="positiveInt" use="required">
            <xs:annotation>
              <xs:documentation>channel number</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="correction" type="xs:float" use="required">
            <xs:annotation>
              <xs:documentation>fraction of affected channel due to contributing</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="channel" type="positiveInt" use="required">
      <xs:annotation>
        <xs:documentation>channel number</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element libra_summary/isotopic_contributions/contributing_channel/affected_channel
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
channel  positiveIntrequired      
documentation 
channel number
correction  xs:floatrequired      
documentation 
fraction of affected channel due to contributing
annotation
documentation 
channel recipient
source
<xs:element name="affected_channel" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>channel recipient</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="channel" type="positiveInt" use="required">
      <xs:annotation>
        <xs:documentation>channel number</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="correction" type="xs:float" use="required">
      <xs:annotation>
        <xs:documentation>fraction of affected channel due to contributing</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element msms_pipeline_analysis
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
content complex
children analysis_summary dataset_derivation msms_run_summary
attributes
Name  Type  Use  Default  Fixed  Annotation
name  xs:string      
documentation 
Summary name (currently not used)
date  xs:dateTimerequired      
documentation 
Date pepXML file was written
summary_xml  xs:stringrequired      
documentation 
Full path self reference
identity constraints
  Name  Refer  Selector  Field(s)  
key  summary_analysis_time    ./pepx:analysis_summary  @time  
@analysis  
keyref  timestamp_analysis_time  summary_analysis_time  ./pepx:msms_run_summary/pepx:analysis_timestamp  @time  
@analysis  
unique  unique_search_summary_basename    ./pepx:msms_run_summary/pepx:search_summary  @base_name  
unique  unique_query_index    ./pepx:msms_run_summary/pepx:spectrum_query  @index  
source
<xs:element name="msms_pipeline_analysis">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="analysis_summary" minOccurs="0" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Summary of analysis subjected to run(s)</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:any namespace="##any" processContents="lax" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Wildcard for summary info customized for a particular analysis</xs:documentation>
              </xs:annotation>
            </xs:any>
          </xs:sequence>
          <xs:attribute name="time" type="xs:dateTime" use="required">
            <xs:annotation>
              <xs:documentation>Time analysis complete (unique id)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="analysis" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Name of analysis program</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="version" type="xs:string">
            <xs:annotation>
              <xs:documentation>Release</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="dataset_derivation" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Source and filtering criteria used to generate dataset</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="data_filter" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:attribute name="number" type="xs:nonNegativeInteger" use="required"/>
                <xs:attribute name="parent_file" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>File from which derived</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="windows_parent" type="xs:string"/>
                <xs:attribute name="description" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>filtering criteria applied to data</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="generation_no" type="xs:nonNegativeInteger" use="required">
            <xs:annotation>
              <xs:documentation>number preceding filter generations</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="msms_run_summary" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Search results for LC/MS/MS run</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="sample_enzyme">
              <xs:annotation>
                <xs:documentation>Defines the net cleavage specificity of an enzyme, chemical reagent, or a mixture of these, for mass spectrometry purposes</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="specificity" minOccurs="0" maxOccurs="unbounded">
                    <xs:annotation>
                      <xs:documentation>Component cleavage specificity. Must be at least one specificity unless enzymeType:fidelity is nonspecific </xs:documentation>
                    </xs:annotation>
                    <xs:complexType>
                      <xs:attribute name="sense" use="required">
                        <xs:annotation>
                          <xs:documentation>Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut</xs:documentation>
                        </xs:annotation>
                        <xs:simpleType>
                          <xs:restriction base="xs:string">
                            <xs:enumeration value="C"/>
                            <xs:enumeration value="N"/>
                          </xs:restriction>
                        </xs:simpleType>
                      </xs:attribute>
                      <xs:attribute name="min_spacing" type="xs:nonNegativeInteger" default="1">
                        <xs:annotation>
                          <xs:documentation>minimum separation between adjacent cleavages</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="cut" use="required">
                        <xs:annotation>
                          <xs:documentation>One or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation>
                        </xs:annotation>
                        <xs:simpleType>
                          <xs:restriction base="xs:string">
                            <xs:minLength value="1"/>
                            <xs:maxLength value="20"/>
                            <xs:pattern value="[A,C-I,K-N,P-T,VWY]+"/>
                          </xs:restriction>
                        </xs:simpleType>
                      </xs:attribute>
                      <xs:attribute name="no_cut" use="optional">
                        <xs:annotation>
                          <xs:documentation>Zero or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation>
                        </xs:annotation>
                        <xs:simpleType>
                          <xs:restriction base="xs:string">
                            <xs:minLength value="0"/>
                            <xs:maxLength value="20"/>
                          </xs:restriction>
                        </xs:simpleType>
                      </xs:attribute>
                    </xs:complexType>
                  </xs:element>
                </xs:sequence>
                <xs:attribute name="name" use="required">
                  <xs:annotation>
                    <xs:documentation>Controlled code name for the enzyme that can be referred to by applications</xs:documentation>
                  </xs:annotation>
                  <xs:simpleType>
                    <xs:restriction base="xs:string">
                      <xs:minLength value="1"/>
                    </xs:restriction>
                  </xs:simpleType>
                </xs:attribute>
                <xs:attribute name="description" type="xs:string" use="optional">
                  <xs:annotation>
                    <xs:documentation>Free text to describe alternative names, special conditions, etc.</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="fidelity" use="optional" default="specific">
                  <xs:annotation>
                    <xs:documentation>Semispecific means that at least one end of a pepide must conform to the cleavage specificity, (unless the peptide was at the terminus of the parent sequence). Nonspecific means that neither end of a peptide must conform to the cleavage specificity.</xs:documentation>
                  </xs:annotation>
                  <xs:simpleType>
                    <xs:restriction base="xs:string">
                      <xs:enumeration value="specific"/>
                      <xs:enumeration value="semispecific"/>
                      <xs:enumeration value="nonspecific"/>
                    </xs:restriction>
                  </xs:simpleType>
                </xs:attribute>
                <xs:attribute name="independent" type="xs:boolean" use="optional" default="1">
                  <xs:annotation>
                    <xs:documentation>If there are multiple specificities and independent is true, then a single peptide cannot exhibit one specificity at one terminus and a different specificity at the other. If independent is false, then a single peptide can exhibit mixed specificities.</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
            <xs:element name="search_summary" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Database search settings</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="search_database" minOccurs="0">
                    <xs:complexType>
                      <xs:attribute name="local_path" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>Full path address of database on local computer</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="URL" type="xs:string"/>
                      <xs:attribute name="database_name" type="xs:string"/>
                      <xs:attribute name="orig_database_url" type="xs:string"/>
                      <xs:attribute name="database_release_date" type="xs:dateTime"/>
                      <xs:attribute name="database_release_identifier" type="xs:string"/>
                      <xs:attribute name="size_in_db_entries" type="xs:nonNegativeInteger"/>
                      <xs:attribute name="size_of_residues" type="xs:nonNegativeInteger"/>
                      <xs:attribute name="type" use="required">
                        <xs:annotation>
                          <xs:documentation>Database type (AA=amino acid, NA=nucleic acid)</xs:documentation>
                        </xs:annotation>
                        <xs:simpleType>
                          <xs:restriction base="xs:string">
                            <xs:enumeration value="AA"/>
                            <xs:enumeration value="NA"/>
                          </xs:restriction>
                        </xs:simpleType>
                      </xs:attribute>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="enzymatic_search_constraint" minOccurs="0">
                    <xs:annotation>
                      <xs:documentation>Required peptide termini</xs:documentation>
                    </xs:annotation>
                    <xs:complexType>
                      <xs:attribute name="enzyme" type="xs:string" use="required"/>
                      <xs:attribute name="max_num_internal_cleavages" type="xs:nonNegativeInteger" use="required">
                        <xs:annotation>
                          <xs:documentation>Maximum number of enzyme cleavage sites allowable within peptide</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="min_number_termini" type="xs:nonNegativeInteger" use="required">
                        <xs:annotation>
                          <xs:documentation>Minimum number of termini compatible with enzymatic cleavage</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="sequence_search_constraint" minOccurs="0" maxOccurs="unbounded">
                    <xs:annotation>
                      <xs:documentation>Required amino acid string</xs:documentation>
                    </xs:annotation>
                    <xs:complexType>
                      <xs:attribute name="sequence" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>Required amino acid string</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="aminoacid_modification" minOccurs="0" maxOccurs="unbounded">
                    <xs:annotation>
                      <xs:documentation>Modified aminoacid, static or variable</xs:documentation>
                    </xs:annotation>
                    <xs:complexType>
                      <xs:attribute name="aminoacid" type="xs:string" use="required"/>
                      <xs:attribute name="massdiff" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>Mass difference with respect to unmodified aminoacid, must begin with either + (nonnegative) or - [e.g. +1.05446 or -2.3342]</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="mass" type="xs:float" use="required">
                        <xs:annotation>
                          <xs:documentation>Mass of modified aminoacid</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="variable" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>Y if both modified and unmodified aminoacid could be present in the dataset, N if only modified aminoacid can be present</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="peptide_terminus" type="xs:string">
                        <xs:annotation>
                          <xs:documentation>whether modification can reside only at protein terminus (specified 'n', 'c', or 'nc')</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="symbol" type="aa_symbolType">
                        <xs:annotation>
                          <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="binary" type="xs:string">
                        <xs:annotation>
                          <xs:documentation>Y if each peptide must have only modified or unmodified aminoacid, N if a peptide may contain both modified and unmodified aminoacid</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="description" type="xs:string"/>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="terminal_modification" minOccurs="0" maxOccurs="unbounded">
                    <xs:annotation>
                      <xs:documentation>Modification to the N or C terminus, static or variable</xs:documentation>
                    </xs:annotation>
                    <xs:complexType>
                      <xs:attribute name="terminus" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>n for N-terminus, c for C-terminus</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="massdiff" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>Mass difference with respect to unmodified terminus</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="mass" type="xs:float" use="required">
                        <xs:annotation>
                          <xs:documentation>Mass of modified terminus</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="variable" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>Y if both modified and unmodified terminus could be present in the dataset, N if only modified terminus can be present</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="symbol" type="term_symbolType">
                        <xs:annotation>
                          <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="protein_terminus" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>whether modification can reside only at protein terminus (specified n or c)</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="description" type="xs:string"/>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
                </xs:sequence>
                <xs:attribute name="base_name" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>Full path location of mzXML file for this search run (without the .mzXML extension)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="search_engine" type="engineType" use="required">
                  <xs:annotation>
                    <xs:documentation>SEQUEST, Mascot, COMET, etc</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="precursor_mass_type" type="massType" use="required">
                  <xs:annotation>
                    <xs:documentation>average or monoisotopic</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="fragment_mass_type" type="massType" use="required">
                  <xs:annotation>
                    <xs:documentation>average or monoisotopic</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="out_data_type" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>Format of file storing the runner up peptides (if not present in pepXML)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="out_data" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>runner up search hit data type extension (e.g. .tgz)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="search_id" type="positiveInt" use="required">
                  <xs:annotation>
                    <xs:documentation>matches id in search hit</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
            <xs:element name="analysis_timestamp" minOccurs="0" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Reference for analysis applied to current run (time corresponds with analysis_summary/@time, id corresponds with analysis_result/@id)</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:sequence>
                  <xs:any namespace="##any" processContents="lax" minOccurs="0">
                    <xs:annotation>
                      <xs:documentation>Wildcard for timestamp info customized for a particular analysis</xs:documentation>
                    </xs:annotation>
                  </xs:any>
                </xs:sequence>
                <xs:attribute name="time" type="xs:dateTime" use="required">
                  <xs:annotation>
                    <xs:documentation>Date of analysis</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="analysis" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>Analysis name</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="id" type="positiveInt" use="required">
                  <xs:annotation>
                    <xs:documentation>Unique identifier for each type of analysis</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
            <xs:element name="spectrum_query" minOccurs="0" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>MS/MS spectrum, precursor ion charge and mass</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="search_result" minOccurs="0" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:sequence>
                        <xs:element name="search_hit" minOccurs="0" maxOccurs="unbounded">
                          <xs:annotation>
                            <xs:documentation>Peptide assignment</xs:documentation>
                          </xs:annotation>
                          <xs:complexType>
                            <xs:sequence>
                              <xs:element name="alternative_protein" minOccurs="0" maxOccurs="unbounded">
                                <xs:annotation>
                                  <xs:documentation>Other protein in search database that contains peptide</xs:documentation>
                                </xs:annotation>
                                <xs:complexType>
                                  <xs:attribute name="protein" type="xs:string" use="required"/>
                                  <xs:attribute name="protein_descr" type="xs:string"/>
                                  <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger"/>
                                  <xs:attribute name="protein_mw" type="xs:double"/>
                                </xs:complexType>
                              </xs:element>
                              <xs:element name="modification_info" minOccurs="0">
                                <xs:annotation>
                                  <xs:documentation>Positions and masses of modifications</xs:documentation>
                                </xs:annotation>
                                <xs:complexType>
                                  <xs:sequence>
                                    <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
                                      <xs:complexType>
                                        <xs:attribute name="position" type="xs:nonNegativeInteger" use="required">
                                          <xs:annotation>
                                            <xs:documentation>modified aminoacid position in peptide [ranging from 1 to peptide length]</xs:documentation>
                                          </xs:annotation>
                                        </xs:attribute>
                                        <xs:attribute name="mass" type="xs:double" use="required">
                                          <xs:annotation>
                                            <xs:documentation>modified mass of aminoacid</xs:documentation>
                                          </xs:annotation>
                                        </xs:attribute>
                                      </xs:complexType>
                                    </xs:element>
                                  </xs:sequence>
                                  <xs:attribute name="mod_nterm_mass" type="xs:double">
                                    <xs:annotation>
                                      <xs:documentation>Mass of modified N terminus</xs:documentation>
                                    </xs:annotation>
                                  </xs:attribute>
                                  <xs:attribute name="mod_cterm_mass" type="xs:double">
                                    <xs:annotation>
                                      <xs:documentation>Mass of modified C terminus</xs:documentation>
                                    </xs:annotation>
                                  </xs:attribute>
                                  <xs:attribute name="modified_peptide" type="xs:string">
                                    <xs:annotation>
                                      <xs:documentation>Peptide sequence (with indicated modifications)</xs:documentation>
                                    </xs:annotation>
                                  </xs:attribute>
                                </xs:complexType>
                              </xs:element>
                              <xs:element name="search_score" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
                              <xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">
                                <xs:complexType>
                                  <xs:sequence>
                                    <xs:any namespace="##any" processContents="lax">
                                      <xs:annotation>
                                        <xs:documentation>Wildcard for result info customized for a particular analysis</xs:documentation>
                                      </xs:annotation>
                                    </xs:any>
                                  </xs:sequence>
                                  <xs:attribute name="analysis" type="xs:string" use="required"/>
                                  <xs:attribute name="id" type="positiveInt" default="1"/>
                                </xs:complexType>
                              </xs:element>
                              <xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
                            </xs:sequence>
                            <xs:attribute name="hit_rank" type="positiveInt" use="required"/>
                            <xs:attribute name="peptide" type="xs:string" use="required">
                              <xs:annotation>
                                <xs:documentation>Peptide aminoacid sequence (with no indicated modifications)</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="peptide_prev_aa" type="xs:string">
                              <xs:annotation>
                                <xs:documentation>Aminoacid preceding peptide (- if none)</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="peptide_next_aa" type="xs:string">
                              <xs:annotation>
                                <xs:documentation>Aminoacid following peptide (- if none)</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="protein" type="xs:string" use="required"/>
                            <xs:attribute name="num_tot_proteins" type="xs:unsignedInt" use="required">
                              <xs:annotation>
                                <xs:documentation>Number of unique proteins in search database containing peptide</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="num_matched_ions" type="xs:nonNegativeInteger">
                              <xs:annotation>
                                <xs:documentation>Number of peptide fragment ions found in spectrum</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="tot_num_ions" type="xs:nonNegativeInteger">
                              <xs:annotation>
                                <xs:documentation>Number of peptide fragment ions predicted for peptide</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="calc_neutral_pep_mass" type="xs:float" use="required"/>
                            <xs:attribute name="massdiff" type="xs:string" use="required">
                              <xs:annotation>
                                <xs:documentation>Mass(precursor ion) - Mass(peptide)</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger">
                              <xs:annotation>
                                <xs:documentation>Number of peptide termini consistent with cleavage by sample enzyme</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="num_missed_cleavages" type="xs:integer">
                              <xs:annotation>
                                <xs:documentation>Number of sample enzyme cleavage sites internal to peptide</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="is_rejected" default="0">
                              <xs:annotation>
                                <xs:documentation>Potential use in future for user manual validation (0 or 1)</xs:documentation>
                              </xs:annotation>
                              <xs:simpleType>
                                <xs:restriction base="xs:nonNegativeInteger">
                                  <xs:enumeration value="0"/>
                                  <xs:enumeration value="1"/>
                                </xs:restriction>
                              </xs:simpleType>
                            </xs:attribute>
                            <xs:attribute name="protein_descr" type="xs:string">
                              <xs:annotation>
                                <xs:documentation>Extracted from search database</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="calc_pI" type="xs:string"/>
                            <xs:attribute name="protein_mw" type="xs:double"/>
                          </xs:complexType>
                          <xs:unique name="unique_result_analysis_id">
                            <xs:annotation>
                              <xs:documentation>analysis and id must be unique within a search_hit</xs:documentation>
                            </xs:annotation>
                            <xs:selector xpath="./pepx:analysis_result"/>
                            <xs:field xpath="@analysis"/>
                            <xs:field xpath="@id"/>
                          </xs:unique>
                        </xs:element>
                      </xs:sequence>
                      <xs:attribute name="search_id" type="positiveInt" default="1">
                        <xs:annotation>
                          <xs:documentation>Unique identifier to search summary</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                    </xs:complexType>
                  </xs:element>
                  <!-- search result -->
                </xs:sequence>
                <xs:attribute name="spectrum" type="xs:string" use="required"/>
                <xs:attribute name="start_scan" type="xs:unsignedInt" use="required">
                  <xs:annotation>
                    <xs:documentation>first scan number integrated into MS/MS spectrum</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="end_scan" type="xs:unsignedInt" use="required">
                  <xs:annotation>
                    <xs:documentation>last scan number integrated into MS/MS spectrum</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="precursor_neutral_mass" type="xs:float" use="required"/>
                <xs:attribute name="assumed_charge" type="xs:nonNegativeInteger" use="required">
                  <xs:annotation>
                    <xs:documentation>Precursor ion charge used for search</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="search_specification" type="xs:string">
                  <xs:annotation>
                    <xs:documentation>Search constraint applied specifically to this query</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="index" type="positiveInt" use="required">
                  <xs:annotation>
                    <xs:documentation>Unique identifier</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
              <xs:unique name="unique_search_id">
                <xs:annotation>
                  <xs:documentation>search_id must be unique within each msms_run_summary</xs:documentation>
                </xs:annotation>
                <xs:selector xpath="./pepx:search_result"/>
                <xs:field xpath="@search_id"/>
              </xs:unique>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="base_name" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>full path file name of mzXML (minus the .mzXML)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="raw_data_type" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>raw data type extension (e.g. .mzXML)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="raw_data" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>raw data type extension (e.g. .mzXML)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="msManufacturer" type="xs:string">
            <xs:annotation>
              <xs:documentation>Manufacturer of MS/MS instrument</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="msModel" type="xs:string">
            <xs:annotation>
              <xs:documentation>Instrument model (cf mzXML)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="msIonization" type="xs:string">
            <xs:annotation>
              <xs:documentation>Instrument model (cf mzXML)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="msMassAnalyzer" type="xs:string">
            <xs:annotation>
              <xs:documentation>Ion trap, etc (cf mzXML)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="msDetector" type="xs:string">
            <xs:annotation>
              <xs:documentation>EMT, etc(cf mzXML)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
        <xs:unique name="unique_timestamp_analysis_time">
          <xs:annotation>
            <xs:documentation>analysis_timestamp analysis and time must be unique within each msms_run_summary</xs:documentation>
          </xs:annotation>
          <xs:selector xpath="./pepx:analysis_timestamp"/>
          <xs:field xpath="@analysis"/>
          <xs:field xpath="@time"/>
        </xs:unique>
        <xs:key name="search_summary_id">
          <xs:selector xpath="./pepx:search_summary"/>
          <xs:field xpath="@search_id"/>
        </xs:key>
        <xs:keyref name="search_result_id" refer="search_summary_id">
          <xs:annotation>
            <xs:documentation>search_id within each search_hit must correspond with that of a search_summary</xs:documentation>
          </xs:annotation>
          <xs:selector xpath="./pepx:spectrum_query/pepx:search_result"/>
          <xs:field xpath="@search_id"/>
        </xs:keyref>
        <xs:key name="timestamp_analysis_id">
          <xs:selector xpath="./pepx:analysis_timestamp"/>
          <xs:field xpath="@analysis"/>
          <xs:field xpath="@id"/>
        </xs:key>
        <xs:keyref name="result_analysis_id" refer="timestamp_analysis_id">
          <xs:annotation>
            <xs:documentation>analysis and id in analysis_result must correspond with those in an analysis_timestamp element</xs:documentation>
          </xs:annotation>
          <xs:selector xpath="./pepx:spectrum_query/pepx:search_result/pepx:search_hit/pepx:analysis_result"/>
          <xs:field xpath="@analysis"/>
          <xs:field xpath="@id"/>
        </xs:keyref>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="name" type="xs:string">
      <xs:annotation>
        <xs:documentation>Summary name (currently not used)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="date" type="xs:dateTime" use="required">
      <xs:annotation>
        <xs:documentation>Date pepXML file was written</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="summary_xml" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Full path self reference</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
  <xs:key name="summary_analysis_time">
    <xs:selector xpath="./pepx:analysis_summary"/>
    <xs:field xpath="@time"/>
    <xs:field xpath="@analysis"/>
  </xs:key>
  <xs:keyref name="timestamp_analysis_time" refer="summary_analysis_time">
    <xs:annotation>
      <xs:documentation>time and analysis within timestamp must correspond with those within analysis_summary element</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="./pepx:msms_run_summary/pepx:analysis_timestamp"/>
    <xs:field xpath="@time"/>
    <xs:field xpath="@analysis"/>
  </xs:keyref>
  <xs:unique name="unique_search_summary_basename">
    <xs:annotation>
      <xs:documentation>search_summary base_name (mzXML file) must be unique within document</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="./pepx:msms_run_summary/pepx:search_summary"/>
    <xs:field xpath="@base_name"/>
  </xs:unique>
  <xs:unique name="unique_query_index">
    <xs:annotation>
      <xs:documentation>spectrum_query index must be unique in document</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="./pepx:msms_run_summary/pepx:spectrum_query"/>
    <xs:field xpath="@index"/>
  </xs:unique>
</xs:element>

element msms_pipeline_analysis/analysis_summary
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
time  xs:dateTimerequired      
documentation 
Time analysis complete (unique id)
analysis  xs:stringrequired      
documentation 
Name of analysis program
version  xs:string      
documentation 
Release
annotation
documentation 
Summary of analysis subjected to run(s)
source
<xs:element name="analysis_summary" minOccurs="0" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Summary of analysis subjected to run(s)</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:any namespace="##any" processContents="lax" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Wildcard for summary info customized for a particular analysis</xs:documentation>
        </xs:annotation>
      </xs:any>
    </xs:sequence>
    <xs:attribute name="time" type="xs:dateTime" use="required">
      <xs:annotation>
        <xs:documentation>Time analysis complete (unique id)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="analysis" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Name of analysis program</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="version" type="xs:string">
      <xs:annotation>
        <xs:documentation>Release</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element msms_pipeline_analysis/dataset_derivation
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
children data_filter
attributes
Name  Type  Use  Default  Fixed  Annotation
generation_no  xs:nonNegativeIntegerrequired      
documentation 
number preceding filter generations
annotation
documentation 
Source and filtering criteria used to generate dataset
source
<xs:element name="dataset_derivation" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Source and filtering criteria used to generate dataset</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="data_filter" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:attribute name="number" type="xs:nonNegativeInteger" use="required"/>
          <xs:attribute name="parent_file" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>File from which derived</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="windows_parent" type="xs:string"/>
          <xs:attribute name="description" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>filtering criteria applied to data</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="generation_no" type="xs:nonNegativeInteger" use="required">
      <xs:annotation>
        <xs:documentation>number preceding filter generations</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element msms_pipeline_analysis/dataset_derivation/data_filter
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
number  xs:nonNegativeIntegerrequired      
parent_file  xs:stringrequired      
documentation 
File from which derived
windows_parent  xs:string      
description  xs:stringrequired      
documentation 
filtering criteria applied to data
source
<xs:element name="data_filter" minOccurs="0" maxOccurs="unbounded">
  <xs:complexType>
    <xs:attribute name="number" type="xs:nonNegativeInteger" use="required"/>
    <xs:attribute name="parent_file" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>File from which derived</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="windows_parent" type="xs:string"/>
    <xs:attribute name="description" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>filtering criteria applied to data</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element msms_pipeline_analysis/msms_run_summary
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
children sample_enzyme search_summary analysis_timestamp spectrum_query
attributes
Name  Type  Use  Default  Fixed  Annotation
base_name  xs:stringrequired      
documentation 
full path file name of mzXML (minus the .mzXML)
raw_data_type  xs:stringrequired      
documentation 
raw data type extension (e.g. .mzXML)
raw_data  xs:stringrequired      
documentation 
raw data type extension (e.g. .mzXML)
msManufacturer  xs:string      
documentation 
Manufacturer of MS/MS instrument
msModel  xs:string      
documentation 
Instrument model (cf mzXML)
msIonization  xs:string      
documentation 
Instrument model (cf mzXML)
msMassAnalyzer  xs:string      
documentation 
Ion trap, etc (cf mzXML)
msDetector  xs:string      
documentation 
EMT, etc(cf mzXML)
identity constraints
  Name  Refer  Selector  Field(s)  
unique  unique_timestamp_analysis_time    ./pepx:analysis_timestamp  @analysis  
@time  
key  search_summary_id    ./pepx:search_summary  @search_id  
keyref  search_result_id  search_summary_id  ./pepx:spectrum_query/pepx:search_result  @search_id  
key  timestamp_analysis_id    ./pepx:analysis_timestamp  @analysis  
@id  
keyref  result_analysis_id  timestamp_analysis_id  ./pepx:spectrum_query/pepx:search_result/pepx:search_hit/pepx:analysis_result  @analysis  
@id  
annotation
documentation 
Search results for LC/MS/MS run
source
<xs:element name="msms_run_summary" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Search results for LC/MS/MS run</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="sample_enzyme">
        <xs:annotation>
          <xs:documentation>Defines the net cleavage specificity of an enzyme, chemical reagent, or a mixture of these, for mass spectrometry purposes</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="specificity" minOccurs="0" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Component cleavage specificity. Must be at least one specificity unless enzymeType:fidelity is nonspecific </xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:attribute name="sense" use="required">
                  <xs:annotation>
                    <xs:documentation>Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut</xs:documentation>
                  </xs:annotation>
                  <xs:simpleType>
                    <xs:restriction base="xs:string">
                      <xs:enumeration value="C"/>
                      <xs:enumeration value="N"/>
                    </xs:restriction>
                  </xs:simpleType>
                </xs:attribute>
                <xs:attribute name="min_spacing" type="xs:nonNegativeInteger" default="1">
                  <xs:annotation>
                    <xs:documentation>minimum separation between adjacent cleavages</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="cut" use="required">
                  <xs:annotation>
                    <xs:documentation>One or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation>
                  </xs:annotation>
                  <xs:simpleType>
                    <xs:restriction base="xs:string">
                      <xs:minLength value="1"/>
                      <xs:maxLength value="20"/>
                      <xs:pattern value="[A,C-I,K-N,P-T,VWY]+"/>
                    </xs:restriction>
                  </xs:simpleType>
                </xs:attribute>
                <xs:attribute name="no_cut" use="optional">
                  <xs:annotation>
                    <xs:documentation>Zero or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation>
                  </xs:annotation>
                  <xs:simpleType>
                    <xs:restriction base="xs:string">
                      <xs:minLength value="0"/>
                      <xs:maxLength value="20"/>
                    </xs:restriction>
                  </xs:simpleType>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="name" use="required">
            <xs:annotation>
              <xs:documentation>Controlled code name for the enzyme that can be referred to by applications</xs:documentation>
            </xs:annotation>
            <xs:simpleType>
              <xs:restriction base="xs:string">
                <xs:minLength value="1"/>
              </xs:restriction>
            </xs:simpleType>
          </xs:attribute>
          <xs:attribute name="description" type="xs:string" use="optional">
            <xs:annotation>
              <xs:documentation>Free text to describe alternative names, special conditions, etc.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="fidelity" use="optional" default="specific">
            <xs:annotation>
              <xs:documentation>Semispecific means that at least one end of a pepide must conform to the cleavage specificity, (unless the peptide was at the terminus of the parent sequence). Nonspecific means that neither end of a peptide must conform to the cleavage specificity.</xs:documentation>
            </xs:annotation>
            <xs:simpleType>
              <xs:restriction base="xs:string">
                <xs:enumeration value="specific"/>
                <xs:enumeration value="semispecific"/>
                <xs:enumeration value="nonspecific"/>
              </xs:restriction>
            </xs:simpleType>
          </xs:attribute>
          <xs:attribute name="independent" type="xs:boolean" use="optional" default="1">
            <xs:annotation>
              <xs:documentation>If there are multiple specificities and independent is true, then a single peptide cannot exhibit one specificity at one terminus and a different specificity at the other. If independent is false, then a single peptide can exhibit mixed specificities.</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="search_summary" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Database search settings</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="search_database" minOccurs="0">
              <xs:complexType>
                <xs:attribute name="local_path" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>Full path address of database on local computer</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="URL" type="xs:string"/>
                <xs:attribute name="database_name" type="xs:string"/>
                <xs:attribute name="orig_database_url" type="xs:string"/>
                <xs:attribute name="database_release_date" type="xs:dateTime"/>
                <xs:attribute name="database_release_identifier" type="xs:string"/>
                <xs:attribute name="size_in_db_entries" type="xs:nonNegativeInteger"/>
                <xs:attribute name="size_of_residues" type="xs:nonNegativeInteger"/>
                <xs:attribute name="type" use="required">
                  <xs:annotation>
                    <xs:documentation>Database type (AA=amino acid, NA=nucleic acid)</xs:documentation>
                  </xs:annotation>
                  <xs:simpleType>
                    <xs:restriction base="xs:string">
                      <xs:enumeration value="AA"/>
                      <xs:enumeration value="NA"/>
                    </xs:restriction>
                  </xs:simpleType>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
            <xs:element name="enzymatic_search_constraint" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Required peptide termini</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:attribute name="enzyme" type="xs:string" use="required"/>
                <xs:attribute name="max_num_internal_cleavages" type="xs:nonNegativeInteger" use="required">
                  <xs:annotation>
                    <xs:documentation>Maximum number of enzyme cleavage sites allowable within peptide</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="min_number_termini" type="xs:nonNegativeInteger" use="required">
                  <xs:annotation>
                    <xs:documentation>Minimum number of termini compatible with enzymatic cleavage</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
            <xs:element name="sequence_search_constraint" minOccurs="0" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Required amino acid string</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:attribute name="sequence" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>Required amino acid string</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
            <xs:element name="aminoacid_modification" minOccurs="0" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Modified aminoacid, static or variable</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:attribute name="aminoacid" type="xs:string" use="required"/>
                <xs:attribute name="massdiff" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>Mass difference with respect to unmodified aminoacid, must begin with either + (nonnegative) or - [e.g. +1.05446 or -2.3342]</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="mass" type="xs:float" use="required">
                  <xs:annotation>
                    <xs:documentation>Mass of modified aminoacid</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="variable" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>Y if both modified and unmodified aminoacid could be present in the dataset, N if only modified aminoacid can be present</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="peptide_terminus" type="xs:string">
                  <xs:annotation>
                    <xs:documentation>whether modification can reside only at protein terminus (specified 'n', 'c', or 'nc')</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="symbol" type="aa_symbolType">
                  <xs:annotation>
                    <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="binary" type="xs:string">
                  <xs:annotation>
                    <xs:documentation>Y if each peptide must have only modified or unmodified aminoacid, N if a peptide may contain both modified and unmodified aminoacid</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="description" type="xs:string"/>
              </xs:complexType>
            </xs:element>
            <xs:element name="terminal_modification" minOccurs="0" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Modification to the N or C terminus, static or variable</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:attribute name="terminus" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>n for N-terminus, c for C-terminus</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="massdiff" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>Mass difference with respect to unmodified terminus</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="mass" type="xs:float" use="required">
                  <xs:annotation>
                    <xs:documentation>Mass of modified terminus</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="variable" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>Y if both modified and unmodified terminus could be present in the dataset, N if only modified terminus can be present</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="symbol" type="term_symbolType">
                  <xs:annotation>
                    <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="protein_terminus" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>whether modification can reside only at protein terminus (specified n or c)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="description" type="xs:string"/>
              </xs:complexType>
            </xs:element>
            <xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
          </xs:sequence>
          <xs:attribute name="base_name" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Full path location of mzXML file for this search run (without the .mzXML extension)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="search_engine" type="engineType" use="required">
            <xs:annotation>
              <xs:documentation>SEQUEST, Mascot, COMET, etc</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="precursor_mass_type" type="massType" use="required">
            <xs:annotation>
              <xs:documentation>average or monoisotopic</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="fragment_mass_type" type="massType" use="required">
            <xs:annotation>
              <xs:documentation>average or monoisotopic</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="out_data_type" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Format of file storing the runner up peptides (if not present in pepXML)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="out_data" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>runner up search hit data type extension (e.g. .tgz)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="search_id" type="positiveInt" use="required">
            <xs:annotation>
              <xs:documentation>matches id in search hit</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="analysis_timestamp" minOccurs="0" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Reference for analysis applied to current run (time corresponds with analysis_summary/@time, id corresponds with analysis_result/@id)</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:any namespace="##any" processContents="lax" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Wildcard for timestamp info customized for a particular analysis</xs:documentation>
              </xs:annotation>
            </xs:any>
          </xs:sequence>
          <xs:attribute name="time" type="xs:dateTime" use="required">
            <xs:annotation>
              <xs:documentation>Date of analysis</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="analysis" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Analysis name</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="id" type="positiveInt" use="required">
            <xs:annotation>
              <xs:documentation>Unique identifier for each type of analysis</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="spectrum_query" minOccurs="0" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>MS/MS spectrum, precursor ion charge and mass</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="search_result" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="search_hit" minOccurs="0" maxOccurs="unbounded">
                    <xs:annotation>
                      <xs:documentation>Peptide assignment</xs:documentation>
                    </xs:annotation>
                    <xs:complexType>
                      <xs:sequence>
                        <xs:element name="alternative_protein" minOccurs="0" maxOccurs="unbounded">
                          <xs:annotation>
                            <xs:documentation>Other protein in search database that contains peptide</xs:documentation>
                          </xs:annotation>
                          <xs:complexType>
                            <xs:attribute name="protein" type="xs:string" use="required"/>
                            <xs:attribute name="protein_descr" type="xs:string"/>
                            <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger"/>
                            <xs:attribute name="protein_mw" type="xs:double"/>
                          </xs:complexType>
                        </xs:element>
                        <xs:element name="modification_info" minOccurs="0">
                          <xs:annotation>
                            <xs:documentation>Positions and masses of modifications</xs:documentation>
                          </xs:annotation>
                          <xs:complexType>
                            <xs:sequence>
                              <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
                                <xs:complexType>
                                  <xs:attribute name="position" type="xs:nonNegativeInteger" use="required">
                                    <xs:annotation>
                                      <xs:documentation>modified aminoacid position in peptide [ranging from 1 to peptide length]</xs:documentation>
                                    </xs:annotation>
                                  </xs:attribute>
                                  <xs:attribute name="mass" type="xs:double" use="required">
                                    <xs:annotation>
                                      <xs:documentation>modified mass of aminoacid</xs:documentation>
                                    </xs:annotation>
                                  </xs:attribute>
                                </xs:complexType>
                              </xs:element>
                            </xs:sequence>
                            <xs:attribute name="mod_nterm_mass" type="xs:double">
                              <xs:annotation>
                                <xs:documentation>Mass of modified N terminus</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="mod_cterm_mass" type="xs:double">
                              <xs:annotation>
                                <xs:documentation>Mass of modified C terminus</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="modified_peptide" type="xs:string">
                              <xs:annotation>
                                <xs:documentation>Peptide sequence (with indicated modifications)</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                          </xs:complexType>
                        </xs:element>
                        <xs:element name="search_score" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
                        <xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">
                          <xs:complexType>
                            <xs:sequence>
                              <xs:any namespace="##any" processContents="lax">
                                <xs:annotation>
                                  <xs:documentation>Wildcard for result info customized for a particular analysis</xs:documentation>
                                </xs:annotation>
                              </xs:any>
                            </xs:sequence>
                            <xs:attribute name="analysis" type="xs:string" use="required"/>
                            <xs:attribute name="id" type="positiveInt" default="1"/>
                          </xs:complexType>
                        </xs:element>
                        <xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
                      </xs:sequence>
                      <xs:attribute name="hit_rank" type="positiveInt" use="required"/>
                      <xs:attribute name="peptide" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>Peptide aminoacid sequence (with no indicated modifications)</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="peptide_prev_aa" type="xs:string">
                        <xs:annotation>
                          <xs:documentation>Aminoacid preceding peptide (- if none)</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="peptide_next_aa" type="xs:string">
                        <xs:annotation>
                          <xs:documentation>Aminoacid following peptide (- if none)</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="protein" type="xs:string" use="required"/>
                      <xs:attribute name="num_tot_proteins" type="xs:unsignedInt" use="required">
                        <xs:annotation>
                          <xs:documentation>Number of unique proteins in search database containing peptide</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="num_matched_ions" type="xs:nonNegativeInteger">
                        <xs:annotation>
                          <xs:documentation>Number of peptide fragment ions found in spectrum</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="tot_num_ions" type="xs:nonNegativeInteger">
                        <xs:annotation>
                          <xs:documentation>Number of peptide fragment ions predicted for peptide</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="calc_neutral_pep_mass" type="xs:float" use="required"/>
                      <xs:attribute name="massdiff" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>Mass(precursor ion) - Mass(peptide)</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger">
                        <xs:annotation>
                          <xs:documentation>Number of peptide termini consistent with cleavage by sample enzyme</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="num_missed_cleavages" type="xs:integer">
                        <xs:annotation>
                          <xs:documentation>Number of sample enzyme cleavage sites internal to peptide</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="is_rejected" default="0">
                        <xs:annotation>
                          <xs:documentation>Potential use in future for user manual validation (0 or 1)</xs:documentation>
                        </xs:annotation>
                        <xs:simpleType>
                          <xs:restriction base="xs:nonNegativeInteger">
                            <xs:enumeration value="0"/>
                            <xs:enumeration value="1"/>
                          </xs:restriction>
                        </xs:simpleType>
                      </xs:attribute>
                      <xs:attribute name="protein_descr" type="xs:string">
                        <xs:annotation>
                          <xs:documentation>Extracted from search database</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="calc_pI" type="xs:string"/>
                      <xs:attribute name="protein_mw" type="xs:double"/>
                    </xs:complexType>
                    <xs:unique name="unique_result_analysis_id">
                      <xs:annotation>
                        <xs:documentation>analysis and id must be unique within a search_hit</xs:documentation>
                      </xs:annotation>
                      <xs:selector xpath="./pepx:analysis_result"/>
                      <xs:field xpath="@analysis"/>
                      <xs:field xpath="@id"/>
                    </xs:unique>
                  </xs:element>
                </xs:sequence>
                <xs:attribute name="search_id" type="positiveInt" default="1">
                  <xs:annotation>
                    <xs:documentation>Unique identifier to search summary</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
            <!-- search result -->
          </xs:sequence>
          <xs:attribute name="spectrum" type="xs:string" use="required"/>
          <xs:attribute name="start_scan" type="xs:unsignedInt" use="required">
            <xs:annotation>
              <xs:documentation>first scan number integrated into MS/MS spectrum</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="end_scan" type="xs:unsignedInt" use="required">
            <xs:annotation>
              <xs:documentation>last scan number integrated into MS/MS spectrum</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="precursor_neutral_mass" type="xs:float" use="required"/>
          <xs:attribute name="assumed_charge" type="xs:nonNegativeInteger" use="required">
            <xs:annotation>
              <xs:documentation>Precursor ion charge used for search</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="search_specification" type="xs:string">
            <xs:annotation>
              <xs:documentation>Search constraint applied specifically to this query</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="index" type="positiveInt" use="required">
            <xs:annotation>
              <xs:documentation>Unique identifier</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
        <xs:unique name="unique_search_id">
          <xs:annotation>
            <xs:documentation>search_id must be unique within each msms_run_summary</xs:documentation>
          </xs:annotation>
          <xs:selector xpath="./pepx:search_result"/>
          <xs:field xpath="@search_id"/>
        </xs:unique>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="base_name" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>full path file name of mzXML (minus the .mzXML)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="raw_data_type" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>raw data type extension (e.g. .mzXML)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="raw_data" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>raw data type extension (e.g. .mzXML)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="msManufacturer" type="xs:string">
      <xs:annotation>
        <xs:documentation>Manufacturer of MS/MS instrument</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="msModel" type="xs:string">
      <xs:annotation>
        <xs:documentation>Instrument model (cf mzXML)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="msIonization" type="xs:string">
      <xs:annotation>
        <xs:documentation>Instrument model (cf mzXML)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="msMassAnalyzer" type="xs:string">
      <xs:annotation>
        <xs:documentation>Ion trap, etc (cf mzXML)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="msDetector" type="xs:string">
      <xs:annotation>
        <xs:documentation>EMT, etc(cf mzXML)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
  <xs:unique name="unique_timestamp_analysis_time">
    <xs:annotation>
      <xs:documentation>analysis_timestamp analysis and time must be unique within each msms_run_summary</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="./pepx:analysis_timestamp"/>
    <xs:field xpath="@analysis"/>
    <xs:field xpath="@time"/>
  </xs:unique>
  <xs:key name="search_summary_id">
    <xs:selector xpath="./pepx:search_summary"/>
    <xs:field xpath="@search_id"/>
  </xs:key>
  <xs:keyref name="search_result_id" refer="search_summary_id">
    <xs:annotation>
      <xs:documentation>search_id within each search_hit must correspond with that of a search_summary</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="./pepx:spectrum_query/pepx:search_result"/>
    <xs:field xpath="@search_id"/>
  </xs:keyref>
  <xs:key name="timestamp_analysis_id">
    <xs:selector xpath="./pepx:analysis_timestamp"/>
    <xs:field xpath="@analysis"/>
    <xs:field xpath="@id"/>
  </xs:key>
  <xs:keyref name="result_analysis_id" refer="timestamp_analysis_id">
    <xs:annotation>
      <xs:documentation>analysis and id in analysis_result must correspond with those in an analysis_timestamp element</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="./pepx:spectrum_query/pepx:search_result/pepx:search_hit/pepx:analysis_result"/>
    <xs:field xpath="@analysis"/>
    <xs:field xpath="@id"/>
  </xs:keyref>
</xs:element>

element msms_pipeline_analysis/msms_run_summary/sample_enzyme
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
children specificity
attributes
Name  Type  Use  Default  Fixed  Annotation
name  required      
documentation 
Controlled code name for the enzyme that can be referred to by applications
description  xs:stringoptional      
documentation 
Free text to describe alternative names, special conditions, etc.
fidelity  optional  specific    
documentation 
Semispecific means that at least one end of a pepide must conform to the cleavage specificity, (unless the peptide was at the terminus of the parent sequence). Nonspecific means that neither end of a peptide must conform to the cleavage specificity.
independent  xs:booleanoptional  1    
documentation 
If there are multiple specificities and independent is true, then a single peptide cannot exhibit one specificity at one terminus and a different specificity at the other. If independent is false, then a single peptide can exhibit mixed specificities.
annotation
documentation 
Defines the net cleavage specificity of an enzyme, chemical reagent, or a mixture of these, for mass spectrometry purposes
source
<xs:element name="sample_enzyme">
  <xs:annotation>
    <xs:documentation>Defines the net cleavage specificity of an enzyme, chemical reagent, or a mixture of these, for mass spectrometry purposes</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="specificity" minOccurs="0" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Component cleavage specificity. Must be at least one specificity unless enzymeType:fidelity is nonspecific </xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="sense" use="required">
            <xs:annotation>
              <xs:documentation>Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut</xs:documentation>
            </xs:annotation>
            <xs:simpleType>
              <xs:restriction base="xs:string">
                <xs:enumeration value="C"/>
                <xs:enumeration value="N"/>
              </xs:restriction>
            </xs:simpleType>
          </xs:attribute>
          <xs:attribute name="min_spacing" type="xs:nonNegativeInteger" default="1">
            <xs:annotation>
              <xs:documentation>minimum separation between adjacent cleavages</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="cut" use="required">
            <xs:annotation>
              <xs:documentation>One or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation>
            </xs:annotation>
            <xs:simpleType>
              <xs:restriction base="xs:string">
                <xs:minLength value="1"/>
                <xs:maxLength value="20"/>
                <xs:pattern value="[A,C-I,K-N,P-T,VWY]+"/>
              </xs:restriction>
            </xs:simpleType>
          </xs:attribute>
          <xs:attribute name="no_cut" use="optional">
            <xs:annotation>
              <xs:documentation>Zero or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation>
            </xs:annotation>
            <xs:simpleType>
              <xs:restriction base="xs:string">
                <xs:minLength value="0"/>
                <xs:maxLength value="20"/>
              </xs:restriction>
            </xs:simpleType>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="name" use="required">
      <xs:annotation>
        <xs:documentation>Controlled code name for the enzyme that can be referred to by applications</xs:documentation>
      </xs:annotation>
      <xs:simpleType>
        <xs:restriction base="xs:string">
          <xs:minLength value="1"/>
        </xs:restriction>
      </xs:simpleType>
    </xs:attribute>
    <xs:attribute name="description" type="xs:string" use="optional">
      <xs:annotation>
        <xs:documentation>Free text to describe alternative names, special conditions, etc.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="fidelity" use="optional" default="specific">
      <xs:annotation>
        <xs:documentation>Semispecific means that at least one end of a pepide must conform to the cleavage specificity, (unless the peptide was at the terminus of the parent sequence). Nonspecific means that neither end of a peptide must conform to the cleavage specificity.</xs:documentation>
      </xs:annotation>
      <xs:simpleType>
        <xs:restriction base="xs:string">
          <xs:enumeration value="specific"/>
          <xs:enumeration value="semispecific"/>
          <xs:enumeration value="nonspecific"/>
        </xs:restriction>
      </xs:simpleType>
    </xs:attribute>
    <xs:attribute name="independent" type="xs:boolean" use="optional" default="1">
      <xs:annotation>
        <xs:documentation>If there are multiple specificities and independent is true, then a single peptide cannot exhibit one specificity at one terminus and a different specificity at the other. If independent is false, then a single peptide can exhibit mixed specificities.</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element msms_pipeline_analysis/msms_run_summary/sample_enzyme/specificity
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
sense  required      
documentation 
Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut
min_spacing  xs:nonNegativeInteger  1    
documentation 
minimum separation between adjacent cleavages
cut  required      
documentation 
One or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site
no_cut  optional      
documentation 
Zero or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site
annotation
documentation 
Component cleavage specificity. Must be at least one specificity unless enzymeType:fidelity is nonspecific 
source
<xs:element name="specificity" minOccurs="0" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Component cleavage specificity. Must be at least one specificity unless enzymeType:fidelity is nonspecific </xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="sense" use="required">
      <xs:annotation>
        <xs:documentation>Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut</xs:documentation>
      </xs:annotation>
      <xs:simpleType>
        <xs:restriction base="xs:string">
          <xs:enumeration value="C"/>
          <xs:enumeration value="N"/>
        </xs:restriction>
      </xs:simpleType>
    </xs:attribute>
    <xs:attribute name="min_spacing" type="xs:nonNegativeInteger" default="1">
      <xs:annotation>
        <xs:documentation>minimum separation between adjacent cleavages</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="cut" use="required">
      <xs:annotation>
        <xs:documentation>One or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation>
      </xs:annotation>
      <xs:simpleType>
        <xs:restriction base="xs:string">
          <xs:minLength value="1"/>
          <xs:maxLength value="20"/>
          <xs:pattern value="[A,C-I,K-N,P-T,VWY]+"/>
        </xs:restriction>
      </xs:simpleType>
    </xs:attribute>
    <xs:attribute name="no_cut" use="optional">
      <xs:annotation>
        <xs:documentation>Zero or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation>
      </xs:annotation>
      <xs:simpleType>
        <xs:restriction base="xs:string">
          <xs:minLength value="0"/>
          <xs:maxLength value="20"/>
        </xs:restriction>
      </xs:simpleType>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element msms_pipeline_analysis/msms_run_summary/search_summary
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
children search_database enzymatic_search_constraint sequence_search_constraint aminoacid_modification terminal_modification parameter
attributes
Name  Type  Use  Default  Fixed  Annotation
base_name  xs:stringrequired      
documentation 
Full path location of mzXML file for this search run (without the .mzXML extension)
search_engine  engineTyperequired      
documentation 
SEQUEST, Mascot, COMET, etc
precursor_mass_type  massTyperequired      
documentation 
average or monoisotopic
fragment_mass_type  massTyperequired      
documentation 
average or monoisotopic
out_data_type  xs:stringrequired      
documentation 
Format of file storing the runner up peptides (if not present in pepXML)
out_data  xs:stringrequired      
documentation 
runner up search hit data type extension (e.g. .tgz)
search_id  positiveIntrequired      
documentation 
matches id in search hit
annotation
documentation 
Database search settings
source
<xs:element name="search_summary" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Database search settings</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="search_database" minOccurs="0">
        <xs:complexType>
          <xs:attribute name="local_path" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Full path address of database on local computer</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="URL" type="xs:string"/>
          <xs:attribute name="database_name" type="xs:string"/>
          <xs:attribute name="orig_database_url" type="xs:string"/>
          <xs:attribute name="database_release_date" type="xs:dateTime"/>
          <xs:attribute name="database_release_identifier" type="xs:string"/>
          <xs:attribute name="size_in_db_entries" type="xs:nonNegativeInteger"/>
          <xs:attribute name="size_of_residues" type="xs:nonNegativeInteger"/>
          <xs:attribute name="type" use="required">
            <xs:annotation>
              <xs:documentation>Database type (AA=amino acid, NA=nucleic acid)</xs:documentation>
            </xs:annotation>
            <xs:simpleType>
              <xs:restriction base="xs:string">
                <xs:enumeration value="AA"/>
                <xs:enumeration value="NA"/>
              </xs:restriction>
            </xs:simpleType>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="enzymatic_search_constraint" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Required peptide termini</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="enzyme" type="xs:string" use="required"/>
          <xs:attribute name="max_num_internal_cleavages" type="xs:nonNegativeInteger" use="required">
            <xs:annotation>
              <xs:documentation>Maximum number of enzyme cleavage sites allowable within peptide</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="min_number_termini" type="xs:nonNegativeInteger" use="required">
            <xs:annotation>
              <xs:documentation>Minimum number of termini compatible with enzymatic cleavage</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="sequence_search_constraint" minOccurs="0" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Required amino acid string</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="sequence" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Required amino acid string</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="aminoacid_modification" minOccurs="0" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Modified aminoacid, static or variable</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="aminoacid" type="xs:string" use="required"/>
          <xs:attribute name="massdiff" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Mass difference with respect to unmodified aminoacid, must begin with either + (nonnegative) or - [e.g. +1.05446 or -2.3342]</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="mass" type="xs:float" use="required">
            <xs:annotation>
              <xs:documentation>Mass of modified aminoacid</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="variable" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Y if both modified and unmodified aminoacid could be present in the dataset, N if only modified aminoacid can be present</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="peptide_terminus" type="xs:string">
            <xs:annotation>
              <xs:documentation>whether modification can reside only at protein terminus (specified 'n', 'c', or 'nc')</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="symbol" type="aa_symbolType">
            <xs:annotation>
              <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="binary" type="xs:string">
            <xs:annotation>
              <xs:documentation>Y if each peptide must have only modified or unmodified aminoacid, N if a peptide may contain both modified and unmodified aminoacid</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="description" type="xs:string"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="terminal_modification" minOccurs="0" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Modification to the N or C terminus, static or variable</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="terminus" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>n for N-terminus, c for C-terminus</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="massdiff" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Mass difference with respect to unmodified terminus</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="mass" type="xs:float" use="required">
            <xs:annotation>
              <xs:documentation>Mass of modified terminus</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="variable" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Y if both modified and unmodified terminus could be present in the dataset, N if only modified terminus can be present</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="symbol" type="term_symbolType">
            <xs:annotation>
              <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="protein_terminus" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>whether modification can reside only at protein terminus (specified n or c)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="description" type="xs:string"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
    </xs:sequence>
    <xs:attribute name="base_name" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Full path location of mzXML file for this search run (without the .mzXML extension)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="search_engine" type="engineType" use="required">
      <xs:annotation>
        <xs:documentation>SEQUEST, Mascot, COMET, etc</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="precursor_mass_type" type="massType" use="required">
      <xs:annotation>
        <xs:documentation>average or monoisotopic</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="fragment_mass_type" type="massType" use="required">
      <xs:annotation>
        <xs:documentation>average or monoisotopic</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="out_data_type" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Format of file storing the runner up peptides (if not present in pepXML)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="out_data" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>runner up search hit data type extension (e.g. .tgz)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="search_id" type="positiveInt" use="required">
      <xs:annotation>
        <xs:documentation>matches id in search hit</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element msms_pipeline_analysis/msms_run_summary/search_summary/search_database
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
local_path  xs:stringrequired      
documentation 
Full path address of database on local computer
URL  xs:string      
database_name  xs:string      
orig_database_url  xs:string      
database_release_date  xs:dateTime      
database_release_identifier  xs:string      
size_in_db_entries  xs:nonNegativeInteger      
size_of_residues  xs:nonNegativeInteger      
type  required      
documentation 
Database type (AA=amino acid, NA=nucleic acid)
source
<xs:element name="search_database" minOccurs="0">
  <xs:complexType>
    <xs:attribute name="local_path" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Full path address of database on local computer</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="URL" type="xs:string"/>
    <xs:attribute name="database_name" type="xs:string"/>
    <xs:attribute name="orig_database_url" type="xs:string"/>
    <xs:attribute name="database_release_date" type="xs:dateTime"/>
    <xs:attribute name="database_release_identifier" type="xs:string"/>
    <xs:attribute name="size_in_db_entries" type="xs:nonNegativeInteger"/>
    <xs:attribute name="size_of_residues" type="xs:nonNegativeInteger"/>
    <xs:attribute name="type" use="required">
      <xs:annotation>
        <xs:documentation>Database type (AA=amino acid, NA=nucleic acid)</xs:documentation>
      </xs:annotation>
      <xs:simpleType>
        <xs:restriction base="xs:string">
          <xs:enumeration value="AA"/>
          <xs:enumeration value="NA"/>
        </xs:restriction>
      </xs:simpleType>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element msms_pipeline_analysis/msms_run_summary/search_summary/enzymatic_search_constraint
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
enzyme  xs:stringrequired      
max_num_internal_cleavages  xs:nonNegativeIntegerrequired      
documentation 
Maximum number of enzyme cleavage sites allowable within peptide
min_number_termini  xs:nonNegativeIntegerrequired      
documentation 
Minimum number of termini compatible with enzymatic cleavage
annotation
documentation 
Required peptide termini
source
<xs:element name="enzymatic_search_constraint" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Required peptide termini</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="enzyme" type="xs:string" use="required"/>
    <xs:attribute name="max_num_internal_cleavages" type="xs:nonNegativeInteger" use="required">
      <xs:annotation>
        <xs:documentation>Maximum number of enzyme cleavage sites allowable within peptide</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="min_number_termini" type="xs:nonNegativeInteger" use="required">
      <xs:annotation>
        <xs:documentation>Minimum number of termini compatible with enzymatic cleavage</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element msms_pipeline_analysis/msms_run_summary/search_summary/sequence_search_constraint
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
sequence  xs:stringrequired      
documentation 
Required amino acid string
annotation
documentation 
Required amino acid string
source
<xs:element name="sequence_search_constraint" minOccurs="0" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Required amino acid string</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="sequence" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Required amino acid string</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element msms_pipeline_analysis/msms_run_summary/search_summary/aminoacid_modification
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
aminoacid  xs:stringrequired      
massdiff  xs:stringrequired      
documentation 
Mass difference with respect to unmodified aminoacid, must begin with either + (nonnegative) or - [e.g. +1.05446 or -2.3342]
mass  xs:floatrequired      
documentation 
Mass of modified aminoacid
variable  xs:stringrequired      
documentation 
Y if both modified and unmodified aminoacid could be present in the dataset, N if only modified aminoacid can be present
peptide_terminus  xs:string      
documentation 
whether modification can reside only at protein terminus (specified 'n', 'c', or 'nc')
symbol  aa_symbolType      
documentation 
Special symbol used by search engine to designate this modification
binary  xs:string      
documentation 
Y if each peptide must have only modified or unmodified aminoacid, N if a peptide may contain both modified and unmodified aminoacid
description  xs:string      
annotation
documentation 
Modified aminoacid, static or variable
source
<xs:element name="aminoacid_modification" minOccurs="0" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Modified aminoacid, static or variable</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="aminoacid" type="xs:string" use="required"/>
    <xs:attribute name="massdiff" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Mass difference with respect to unmodified aminoacid, must begin with either + (nonnegative) or - [e.g. +1.05446 or -2.3342]</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="mass" type="xs:float" use="required">
      <xs:annotation>
        <xs:documentation>Mass of modified aminoacid</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="variable" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Y if both modified and unmodified aminoacid could be present in the dataset, N if only modified aminoacid can be present</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="peptide_terminus" type="xs:string">
      <xs:annotation>
        <xs:documentation>whether modification can reside only at protein terminus (specified 'n', 'c', or 'nc')</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="symbol" type="aa_symbolType">
      <xs:annotation>
        <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="binary" type="xs:string">
      <xs:annotation>
        <xs:documentation>Y if each peptide must have only modified or unmodified aminoacid, N if a peptide may contain both modified and unmodified aminoacid</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="description" type="xs:string"/>
  </xs:complexType>
</xs:element>

element msms_pipeline_analysis/msms_run_summary/search_summary/terminal_modification
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
terminus  xs:stringrequired      
documentation 
n for N-terminus, c for C-terminus
massdiff  xs:stringrequired      
documentation 
Mass difference with respect to unmodified terminus
mass  xs:floatrequired      
documentation 
Mass of modified terminus
variable  xs:stringrequired      
documentation 
Y if both modified and unmodified terminus could be present in the dataset, N if only modified terminus can be present
symbol  term_symbolType      
documentation 
Special symbol used by search engine to designate this modification
protein_terminus  xs:stringrequired      
documentation 
whether modification can reside only at protein terminus (specified n or c)
description  xs:string      
annotation
documentation 
Modification to the N or C terminus, static or variable
source
<xs:element name="terminal_modification" minOccurs="0" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Modification to the N or C terminus, static or variable</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="terminus" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>n for N-terminus, c for C-terminus</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="massdiff" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Mass difference with respect to unmodified terminus</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="mass" type="xs:float" use="required">
      <xs:annotation>
        <xs:documentation>Mass of modified terminus</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="variable" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Y if both modified and unmodified terminus could be present in the dataset, N if only modified terminus can be present</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="symbol" type="term_symbolType">
      <xs:annotation>
        <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="protein_terminus" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>whether modification can reside only at protein terminus (specified n or c)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="description" type="xs:string"/>
  </xs:complexType>
</xs:element>

element msms_pipeline_analysis/msms_run_summary/search_summary/parameter
diagram
namespace http://regis-web.systemsbiology.net/pepXML
type nameValueType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
name  xs:stringrequired      
value  xs:anySimpleTyperequired      
type  xs:anySimpleType      
source
<xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>

element msms_pipeline_analysis/msms_run_summary/analysis_timestamp
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
time  xs:dateTimerequired      
documentation 
Date of analysis
analysis  xs:stringrequired      
documentation 
Analysis name
id  positiveIntrequired      
documentation 
Unique identifier for each type of analysis
annotation
documentation 
Reference for analysis applied to current run (time corresponds with analysis_summary/@time, id corresponds with analysis_result/@id)
source
<xs:element name="analysis_timestamp" minOccurs="0" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Reference for analysis applied to current run (time corresponds with analysis_summary/@time, id corresponds with analysis_result/@id)</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:any namespace="##any" processContents="lax" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Wildcard for timestamp info customized for a particular analysis</xs:documentation>
        </xs:annotation>
      </xs:any>
    </xs:sequence>
    <xs:attribute name="time" type="xs:dateTime" use="required">
      <xs:annotation>
        <xs:documentation>Date of analysis</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="analysis" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Analysis name</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="id" type="positiveInt" use="required">
      <xs:annotation>
        <xs:documentation>Unique identifier for each type of analysis</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element msms_pipeline_analysis/msms_run_summary/spectrum_query
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
children search_result
attributes
Name  Type  Use  Default  Fixed  Annotation
spectrum  xs:stringrequired      
start_scan  xs:unsignedIntrequired      
documentation 
first scan number integrated into MS/MS spectrum
end_scan  xs:unsignedIntrequired      
documentation 
last scan number integrated into MS/MS spectrum
precursor_neutral_mass  xs:floatrequired      
assumed_charge  xs:nonNegativeIntegerrequired      
documentation 
Precursor ion charge used for search
search_specification  xs:string      
documentation 
Search constraint applied specifically to this query
index  positiveIntrequired      
documentation 
Unique identifier
identity constraints
  Name  Refer  Selector  Field(s)  
unique  unique_search_id    ./pepx:search_result  @search_id  
annotation
documentation 
MS/MS spectrum, precursor ion charge and mass
source
<xs:element name="spectrum_query" minOccurs="0" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>MS/MS spectrum, precursor ion charge and mass</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="search_result" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="search_hit" minOccurs="0" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Peptide assignment</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="alternative_protein" minOccurs="0" maxOccurs="unbounded">
                    <xs:annotation>
                      <xs:documentation>Other protein in search database that contains peptide</xs:documentation>
                    </xs:annotation>
                    <xs:complexType>
                      <xs:attribute name="protein" type="xs:string" use="required"/>
                      <xs:attribute name="protein_descr" type="xs:string"/>
                      <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger"/>
                      <xs:attribute name="protein_mw" type="xs:double"/>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="modification_info" minOccurs="0">
                    <xs:annotation>
                      <xs:documentation>Positions and masses of modifications</xs:documentation>
                    </xs:annotation>
                    <xs:complexType>
                      <xs:sequence>
                        <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
                          <xs:complexType>
                            <xs:attribute name="position" type="xs:nonNegativeInteger" use="required">
                              <xs:annotation>
                                <xs:documentation>modified aminoacid position in peptide [ranging from 1 to peptide length]</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="mass" type="xs:double" use="required">
                              <xs:annotation>
                                <xs:documentation>modified mass of aminoacid</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                          </xs:complexType>
                        </xs:element>
                      </xs:sequence>
                      <xs:attribute name="mod_nterm_mass" type="xs:double">
                        <xs:annotation>
                          <xs:documentation>Mass of modified N terminus</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="mod_cterm_mass" type="xs:double">
                        <xs:annotation>
                          <xs:documentation>Mass of modified C terminus</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="modified_peptide" type="xs:string">
                        <xs:annotation>
                          <xs:documentation>Peptide sequence (with indicated modifications)</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="search_score" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
                  <xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:sequence>
                        <xs:any namespace="##any" processContents="lax">
                          <xs:annotation>
                            <xs:documentation>Wildcard for result info customized for a particular analysis</xs:documentation>
                          </xs:annotation>
                        </xs:any>
                      </xs:sequence>
                      <xs:attribute name="analysis" type="xs:string" use="required"/>
                      <xs:attribute name="id" type="positiveInt" default="1"/>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
                </xs:sequence>
                <xs:attribute name="hit_rank" type="positiveInt" use="required"/>
                <xs:attribute name="peptide" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>Peptide aminoacid sequence (with no indicated modifications)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="peptide_prev_aa" type="xs:string">
                  <xs:annotation>
                    <xs:documentation>Aminoacid preceding peptide (- if none)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="peptide_next_aa" type="xs:string">
                  <xs:annotation>
                    <xs:documentation>Aminoacid following peptide (- if none)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="protein" type="xs:string" use="required"/>
                <xs:attribute name="num_tot_proteins" type="xs:unsignedInt" use="required">
                  <xs:annotation>
                    <xs:documentation>Number of unique proteins in search database containing peptide</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="num_matched_ions" type="xs:nonNegativeInteger">
                  <xs:annotation>
                    <xs:documentation>Number of peptide fragment ions found in spectrum</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="tot_num_ions" type="xs:nonNegativeInteger">
                  <xs:annotation>
                    <xs:documentation>Number of peptide fragment ions predicted for peptide</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="calc_neutral_pep_mass" type="xs:float" use="required"/>
                <xs:attribute name="massdiff" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>Mass(precursor ion) - Mass(peptide)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger">
                  <xs:annotation>
                    <xs:documentation>Number of peptide termini consistent with cleavage by sample enzyme</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="num_missed_cleavages" type="xs:integer">
                  <xs:annotation>
                    <xs:documentation>Number of sample enzyme cleavage sites internal to peptide</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="is_rejected" default="0">
                  <xs:annotation>
                    <xs:documentation>Potential use in future for user manual validation (0 or 1)</xs:documentation>
                  </xs:annotation>
                  <xs:simpleType>
                    <xs:restriction base="xs:nonNegativeInteger">
                      <xs:enumeration value="0"/>
                      <xs:enumeration value="1"/>
                    </xs:restriction>
                  </xs:simpleType>
                </xs:attribute>
                <xs:attribute name="protein_descr" type="xs:string">
                  <xs:annotation>
                    <xs:documentation>Extracted from search database</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="calc_pI" type="xs:string"/>
                <xs:attribute name="protein_mw" type="xs:double"/>
              </xs:complexType>
              <xs:unique name="unique_result_analysis_id">
                <xs:annotation>
                  <xs:documentation>analysis and id must be unique within a search_hit</xs:documentation>
                </xs:annotation>
                <xs:selector xpath="./pepx:analysis_result"/>
                <xs:field xpath="@analysis"/>
                <xs:field xpath="@id"/>
              </xs:unique>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="search_id" type="positiveInt" default="1">
            <xs:annotation>
              <xs:documentation>Unique identifier to search summary</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <!-- search result -->
    </xs:sequence>
    <xs:attribute name="spectrum" type="xs:string" use="required"/>
    <xs:attribute name="start_scan" type="xs:unsignedInt" use="required">
      <xs:annotation>
        <xs:documentation>first scan number integrated into MS/MS spectrum</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="end_scan" type="xs:unsignedInt" use="required">
      <xs:annotation>
        <xs:documentation>last scan number integrated into MS/MS spectrum</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="precursor_neutral_mass" type="xs:float" use="required"/>
    <xs:attribute name="assumed_charge" type="xs:nonNegativeInteger" use="required">
      <xs:annotation>
        <xs:documentation>Precursor ion charge used for search</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="search_specification" type="xs:string">
      <xs:annotation>
        <xs:documentation>Search constraint applied specifically to this query</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="index" type="positiveInt" use="required">
      <xs:annotation>
        <xs:documentation>Unique identifier</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
  <xs:unique name="unique_search_id">
    <xs:annotation>
      <xs:documentation>search_id must be unique within each msms_run_summary</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="./pepx:search_result"/>
    <xs:field xpath="@search_id"/>
  </xs:unique>
</xs:element>

element msms_pipeline_analysis/msms_run_summary/spectrum_query/search_result
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
children search_hit
attributes
Name  Type  Use  Default  Fixed  Annotation
search_id  positiveInt  1    
documentation 
Unique identifier to search summary
source
<xs:element name="search_result" minOccurs="0" maxOccurs="unbounded">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="search_hit" minOccurs="0" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Peptide assignment</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="alternative_protein" minOccurs="0" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Other protein in search database that contains peptide</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:attribute name="protein" type="xs:string" use="required"/>
                <xs:attribute name="protein_descr" type="xs:string"/>
                <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger"/>
                <xs:attribute name="protein_mw" type="xs:double"/>
              </xs:complexType>
            </xs:element>
            <xs:element name="modification_info" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Positions and masses of modifications</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:attribute name="position" type="xs:nonNegativeInteger" use="required">
                        <xs:annotation>
                          <xs:documentation>modified aminoacid position in peptide [ranging from 1 to peptide length]</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="mass" type="xs:double" use="required">
                        <xs:annotation>
                          <xs:documentation>modified mass of aminoacid</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                    </xs:complexType>
                  </xs:element>
                </xs:sequence>
                <xs:attribute name="mod_nterm_mass" type="xs:double">
                  <xs:annotation>
                    <xs:documentation>Mass of modified N terminus</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="mod_cterm_mass" type="xs:double">
                  <xs:annotation>
                    <xs:documentation>Mass of modified C terminus</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="modified_peptide" type="xs:string">
                  <xs:annotation>
                    <xs:documentation>Peptide sequence (with indicated modifications)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
            <xs:element name="search_score" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
            <xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:sequence>
                  <xs:any namespace="##any" processContents="lax">
                    <xs:annotation>
                      <xs:documentation>Wildcard for result info customized for a particular analysis</xs:documentation>
                    </xs:annotation>
                  </xs:any>
                </xs:sequence>
                <xs:attribute name="analysis" type="xs:string" use="required"/>
                <xs:attribute name="id" type="positiveInt" default="1"/>
              </xs:complexType>
            </xs:element>
            <xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
          </xs:sequence>
          <xs:attribute name="hit_rank" type="positiveInt" use="required"/>
          <xs:attribute name="peptide" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Peptide aminoacid sequence (with no indicated modifications)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="peptide_prev_aa" type="xs:string">
            <xs:annotation>
              <xs:documentation>Aminoacid preceding peptide (- if none)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="peptide_next_aa" type="xs:string">
            <xs:annotation>
              <xs:documentation>Aminoacid following peptide (- if none)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="protein" type="xs:string" use="required"/>
          <xs:attribute name="num_tot_proteins" type="xs:unsignedInt" use="required">
            <xs:annotation>
              <xs:documentation>Number of unique proteins in search database containing peptide</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="num_matched_ions" type="xs:nonNegativeInteger">
            <xs:annotation>
              <xs:documentation>Number of peptide fragment ions found in spectrum</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="tot_num_ions" type="xs:nonNegativeInteger">
            <xs:annotation>
              <xs:documentation>Number of peptide fragment ions predicted for peptide</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="calc_neutral_pep_mass" type="xs:float" use="required"/>
          <xs:attribute name="massdiff" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Mass(precursor ion) - Mass(peptide)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger">
            <xs:annotation>
              <xs:documentation>Number of peptide termini consistent with cleavage by sample enzyme</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="num_missed_cleavages" type="xs:integer">
            <xs:annotation>
              <xs:documentation>Number of sample enzyme cleavage sites internal to peptide</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="is_rejected" default="0">
            <xs:annotation>
              <xs:documentation>Potential use in future for user manual validation (0 or 1)</xs:documentation>
            </xs:annotation>
            <xs:simpleType>
              <xs:restriction base="xs:nonNegativeInteger">
                <xs:enumeration value="0"/>
                <xs:enumeration value="1"/>
              </xs:restriction>
            </xs:simpleType>
          </xs:attribute>
          <xs:attribute name="protein_descr" type="xs:string">
            <xs:annotation>
              <xs:documentation>Extracted from search database</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="calc_pI" type="xs:string"/>
          <xs:attribute name="protein_mw" type="xs:double"/>
        </xs:complexType>
        <xs:unique name="unique_result_analysis_id">
          <xs:annotation>
            <xs:documentation>analysis and id must be unique within a search_hit</xs:documentation>
          </xs:annotation>
          <xs:selector xpath="./pepx:analysis_result"/>
          <xs:field xpath="@analysis"/>
          <xs:field xpath="@id"/>
        </xs:unique>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="search_id" type="positiveInt" default="1">
      <xs:annotation>
        <xs:documentation>Unique identifier to search summary</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element msms_pipeline_analysis/msms_run_summary/spectrum_query/search_result/search_hit
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
children alternative_protein modification_info search_score analysis_result parameter
attributes
Name  Type  Use  Default  Fixed  Annotation
hit_rank  positiveIntrequired      
peptide  xs:stringrequired      
documentation 
Peptide aminoacid sequence (with no indicated modifications)
peptide_prev_aa  xs:string      
documentation 
Aminoacid preceding peptide (- if none)
peptide_next_aa  xs:string      
documentation 
Aminoacid following peptide (- if none)
protein  xs:stringrequired      
num_tot_proteins  xs:unsignedIntrequired      
documentation 
Number of unique proteins in search database containing peptide
num_matched_ions  xs:nonNegativeInteger      
documentation 
Number of peptide fragment ions found in spectrum
tot_num_ions  xs:nonNegativeInteger      
documentation 
Number of peptide fragment ions predicted for peptide
calc_neutral_pep_mass  xs:floatrequired      
massdiff  xs:stringrequired      
documentation 
Mass(precursor ion) - Mass(peptide)
num_tol_term  xs:nonNegativeInteger      
documentation 
Number of peptide termini consistent with cleavage by sample enzyme
num_missed_cleavages  xs:integer      
documentation 
Number of sample enzyme cleavage sites internal to peptide
is_rejected    0    
documentation 
Potential use in future for user manual validation (0 or 1)
protein_descr  xs:string      
documentation 
Extracted from search database
calc_pI  xs:string      
protein_mw  xs:double      
identity constraints
  Name  Refer  Selector  Field(s)  
unique  unique_result_analysis_id    ./pepx:analysis_result  @analysis  
@id  
annotation
documentation 
Peptide assignment
source
<xs:element name="search_hit" minOccurs="0" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Peptide assignment</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="alternative_protein" minOccurs="0" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Other protein in search database that contains peptide</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="protein" type="xs:string" use="required"/>
          <xs:attribute name="protein_descr" type="xs:string"/>
          <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger"/>
          <xs:attribute name="protein_mw" type="xs:double"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="modification_info" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Positions and masses of modifications</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:attribute name="position" type="xs:nonNegativeInteger" use="required">
                  <xs:annotation>
                    <xs:documentation>modified aminoacid position in peptide [ranging from 1 to peptide length]</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="mass" type="xs:double" use="required">
                  <xs:annotation>
                    <xs:documentation>modified mass of aminoacid</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="mod_nterm_mass" type="xs:double">
            <xs:annotation>
              <xs:documentation>Mass of modified N terminus</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="mod_cterm_mass" type="xs:double">
            <xs:annotation>
              <xs:documentation>Mass of modified C terminus</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="modified_peptide" type="xs:string">
            <xs:annotation>
              <xs:documentation>Peptide sequence (with indicated modifications)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="search_score" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
      <xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:sequence>
            <xs:any namespace="##any" processContents="lax">
              <xs:annotation>
                <xs:documentation>Wildcard for result info customized for a particular analysis</xs:documentation>
              </xs:annotation>
            </xs:any>
          </xs:sequence>
          <xs:attribute name="analysis" type="xs:string" use="required"/>
          <xs:attribute name="id" type="positiveInt" default="1"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
    </xs:sequence>
    <xs:attribute name="hit_rank" type="positiveInt" use="required"/>
    <xs:attribute name="peptide" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Peptide aminoacid sequence (with no indicated modifications)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="peptide_prev_aa" type="xs:string">
      <xs:annotation>
        <xs:documentation>Aminoacid preceding peptide (- if none)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="peptide_next_aa" type="xs:string">
      <xs:annotation>
        <xs:documentation>Aminoacid following peptide (- if none)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="protein" type="xs:string" use="required"/>
    <xs:attribute name="num_tot_proteins" type="xs:unsignedInt" use="required">
      <xs:annotation>
        <xs:documentation>Number of unique proteins in search database containing peptide</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="num_matched_ions" type="xs:nonNegativeInteger">
      <xs:annotation>
        <xs:documentation>Number of peptide fragment ions found in spectrum</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="tot_num_ions" type="xs:nonNegativeInteger">
      <xs:annotation>
        <xs:documentation>Number of peptide fragment ions predicted for peptide</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="calc_neutral_pep_mass" type="xs:float" use="required"/>
    <xs:attribute name="massdiff" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Mass(precursor ion) - Mass(peptide)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger">
      <xs:annotation>
        <xs:documentation>Number of peptide termini consistent with cleavage by sample enzyme</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="num_missed_cleavages" type="xs:integer">
      <xs:annotation>
        <xs:documentation>Number of sample enzyme cleavage sites internal to peptide</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="is_rejected" default="0">
      <xs:annotation>
        <xs:documentation>Potential use in future for user manual validation (0 or 1)</xs:documentation>
      </xs:annotation>
      <xs:simpleType>
        <xs:restriction base="xs:nonNegativeInteger">
          <xs:enumeration value="0"/>
          <xs:enumeration value="1"/>
        </xs:restriction>
      </xs:simpleType>
    </xs:attribute>
    <xs:attribute name="protein_descr" type="xs:string">
      <xs:annotation>
        <xs:documentation>Extracted from search database</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="calc_pI" type="xs:string"/>
    <xs:attribute name="protein_mw" type="xs:double"/>
  </xs:complexType>
  <xs:unique name="unique_result_analysis_id">
    <xs:annotation>
      <xs:documentation>analysis and id must be unique within a search_hit</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="./pepx:analysis_result"/>
    <xs:field xpath="@analysis"/>
    <xs:field xpath="@id"/>
  </xs:unique>
</xs:element>

element msms_pipeline_analysis/msms_run_summary/spectrum_query/search_result/search_hit/alternative_protein
diagram
namespace http://regis-web.systemsbiology.net/pepXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
protein  xs:stringrequired      
protein_descr  xs:string      
num_tol_term  xs:nonNegativeInteger      
protein_mw  xs:double      
annotation
documentation 
Other protein in search database that contains peptide
source
<xs:element name="alternative_protein" minOccurs="0" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>Other protein in search database that contains peptide</xs:documentation>
  </xs:annotation>
  <