Schema protXML_v3.xsd


schema location:  http://localhost/protXML_v3.xsd
attribute form default: 
element form default:  qualified
targetNamespace:  http://regis-web.systemsbiology.net/protXML
 
Elements  Simple types 
ASAP_prot_analysis_summary  positiveInt 
ASAP_pvalue_analysis_summary 
ASAPRatio 
ASAPRatio_pvalue 
libra_result 
libra_summary 
protein_summary 
proteinprophet_details 
XPress_analysis_summary 


element ASAP_prot_analysis_summary
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
version  xs:string      
binary_ref_files  xs:string      
min_peptide_probability  xs:doublerequired      
min_peptide_weight  xs:doublerequired      
min_protein_probability  xs:doublerequired      
reference_isotope  xs:string      
source 
<xs:element name="ASAP_prot_analysis_summary">
  <xs:complexType>
    <xs:attribute name="version" type="xs:string"/>
    <xs:attribute name="binary_ref_files" type="xs:string"/>
    <xs:attribute name="min_peptide_probability" type="xs:double" use="required"/>
    <xs:attribute name="min_peptide_weight" type="xs:double" use="required"/>
    <xs:attribute name="min_protein_probability" type="xs:double" use="required"/>
    <xs:attribute name="reference_isotope" type="xs:string"/>
  </xs:complexType>
</xs:element>

element ASAP_pvalue_analysis_summary
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
asapratio_id  xs:nonNegativeInteger  1    
background_ratio_mean  xs:doublerequired      
background_ratio_stdev  xs:doublerequired      
background_fitting_error  xs:doublerequired      
analysis_distribution_file  xs:stringrequired      
full_analysis_distr_file  xs:string      
asap_prot_id  xs:nonNegativeInteger  1    
source 
<xs:element name="ASAP_pvalue_analysis_summary">
  <xs:complexType>
    <xs:attribute name="asapratio_id" type="xs:nonNegativeInteger" default="1"/>
    <xs:attribute name="background_ratio_mean" type="xs:double" use="required"/>
    <xs:attribute name="background_ratio_stdev" type="xs:double" use="required"/>
    <xs:attribute name="background_fitting_error" type="xs:double" use="required"/>
    <xs:attribute name="analysis_distribution_file" type="xs:string" use="required"/>
    <xs:attribute name="full_analysis_distr_file" type="xs:string"/>
    <xs:attribute name="asap_prot_id" type="xs:nonNegativeInteger" default="1"/>
  </xs:complexType>
</xs:element>

element ASAPRatio
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
content complex
children ASAP_Seq
attributes
Name  Type  Use  Default  Fixed  Annotation
ratio_mean  xs:doublerequired      
ratio_standard_dev  xs:doublerequired      
ratio_number_peptides  xs:nonNegativeIntegerrequired      
heavy2light_ratio_mean  xs:double      
heavy2light_ratio_standard_dev  xs:double      
description  xs:string      
status  xs:string      
peptide_inds  xs:string      
annotation
documentation 
Results of ASAPRatio quantitation of protein
source 
<xs:element name="ASAPRatio">
  <xs:annotation>
    <xs:documentation>Results of ASAPRatio quantitation of protein</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="ASAP_Seq" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="ASAP_Peak" maxOccurs="unbounded">
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="ASAP_Dta" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:attribute name="peptide_index" type="xs:string" use="required"/>
                      <xs:attribute name="include" type="xs:string" use="required"/>
                    </xs:complexType>
                  </xs:element>
                </xs:sequence>
                <xs:attribute name="status" type="xs:string" use="required"/>
                <xs:attribute name="include" type="xs:string" use="required"/>
                <xs:attribute name="datanum" type="xs:nonNegativeInteger" use="required"/>
                <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
                <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
                <xs:attribute name="weight" type="xs:double" use="required"/>
                <xs:attribute name="peptide_binary_ind" type="xs:string" use="required"/>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="status" type="xs:string" use="required"/>
          <xs:attribute name="include" type="xs:string" use="required"/>
          <xs:attribute name="datanum" type="xs:nonNegativeInteger" use="required"/>
          <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
          <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
          <xs:attribute name="weight" type="xs:double" use="required"/>
          <xs:attribute name="light_sequence" type="xs:string" use="required"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
    <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
    <xs:attribute name="ratio_number_peptides" type="xs:nonNegativeInteger" use="required"/>
    <xs:attribute name="heavy2light_ratio_mean" type="xs:double"/>
    <xs:attribute name="heavy2light_ratio_standard_dev" type="xs:double"/>
    <xs:attribute name="description" type="xs:string"/>
    <xs:attribute name="status" type="xs:string"/>
    <xs:attribute name="peptide_inds" type="xs:string"/>
  </xs:complexType>
</xs:element>

element ASAPRatio/ASAP_Seq
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
children ASAP_Peak
attributes
Name  Type  Use  Default  Fixed  Annotation
status  xs:stringrequired      
include  xs:stringrequired      
datanum  xs:nonNegativeIntegerrequired      
ratio_mean  xs:doublerequired      
ratio_standard_dev  xs:doublerequired      
weight  xs:doublerequired      
light_sequence  xs:stringrequired      
source 
<xs:element name="ASAP_Seq" minOccurs="0" maxOccurs="unbounded">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="ASAP_Peak" maxOccurs="unbounded">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="ASAP_Dta" maxOccurs="unbounded">
              <xs:complexType>
                <xs:attribute name="peptide_index" type="xs:string" use="required"/>
                <xs:attribute name="include" type="xs:string" use="required"/>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="status" type="xs:string" use="required"/>
          <xs:attribute name="include" type="xs:string" use="required"/>
          <xs:attribute name="datanum" type="xs:nonNegativeInteger" use="required"/>
          <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
          <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
          <xs:attribute name="weight" type="xs:double" use="required"/>
          <xs:attribute name="peptide_binary_ind" type="xs:string" use="required"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="status" type="xs:string" use="required"/>
    <xs:attribute name="include" type="xs:string" use="required"/>
    <xs:attribute name="datanum" type="xs:nonNegativeInteger" use="required"/>
    <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
    <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
    <xs:attribute name="weight" type="xs:double" use="required"/>
    <xs:attribute name="light_sequence" type="xs:string" use="required"/>
  </xs:complexType>
</xs:element>

element ASAPRatio/ASAP_Seq/ASAP_Peak
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
children ASAP_Dta
attributes
Name  Type  Use  Default  Fixed  Annotation
status  xs:stringrequired      
include  xs:stringrequired      
datanum  xs:nonNegativeIntegerrequired      
ratio_mean  xs:doublerequired      
ratio_standard_dev  xs:doublerequired      
weight  xs:doublerequired      
peptide_binary_ind  xs:stringrequired      
source 
<xs:element name="ASAP_Peak" maxOccurs="unbounded">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="ASAP_Dta" maxOccurs="unbounded">
        <xs:complexType>
          <xs:attribute name="peptide_index" type="xs:string" use="required"/>
          <xs:attribute name="include" type="xs:string" use="required"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="status" type="xs:string" use="required"/>
    <xs:attribute name="include" type="xs:string" use="required"/>
    <xs:attribute name="datanum" type="xs:nonNegativeInteger" use="required"/>
    <xs:attribute name="ratio_mean" type="xs:double" use="required"/>
    <xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
    <xs:attribute name="weight" type="xs:double" use="required"/>
    <xs:attribute name="peptide_binary_ind" type="xs:string" use="required"/>
  </xs:complexType>
</xs:element>

element ASAPRatio/ASAP_Seq/ASAP_Peak/ASAP_Dta
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
peptide_index  xs:stringrequired      
include  xs:stringrequired      
source 
<xs:element name="ASAP_Dta" maxOccurs="unbounded">
  <xs:complexType>
    <xs:attribute name="peptide_index" type="xs:string" use="required"/>
    <xs:attribute name="include" type="xs:string" use="required"/>
  </xs:complexType>
</xs:element>

element ASAPRatio_pvalue
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
adj_ratio_mean  xs:doublerequired      
documentation 
Ratio adjusted for dataset mean value
adj_ratio_standard_dev  xs:doublerequired      
documentation 
Error adjusted for dataset mean value
heavy2light_adj_ratio_mean  xs:double      
documentation 
Heavy2light ratio adjusted for dataset mean value
heavy2light_adj_ratio_standard_dev  xs:double      
documentation 
Heavy2light error adjusted for dataset mean value
pvalue  xs:double      
documentation 
pvalue (probability of ratio due by chance to 1:1 protein)
decimal_pvalue  xs:double      
documentation 
decimal representation of pvalue
annotation
documentation 
Results of ASAPRatio pvalue analysis (adjusting ASAPRatio ratios for offset of dataset, and determining whether ratios are significantly different from chance values originating from 1:1 proteins)
source 
<xs:element name="ASAPRatio_pvalue">
  <xs:annotation>
    <xs:documentation>Results of ASAPRatio pvalue analysis (adjusting ASAPRatio ratios for offset of dataset, and determining whether ratios are significantly different from chance values originating from 1:1 proteins)</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="adj_ratio_mean" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>Ratio adjusted for dataset mean value</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="adj_ratio_standard_dev" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>Error adjusted for dataset mean value</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="heavy2light_adj_ratio_mean" type="xs:double">
      <xs:annotation>
        <xs:documentation>Heavy2light ratio adjusted for dataset mean value</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="heavy2light_adj_ratio_standard_dev" type="xs:double">
      <xs:annotation>
        <xs:documentation>Heavy2light error adjusted for dataset mean value</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="pvalue" type="xs:double">
      <xs:annotation>
        <xs:documentation>pvalue (probability of ratio due by chance to 1:1 protein)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="decimal_pvalue" type="xs:double">
      <xs:annotation>
        <xs:documentation>decimal representation of pvalue</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element libra_result
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
content complex
children intensity
attributes
Name  Type  Use  Default  Fixed  Annotation
number  xs:nonNegativeIntegerrequired      
identity constraints
  Name  Refer  Selector  Field(s)  
unique  libra_result_channel_index    .  @channel  
source 
<xs:element name="libra_result">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="intensity" maxOccurs="unbounded">
        <xs:complexType>
          <xs:attribute name="mz" type="xs:float" use="required"/>
          <xs:attribute name="ratio" type="xs:float" use="required"/>
          <xs:attribute name="error" type="xs:float" use="required"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="number" type="xs:nonNegativeInteger" use="required"/>
  </xs:complexType>
  <xs:unique name="libra_result_channel_index">
    <xs:selector xpath="."/>
    <xs:field xpath="@channel"/>
  </xs:unique>
</xs:element>

element libra_result/intensity
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
mz  xs:floatrequired      
ratio  xs:floatrequired      
error  xs:floatrequired      
source 
<xs:element name="intensity" maxOccurs="unbounded">
  <xs:complexType>
    <xs:attribute name="mz" type="xs:float" use="required"/>
    <xs:attribute name="ratio" type="xs:float" use="required"/>
    <xs:attribute name="error" type="xs:float" use="required"/>
  </xs:complexType>
</xs:element>

element libra_summary
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
content complex
children fragment_masses isotopic_contributions
attributes
Name  Type  Use  Default  Fixed  Annotation
mass_tolerance  xs:floatrequired      
centroiding_preference  xs:intrequired      
normalization  xs:intrequired      
output_type  xs:intrequired      
channel_code  xs:string      
min_pep_prob  xs:floatrequired      
min_pep_wt  xs:floatrequired      
min_prot_prob  xs:floatrequired      
identity constraints
  Name  Refer  Selector  Field(s)  
key  libra_channel_index    ./protx:fragment_masses  @channel  
keyref  libra_contr_channel_index_ref  libra_channel_index  ./protx:isotopic_contributions/protx:contributing_channel  @channel  
keyref  libra_aff_channel_index_ref  libra_channel_index  ./protx:isotopic_contributions/protx:contributing_channel/protx:affected_channel  @channel  
source 
<xs:element name="libra_summary">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="fragment_masses" maxOccurs="unbounded">
        <xs:complexType>
          <xs:attribute name="channel" type="positiveInt" use="required"/>
          <xs:attribute name="mz" type="xs:float" use="required"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="isotopic_contributions" minOccurs="0">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="contributing_channel" maxOccurs="unbounded">
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="affected_channel" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:attribute name="channel" type="positiveInt" use="required"/>
                      <xs:attribute name="correction" type="xs:float" use="required"/>
                    </xs:complexType>
                  </xs:element>
                </xs:sequence>
                <xs:attribute name="channel" type="positiveInt" use="required"/>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="mass_tolerance" type="xs:float" use="required"/>
    <xs:attribute name="centroiding_preference" type="xs:int" use="required"/>
    <xs:attribute name="normalization" type="xs:int" use="required"/>
    <xs:attribute name="output_type" type="xs:int" use="required"/>
    <xs:attribute name="channel_code" type="xs:string"/>
    <xs:attribute name="min_pep_prob" type="xs:float" use="required"/>
    <xs:attribute name="min_pep_wt" type="xs:float" use="required"/>
    <xs:attribute name="min_prot_prob" type="xs:float" use="required"/>
  </xs:complexType>
  <xs:key name="libra_channel_index">
    <xs:selector xpath="./protx:fragment_masses"/>
    <xs:field xpath="@channel"/>
  </xs:key>
  <xs:keyref name="libra_contr_channel_index_ref" refer="libra_channel_index">
    <xs:selector xpath="./protx:isotopic_contributions/protx:contributing_channel"/>
    <xs:field xpath="@channel"/>
  </xs:keyref>
  <xs:keyref name="libra_aff_channel_index_ref" refer="libra_channel_index">
    <xs:selector xpath="./protx:isotopic_contributions/protx:contributing_channel/protx:affected_channel"/>
    <xs:field xpath="@channel"/>
  </xs:keyref>
</xs:element>

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

element libra_summary/isotopic_contributions
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
children contributing_channel
source 
<xs:element name="isotopic_contributions" minOccurs="0">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="contributing_channel" maxOccurs="unbounded">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="affected_channel" maxOccurs="unbounded">
              <xs:complexType>
                <xs:attribute name="channel" type="positiveInt" use="required"/>
                <xs:attribute name="correction" type="xs:float" use="required"/>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="channel" type="positiveInt" use="required"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
  </xs:complexType>
</xs:element>

element libra_summary/isotopic_contributions/contributing_channel
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
children affected_channel
attributes
Name  Type  Use  Default  Fixed  Annotation
channel  positiveIntrequired      
source 
<xs:element name="contributing_channel" maxOccurs="unbounded">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="affected_channel" maxOccurs="unbounded">
        <xs:complexType>
          <xs:attribute name="channel" type="positiveInt" use="required"/>
          <xs:attribute name="correction" type="xs:float" use="required"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="channel" type="positiveInt" use="required"/>
  </xs:complexType>
</xs:element>

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

element protein_summary
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
content complex
children protein_summary_header analysis_summary dataset_derivation protein_group
attributes
Name  Type  Use  Default  Fixed  Annotation
summary_xml  xs:string      
identity constraints
  Name  Refer  Selector  Field(s)  
key  summary_analysis_id    ./protx:analysis_summary  @analysis  
@id  
keyref  result_analysis_id  summary_analysis_id  ./protx:protein_group/protx:protein/protx:analysis_result  @analysis  
@id  
unique  unique_group_number    ./protx:protein_group  @group_number  
source 
<xs:element name="protein_summary">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="protein_summary_header">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="program_details">
              <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 used to infer protein identifications</xs:documentation>
                    </xs:annotation>
                  </xs:any>
                </xs:sequence>
                <xs:attribute name="analysis" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>Name of analysis used for protein identifications</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="time" type="xs:dateTime" use="required">
                  <xs:annotation>
                    <xs:documentation>Time of analysis</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="version" type="xs:string"/>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="reference_database" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>full path database name</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="win-cyg_reference_database" type="xs:string">
            <xs:annotation>
              <xs:documentation>windows full path database</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="residue_substitution_list" type="xs:string">
            <xs:annotation>
              <xs:documentation>residues considered equivalent when comparing peptides</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="organism" type="xs:string">
            <xs:annotation>
              <xs:documentation>sample organism (used for annotation purposes)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="source_files" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>input pepXML files</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="source_files_alt" type="xs:string" use="required"/>
          <xs:attribute name="win-cyg_source_files" type="xs:string">
            <xs:annotation>
              <xs:documentation>windows pepXML file names</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="source_file_xtn" type="xs:string">
            <xs:annotation>
              <xs:documentation>file type (if not pepXML)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="min_peptide_probability" type="xs:double" use="required">
            <xs:annotation>
              <xs:documentation>minimum adjusted peptide probability contributing to protein probability</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="min_peptide_weight" type="xs:double" use="required">
            <xs:annotation>
              <xs:documentation>minimum peptide weight contributing to protein probability</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="num_predicted_correct_prots" type="xs:double" use="required">
            <xs:annotation>
              <xs:documentation>total number of predicted correct protein ids (sum of probabilities)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="num_input_1_spectra" type="xs:integer" use="required">
            <xs:annotation>
              <xs:documentation>number of spectra from 1+ precursor ions</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="num_input_2_spectra" type="xs:integer" use="required">
            <xs:annotation>
              <xs:documentation>number of spectra from 2+ precursor ions</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="num_input_3_spectra" type="xs:integer" use="required">
            <xs:annotation>
              <xs:documentation>number of spectra from 3+ precursor ions</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="initial_min_peptide_prob" type="xs:double" use="required">
            <xs:annotation>
              <xs:documentation>minimum initial peptide probability to contribute to analysis</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="total_no_spectrum_ids" type="xs:double">
            <xs:annotation>
              <xs:documentation>total estimated number of correct peptide assignments in dataset</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="sample_enzyme" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>enzyme applied to sample prior to MS/MS</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="analysis_summary" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:sequence>
            <xs:any namespace="##any" processContents="lax" minOccurs="0">
              <xs:annotation>
                <xs:documentation>time of analysis</xs:documentation>
              </xs:annotation>
            </xs:any>
          </xs:sequence>
          <xs:attribute name="analysis" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>name of protein-level analysis</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="time" type="xs:dateTime" use="required">
            <xs:annotation>
              <xs:documentation>time of analysis</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="id" type="xs:nonNegativeInteger" use="required">
            <xs:annotation>
              <xs:documentation>unique id corresponding with analysis_result elements</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="dataset_derivation">
        <xs:annotation>
          <xs:documentation>Source and filtering criteria used to generate dataset</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence minOccurs="0" maxOccurs="unbounded">
            <xs:element name="data_filter">
              <xs:complexType>
                <xs:attribute name="number" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>generation number (0 is root)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <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:string" use="required">
            <xs:annotation>
              <xs:documentation>number preceding filter generations</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="protein_group" maxOccurs="unbounded">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="protein" maxOccurs="unbounded">
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="parameter" minOccurs="0" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:simpleContent>
                        <xs:extension base="xs:anySimpleType">
                          <xs:attribute name="name" type="xs:string" use="required"/>
                          <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
                          <xs:attribute name="type" type="xs:anySimpleType"/>
                        </xs:extension>
                      </xs:simpleContent>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:sequence>
                        <xs:any namespace="##any" processContents="lax">
                          <xs:annotation>
                            <xs:documentation>wildcard to be substituted with element storing analysis-specific result info</xs:documentation>
                          </xs:annotation>
                        </xs:any>
                      </xs:sequence>
                      <xs:attribute name="analysis" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>name of protein level analysis</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="id" type="xs:nonNegativeInteger" default="1">
                        <xs:annotation>
                          <xs:documentation>unique identifier to analysis_summary element</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="annotation" minOccurs="0">
                    <xs:complexType>
                      <xs:attribute name="protein_description" type="xs:string" use="required"/>
                      <xs:attribute name="ipi_name" type="xs:string"/>
                      <xs:attribute name="refseq_name" type="xs:string"/>
                      <xs:attribute name="swissprot_name" type="xs:string"/>
                      <xs:attribute name="ensembl_name" type="xs:string"/>
                      <xs:attribute name="trembl_name" type="xs:string"/>
                      <xs:attribute name="locus_link_name" type="xs:string"/>
                      <xs:attribute name="flybase" type="xs:string"/>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="indistinguishable_protein" minOccurs="0" maxOccurs="unbounded">
                    <xs:annotation>
                      <xs:documentation>other protein sharing corresponding peptides</xs:documentation>
                    </xs:annotation>
                    <xs:complexType>
                      <xs:sequence>
                        <xs:element name="annotation" minOccurs="0">
                          <xs:annotation>
                            <xs:documentation>protein description</xs:documentation>
                          </xs:annotation>
                          <xs:complexType>
                            <xs:attribute name="protein_description" type="xs:string" use="required">
                              <xs:annotation>
                                <xs:documentation>description</xs:documentation>
                              </xs:annotation>
                            </xs:attribute>
                            <xs:attribute name="ipi_name" type="xs:string"/>
                            <xs:attribute name="refseq_name" type="xs:string"/>
                            <xs:attribute name="swissprot_name" type="xs:string"/>
                            <xs:attribute name="ensembl_name" type="xs:string"/>
                            <xs:attribute name="trembl_name" type="xs:string"/>
                            <xs:attribute name="locus_link_name" type="xs:string"/>
                            <xs:attribute name="flybase" type="xs:string"/>
                          </xs:complexType>
                        </xs:element>
                      </xs:sequence>
                      <xs:attribute name="protein_name" type="xs:string" use="required"/>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="peptide" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:sequence>
                        <xs:element name="parameter" minOccurs="0" maxOccurs="unbounded">
                          <xs:complexType>
                            <xs:simpleContent>
                              <xs:extension base="xs:anySimpleType">
                                <xs:attribute name="name" type="xs:string" use="required"/>
                                <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
                                <xs:attribute name="type" type="xs:anySimpleType"/>
                              </xs:extension>
                            </xs:simpleContent>
                          </xs:complexType>
                        </xs:element>
                        <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
                          <xs:complexType>
                            <xs:sequence>
                              <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
                                <xs:complexType>
                                  <xs:attribute name="position" type="xs:string" use="required"/>
                                  <xs:attribute name="mass" type="xs:string" use="required"/>
                                </xs:complexType>
                              </xs:element>
                            </xs:sequence>
                            <xs:attribute name="mod_nterm_mass" type="xs:string"/>
                            <xs:attribute name="mod_cterm_mass" type="xs:string"/>
                            <xs:attribute name="modified_peptide" type="xs:string"/>
                          </xs:complexType>
                        </xs:element>
                        <xs:element name="peptide_parent_protein" minOccurs="0" maxOccurs="unbounded">
                          <xs:complexType>
                            <xs:attribute name="protein_name" type="xs:string" use="required"/>
                          </xs:complexType>
                        </xs:element>
                        <xs:element name="indistinguishable_peptide" minOccurs="0" maxOccurs="unbounded">
                          <xs:complexType>
                            <xs:sequence>
                              <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
                                <xs:complexType>
                                  <xs:sequence>
                                    <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
                                      <xs:complexType>
                                        <xs:attribute name="position" type="xs:string" use="required"/>
                                        <xs:attribute name="mass" type="xs:string" use="required"/>
                                      </xs:complexType>
                                    </xs:element>
                                  </xs:sequence>
                                  <xs:attribute name="mod_nterm_mass" type="xs:string"/>
                                  <xs:attribute name="mod_cterm_mass" type="xs:string"/>
                                  <xs:attribute name="modified_peptide" type="xs:string"/>
                                </xs:complexType>
                              </xs:element>
                            </xs:sequence>
                            <xs:attribute name="peptide_sequence" type="xs:string" use="required"/>
                          </xs:complexType>
                        </xs:element>
                      </xs:sequence>
                      <xs:attribute name="peptide_sequence" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>unmodified aa sequence</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="charge" type="xs:positiveInteger" use="required">
                        <xs:annotation>
                          <xs:documentation>precursor ion charge</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="initial_probability" type="xs:double" use="required">
                        <xs:annotation>
                          <xs:documentation>prior to nsp adjustment</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="nsp_adjusted_probability" type="xs:double" use="optional">
                        <xs:annotation>
                          <xs:documentation>after nsp adjustment</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="peptide_group_designator" type="xs:string">
                        <xs:annotation>
                          <xs:documentation>link to spectra with other precursor ion charges assigned to same peptide</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="weight" type="xs:double" default="1.0"/>
                      <xs:attribute name="is_nondegenerate_evidence" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>confidence that peptide corresponds with this protein (rather than others in which it occurs)</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="n_enzymatic_termini" type="xs:nonNegativeInteger" use="required">
                        <xs:annotation>
                          <xs:documentation>number of termini consistent with proteolytic cleavage</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="n_sibling_peptides" type="xs:double">
                        <xs:annotation>
                          <xs:documentation>estimated number of sibling peptides (other identified peptides corresponding to same protein)</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="n_sibling_peptides_bin" type="xs:integer" default="0">
                        <xs:annotation>
                          <xs:documentation>discretized nsp value</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="n_instances" type="xs:integer" use="required">
                        <xs:annotation>
                          <xs:documentation>number of times peptide assigned to spectrum of precursor ion charge in dataset</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="calc_neutral_pep_mass" type="xs:double"/>
                      <xs:attribute name="is_contributing_evidence" type="xs:string" use="required"/>
                    </xs:complexType>
                  </xs:element>
                </xs:sequence>
                <xs:attribute name="protein_name" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>database protein name</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="probability" type="xs:double" use="required">
                  <xs:annotation>
                    <xs:documentation>confidence of protein id</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="percent_coverage" type="xs:double">
                  <xs:annotation>
                    <xs:documentation>percent of protein sequence covered by corresponding peptides</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="n_indistinguishable_proteins" type="xs:integer" use="required">
                  <xs:annotation>
                    <xs:documentation>number of proteins with identical corresponding peptides</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="unique_stripped_peptides" type="xs:string"/>
                <xs:attribute name="group_sibling_id" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>protein group id</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="total_number_peptides" type="xs:integer">
                  <xs:annotation>
                    <xs:documentation>total number of corresponding peptides that contributed to protein probability</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="subsuming_protein_entry" type="xs:string">
                  <xs:annotation>
                    <xs:documentation>name of portein containing all corresponding peptides, and more</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="pct_spectrum_ids" type="xs:string">
                  <xs:annotation>
                    <xs:documentation>fraction of correct dataset peptide identifications corresponding to protein</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
              <xs:unique name="unique_result_analysis_id">
                <xs:annotation>
                  <xs:documentation>can only have one analysis/id combination within each protein element</xs:documentation>
                </xs:annotation>
                <xs:selector xpath="./protx:analysis_result"/>
                <xs:field xpath="@analysis"/>
                <xs:field xpath="@id"/>
              </xs:unique>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="group_number" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>index</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="pseudo_name" type="xs:string"/>
          <xs:attribute name="probability" type="xs:double" use="required">
            <xs:annotation>
              <xs:documentation>group probability (taking contributions from all group member proteins)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
        <xs:unique name="unique_group_sibling_id">
          <xs:annotation>
            <xs:documentation>Each group_sibling_id must be unique within a protein group</xs:documentation>
          </xs:annotation>
          <xs:selector xpath="./protx:protein"/>
          <xs:field xpath="@group_sibling_id"/>
        </xs:unique>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="summary_xml" type="xs:string"/>
  </xs:complexType>
  <xs:key name="summary_analysis_id">
    <xs:selector xpath="./protx:analysis_summary"/>
    <xs:field xpath="@analysis"/>
    <xs:field xpath="@id"/>
  </xs:key>
  <xs:keyref name="result_analysis_id" refer="summary_analysis_id">
    <xs:annotation>
      <xs:documentation>analysis and id must correspond with those fields in an analysis_summary element</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="./protx:protein_group/protx:protein/protx:analysis_result"/>
    <xs:field xpath="@analysis"/>
    <xs:field xpath="@id"/>
  </xs:keyref>
  <xs:unique name="unique_group_number">
    <xs:annotation>
      <xs:documentation>Requires group numbers be unique for entire dataset</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="./protx:protein_group"/>
    <xs:field xpath="@group_number"/>
  </xs:unique>
</xs:element>

element protein_summary/protein_summary_header
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
children program_details
attributes
Name  Type  Use  Default  Fixed  Annotation
reference_database  xs:stringrequired      
documentation 
full path database name
win-cyg_reference_database  xs:string      
documentation 
windows full path database
residue_substitution_list  xs:string      
documentation 
residues considered equivalent when comparing peptides
organism  xs:string      
documentation 
sample organism (used for annotation purposes)
source_files  xs:stringrequired      
documentation 
input pepXML files
source_files_alt  xs:stringrequired      
win-cyg_source_files  xs:string      
documentation 
windows pepXML file names
source_file_xtn  xs:string      
documentation 
file type (if not pepXML)
min_peptide_probability  xs:doublerequired      
documentation 
minimum adjusted peptide probability contributing to protein probability
min_peptide_weight  xs:doublerequired      
documentation 
minimum peptide weight contributing to protein probability
num_predicted_correct_prots  xs:doublerequired      
documentation 
total number of predicted correct protein ids (sum of probabilities)
num_input_1_spectra  xs:integerrequired      
documentation 
number of spectra from 1+ precursor ions
num_input_2_spectra  xs:integerrequired      
documentation 
number of spectra from 2+ precursor ions
num_input_3_spectra  xs:integerrequired      
documentation 
number of spectra from 3+ precursor ions
initial_min_peptide_prob  xs:doublerequired      
documentation 
minimum initial peptide probability to contribute to analysis
total_no_spectrum_ids  xs:double      
documentation 
total estimated number of correct peptide assignments in dataset
sample_enzyme  xs:stringrequired      
documentation 
enzyme applied to sample prior to MS/MS
source 
<xs:element name="protein_summary_header">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="program_details">
        <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 used to infer protein identifications</xs:documentation>
              </xs:annotation>
            </xs:any>
          </xs:sequence>
          <xs:attribute name="analysis" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>Name of analysis used for protein identifications</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="time" type="xs:dateTime" use="required">
            <xs:annotation>
              <xs:documentation>Time of analysis</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="version" type="xs:string"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="reference_database" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>full path database name</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="win-cyg_reference_database" type="xs:string">
      <xs:annotation>
        <xs:documentation>windows full path database</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="residue_substitution_list" type="xs:string">
      <xs:annotation>
        <xs:documentation>residues considered equivalent when comparing peptides</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="organism" type="xs:string">
      <xs:annotation>
        <xs:documentation>sample organism (used for annotation purposes)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="source_files" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>input pepXML files</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="source_files_alt" type="xs:string" use="required"/>
    <xs:attribute name="win-cyg_source_files" type="xs:string">
      <xs:annotation>
        <xs:documentation>windows pepXML file names</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="source_file_xtn" type="xs:string">
      <xs:annotation>
        <xs:documentation>file type (if not pepXML)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="min_peptide_probability" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>minimum adjusted peptide probability contributing to protein probability</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="min_peptide_weight" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>minimum peptide weight contributing to protein probability</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="num_predicted_correct_prots" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>total number of predicted correct protein ids (sum of probabilities)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="num_input_1_spectra" type="xs:integer" use="required">
      <xs:annotation>
        <xs:documentation>number of spectra from 1+ precursor ions</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="num_input_2_spectra" type="xs:integer" use="required">
      <xs:annotation>
        <xs:documentation>number of spectra from 2+ precursor ions</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="num_input_3_spectra" type="xs:integer" use="required">
      <xs:annotation>
        <xs:documentation>number of spectra from 3+ precursor ions</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="initial_min_peptide_prob" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>minimum initial peptide probability to contribute to analysis</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="total_no_spectrum_ids" type="xs:double">
      <xs:annotation>
        <xs:documentation>total estimated number of correct peptide assignments in dataset</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="sample_enzyme" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>enzyme applied to sample prior to MS/MS</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element protein_summary/protein_summary_header/program_details
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
analysis  xs:stringrequired      
documentation 
Name of analysis used for protein identifications
time  xs:dateTimerequired      
documentation 
Time of analysis
version  xs:string      
source 
<xs:element name="program_details">
  <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 used to infer protein identifications</xs:documentation>
        </xs:annotation>
      </xs:any>
    </xs:sequence>
    <xs:attribute name="analysis" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>Name of analysis used for protein identifications</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="time" type="xs:dateTime" use="required">
      <xs:annotation>
        <xs:documentation>Time of analysis</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="version" type="xs:string"/>
  </xs:complexType>
</xs:element>

element protein_summary/analysis_summary
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
analysis  xs:stringrequired      
documentation 
name of protein-level analysis
time  xs:dateTimerequired      
documentation 
time of analysis
id  xs:nonNegativeIntegerrequired      
documentation 
unique id corresponding with analysis_result elements
source 
<xs:element name="analysis_summary" minOccurs="0" maxOccurs="unbounded">
  <xs:complexType>
    <xs:sequence>
      <xs:any namespace="##any" processContents="lax" minOccurs="0">
        <xs:annotation>
          <xs:documentation>time of analysis</xs:documentation>
        </xs:annotation>
      </xs:any>
    </xs:sequence>
    <xs:attribute name="analysis" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>name of protein-level analysis</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="time" type="xs:dateTime" use="required">
      <xs:annotation>
        <xs:documentation>time of analysis</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="id" type="xs:nonNegativeInteger" use="required">
      <xs:annotation>
        <xs:documentation>unique id corresponding with analysis_result elements</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element protein_summary/dataset_derivation
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
children data_filter
attributes
Name  Type  Use  Default  Fixed  Annotation
generation_no  xs:stringrequired      
documentation 
number preceding filter generations
annotation
documentation 
Source and filtering criteria used to generate dataset
source 
<xs:element name="dataset_derivation">
  <xs:annotation>
    <xs:documentation>Source and filtering criteria used to generate dataset</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence minOccurs="0" maxOccurs="unbounded">
      <xs:element name="data_filter">
        <xs:complexType>
          <xs:attribute name="number" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>generation number (0 is root)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <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:string" use="required">
      <xs:annotation>
        <xs:documentation>number preceding filter generations</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element protein_summary/dataset_derivation/data_filter
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
number  xs:stringrequired      
documentation 
generation number (0 is root)
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">
  <xs:complexType>
    <xs:attribute name="number" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>generation number (0 is root)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <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 protein_summary/protein_group
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
children protein
attributes
Name  Type  Use  Default  Fixed  Annotation
group_number  xs:stringrequired      
documentation 
index
pseudo_name  xs:string      
probability  xs:doublerequired      
documentation 
group probability (taking contributions from all group member proteins)
identity constraints
  Name  Refer  Selector  Field(s)  
unique  unique_group_sibling_id    ./protx:protein  @group_sibling_id  
source 
<xs:element name="protein_group" maxOccurs="unbounded">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="protein" maxOccurs="unbounded">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="parameter" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:simpleContent>
                  <xs:extension base="xs:anySimpleType">
                    <xs:attribute name="name" type="xs:string" use="required"/>
                    <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
                    <xs:attribute name="type" type="xs:anySimpleType"/>
                  </xs:extension>
                </xs:simpleContent>
              </xs:complexType>
            </xs:element>
            <xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:sequence>
                  <xs:any namespace="##any" processContents="lax">
                    <xs:annotation>
                      <xs:documentation>wildcard to be substituted with element storing analysis-specific result info</xs:documentation>
                    </xs:annotation>
                  </xs:any>
                </xs:sequence>
                <xs:attribute name="analysis" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>name of protein level analysis</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="id" type="xs:nonNegativeInteger" default="1">
                  <xs:annotation>
                    <xs:documentation>unique identifier to analysis_summary element</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
            <xs:element name="annotation" minOccurs="0">
              <xs:complexType>
                <xs:attribute name="protein_description" type="xs:string" use="required"/>
                <xs:attribute name="ipi_name" type="xs:string"/>
                <xs:attribute name="refseq_name" type="xs:string"/>
                <xs:attribute name="swissprot_name" type="xs:string"/>
                <xs:attribute name="ensembl_name" type="xs:string"/>
                <xs:attribute name="trembl_name" type="xs:string"/>
                <xs:attribute name="locus_link_name" type="xs:string"/>
                <xs:attribute name="flybase" type="xs:string"/>
              </xs:complexType>
            </xs:element>
            <xs:element name="indistinguishable_protein" minOccurs="0" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>other protein sharing corresponding peptides</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="annotation" minOccurs="0">
                    <xs:annotation>
                      <xs:documentation>protein description</xs:documentation>
                    </xs:annotation>
                    <xs:complexType>
                      <xs:attribute name="protein_description" type="xs:string" use="required">
                        <xs:annotation>
                          <xs:documentation>description</xs:documentation>
                        </xs:annotation>
                      </xs:attribute>
                      <xs:attribute name="ipi_name" type="xs:string"/>
                      <xs:attribute name="refseq_name" type="xs:string"/>
                      <xs:attribute name="swissprot_name" type="xs:string"/>
                      <xs:attribute name="ensembl_name" type="xs:string"/>
                      <xs:attribute name="trembl_name" type="xs:string"/>
                      <xs:attribute name="locus_link_name" type="xs:string"/>
                      <xs:attribute name="flybase" type="xs:string"/>
                    </xs:complexType>
                  </xs:element>
                </xs:sequence>
                <xs:attribute name="protein_name" type="xs:string" use="required"/>
              </xs:complexType>
            </xs:element>
            <xs:element name="peptide" maxOccurs="unbounded">
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="parameter" minOccurs="0" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:simpleContent>
                        <xs:extension base="xs:anySimpleType">
                          <xs:attribute name="name" type="xs:string" use="required"/>
                          <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
                          <xs:attribute name="type" type="xs:anySimpleType"/>
                        </xs:extension>
                      </xs:simpleContent>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:sequence>
                        <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
                          <xs:complexType>
                            <xs:attribute name="position" type="xs:string" use="required"/>
                            <xs:attribute name="mass" type="xs:string" use="required"/>
                          </xs:complexType>
                        </xs:element>
                      </xs:sequence>
                      <xs:attribute name="mod_nterm_mass" type="xs:string"/>
                      <xs:attribute name="mod_cterm_mass" type="xs:string"/>
                      <xs:attribute name="modified_peptide" type="xs:string"/>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="peptide_parent_protein" minOccurs="0" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:attribute name="protein_name" type="xs:string" use="required"/>
                    </xs:complexType>
                  </xs:element>
                  <xs:element name="indistinguishable_peptide" minOccurs="0" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:sequence>
                        <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
                          <xs:complexType>
                            <xs:sequence>
                              <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
                                <xs:complexType>
                                  <xs:attribute name="position" type="xs:string" use="required"/>
                                  <xs:attribute name="mass" type="xs:string" use="required"/>
                                </xs:complexType>
                              </xs:element>
                            </xs:sequence>
                            <xs:attribute name="mod_nterm_mass" type="xs:string"/>
                            <xs:attribute name="mod_cterm_mass" type="xs:string"/>
                            <xs:attribute name="modified_peptide" type="xs:string"/>
                          </xs:complexType>
                        </xs:element>
                      </xs:sequence>
                      <xs:attribute name="peptide_sequence" type="xs:string" use="required"/>
                    </xs:complexType>
                  </xs:element>
                </xs:sequence>
                <xs:attribute name="peptide_sequence" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>unmodified aa sequence</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="charge" type="xs:positiveInteger" use="required">
                  <xs:annotation>
                    <xs:documentation>precursor ion charge</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="initial_probability" type="xs:double" use="required">
                  <xs:annotation>
                    <xs:documentation>prior to nsp adjustment</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="nsp_adjusted_probability" type="xs:double" use="optional">
                  <xs:annotation>
                    <xs:documentation>after nsp adjustment</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="peptide_group_designator" type="xs:string">
                  <xs:annotation>
                    <xs:documentation>link to spectra with other precursor ion charges assigned to same peptide</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="weight" type="xs:double" default="1.0"/>
                <xs:attribute name="is_nondegenerate_evidence" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>confidence that peptide corresponds with this protein (rather than others in which it occurs)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="n_enzymatic_termini" type="xs:nonNegativeInteger" use="required">
                  <xs:annotation>
                    <xs:documentation>number of termini consistent with proteolytic cleavage</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="n_sibling_peptides" type="xs:double">
                  <xs:annotation>
                    <xs:documentation>estimated number of sibling peptides (other identified peptides corresponding to same protein)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="n_sibling_peptides_bin" type="xs:integer" default="0">
                  <xs:annotation>
                    <xs:documentation>discretized nsp value</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="n_instances" type="xs:integer" use="required">
                  <xs:annotation>
                    <xs:documentation>number of times peptide assigned to spectrum of precursor ion charge in dataset</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="calc_neutral_pep_mass" type="xs:double"/>
                <xs:attribute name="is_contributing_evidence" type="xs:string" use="required"/>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="protein_name" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>database protein name</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="probability" type="xs:double" use="required">
            <xs:annotation>
              <xs:documentation>confidence of protein id</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="percent_coverage" type="xs:double">
            <xs:annotation>
              <xs:documentation>percent of protein sequence covered by corresponding peptides</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="n_indistinguishable_proteins" type="xs:integer" use="required">
            <xs:annotation>
              <xs:documentation>number of proteins with identical corresponding peptides</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="unique_stripped_peptides" type="xs:string"/>
          <xs:attribute name="group_sibling_id" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>protein group id</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="total_number_peptides" type="xs:integer">
            <xs:annotation>
              <xs:documentation>total number of corresponding peptides that contributed to protein probability</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="subsuming_protein_entry" type="xs:string">
            <xs:annotation>
              <xs:documentation>name of portein containing all corresponding peptides, and more</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="pct_spectrum_ids" type="xs:string">
            <xs:annotation>
              <xs:documentation>fraction of correct dataset peptide identifications corresponding to protein</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
        <xs:unique name="unique_result_analysis_id">
          <xs:annotation>
            <xs:documentation>can only have one analysis/id combination within each protein element</xs:documentation>
          </xs:annotation>
          <xs:selector xpath="./protx:analysis_result"/>
          <xs:field xpath="@analysis"/>
          <xs:field xpath="@id"/>
        </xs:unique>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="group_number" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>index</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="pseudo_name" type="xs:string"/>
    <xs:attribute name="probability" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>group probability (taking contributions from all group member proteins)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
  <xs:unique name="unique_group_sibling_id">
    <xs:annotation>
      <xs:documentation>Each group_sibling_id must be unique within a protein group</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="./protx:protein"/>
    <xs:field xpath="@group_sibling_id"/>
  </xs:unique>
</xs:element>

element protein_summary/protein_group/protein
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
children parameter analysis_result annotation indistinguishable_protein peptide
attributes
Name  Type  Use  Default  Fixed  Annotation
protein_name  xs:stringrequired      
documentation 
database protein name
probability  xs:doublerequired      
documentation 
confidence of protein id
percent_coverage  xs:double      
documentation 
percent of protein sequence covered by corresponding peptides
n_indistinguishable_proteins  xs:integerrequired      
documentation 
number of proteins with identical corresponding peptides
unique_stripped_peptides  xs:string      
group_sibling_id  xs:stringrequired      
documentation 
protein group id
total_number_peptides  xs:integer      
documentation 
total number of corresponding peptides that contributed to protein probability
subsuming_protein_entry  xs:string      
documentation 
name of portein containing all corresponding peptides, and more
pct_spectrum_ids  xs:string      
documentation 
fraction of correct dataset peptide identifications corresponding to protein
identity constraints
  Name  Refer  Selector  Field(s)  
unique  unique_result_analysis_id    ./protx:analysis_result  @analysis  
@id  
source 
<xs:element name="protein" maxOccurs="unbounded">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="parameter" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:simpleContent>
            <xs:extension base="xs:anySimpleType">
              <xs:attribute name="name" type="xs:string" use="required"/>
              <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
              <xs:attribute name="type" type="xs:anySimpleType"/>
            </xs:extension>
          </xs:simpleContent>
        </xs:complexType>
      </xs:element>
      <xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:sequence>
            <xs:any namespace="##any" processContents="lax">
              <xs:annotation>
                <xs:documentation>wildcard to be substituted with element storing analysis-specific result info</xs:documentation>
              </xs:annotation>
            </xs:any>
          </xs:sequence>
          <xs:attribute name="analysis" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>name of protein level analysis</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="id" type="xs:nonNegativeInteger" default="1">
            <xs:annotation>
              <xs:documentation>unique identifier to analysis_summary element</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
      <xs:element name="annotation" minOccurs="0">
        <xs:complexType>
          <xs:attribute name="protein_description" type="xs:string" use="required"/>
          <xs:attribute name="ipi_name" type="xs:string"/>
          <xs:attribute name="refseq_name" type="xs:string"/>
          <xs:attribute name="swissprot_name" type="xs:string"/>
          <xs:attribute name="ensembl_name" type="xs:string"/>
          <xs:attribute name="trembl_name" type="xs:string"/>
          <xs:attribute name="locus_link_name" type="xs:string"/>
          <xs:attribute name="flybase" type="xs:string"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="indistinguishable_protein" minOccurs="0" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>other protein sharing corresponding peptides</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="annotation" minOccurs="0">
              <xs:annotation>
                <xs:documentation>protein description</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:attribute name="protein_description" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>description</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="ipi_name" type="xs:string"/>
                <xs:attribute name="refseq_name" type="xs:string"/>
                <xs:attribute name="swissprot_name" type="xs:string"/>
                <xs:attribute name="ensembl_name" type="xs:string"/>
                <xs:attribute name="trembl_name" type="xs:string"/>
                <xs:attribute name="locus_link_name" type="xs:string"/>
                <xs:attribute name="flybase" type="xs:string"/>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="protein_name" type="xs:string" use="required"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="peptide" maxOccurs="unbounded">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="parameter" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:simpleContent>
                  <xs:extension base="xs:anySimpleType">
                    <xs:attribute name="name" type="xs:string" use="required"/>
                    <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
                    <xs:attribute name="type" type="xs:anySimpleType"/>
                  </xs:extension>
                </xs:simpleContent>
              </xs:complexType>
            </xs:element>
            <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:attribute name="position" type="xs:string" use="required"/>
                      <xs:attribute name="mass" type="xs:string" use="required"/>
                    </xs:complexType>
                  </xs:element>
                </xs:sequence>
                <xs:attribute name="mod_nterm_mass" type="xs:string"/>
                <xs:attribute name="mod_cterm_mass" type="xs:string"/>
                <xs:attribute name="modified_peptide" type="xs:string"/>
              </xs:complexType>
            </xs:element>
            <xs:element name="peptide_parent_protein" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:attribute name="protein_name" type="xs:string" use="required"/>
              </xs:complexType>
            </xs:element>
            <xs:element name="indistinguishable_peptide" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:sequence>
                        <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
                          <xs:complexType>
                            <xs:attribute name="position" type="xs:string" use="required"/>
                            <xs:attribute name="mass" type="xs:string" use="required"/>
                          </xs:complexType>
                        </xs:element>
                      </xs:sequence>
                      <xs:attribute name="mod_nterm_mass" type="xs:string"/>
                      <xs:attribute name="mod_cterm_mass" type="xs:string"/>
                      <xs:attribute name="modified_peptide" type="xs:string"/>
                    </xs:complexType>
                  </xs:element>
                </xs:sequence>
                <xs:attribute name="peptide_sequence" type="xs:string" use="required"/>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="peptide_sequence" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>unmodified aa sequence</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="charge" type="xs:positiveInteger" use="required">
            <xs:annotation>
              <xs:documentation>precursor ion charge</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="initial_probability" type="xs:double" use="required">
            <xs:annotation>
              <xs:documentation>prior to nsp adjustment</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="nsp_adjusted_probability" type="xs:double" use="optional">
            <xs:annotation>
              <xs:documentation>after nsp adjustment</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="peptide_group_designator" type="xs:string">
            <xs:annotation>
              <xs:documentation>link to spectra with other precursor ion charges assigned to same peptide</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="weight" type="xs:double" default="1.0"/>
          <xs:attribute name="is_nondegenerate_evidence" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>confidence that peptide corresponds with this protein (rather than others in which it occurs)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="n_enzymatic_termini" type="xs:nonNegativeInteger" use="required">
            <xs:annotation>
              <xs:documentation>number of termini consistent with proteolytic cleavage</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="n_sibling_peptides" type="xs:double">
            <xs:annotation>
              <xs:documentation>estimated number of sibling peptides (other identified peptides corresponding to same protein)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="n_sibling_peptides_bin" type="xs:integer" default="0">
            <xs:annotation>
              <xs:documentation>discretized nsp value</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="n_instances" type="xs:integer" use="required">
            <xs:annotation>
              <xs:documentation>number of times peptide assigned to spectrum of precursor ion charge in dataset</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="calc_neutral_pep_mass" type="xs:double"/>
          <xs:attribute name="is_contributing_evidence" type="xs:string" use="required"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="protein_name" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>database protein name</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="probability" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>confidence of protein id</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="percent_coverage" type="xs:double">
      <xs:annotation>
        <xs:documentation>percent of protein sequence covered by corresponding peptides</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="n_indistinguishable_proteins" type="xs:integer" use="required">
      <xs:annotation>
        <xs:documentation>number of proteins with identical corresponding peptides</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="unique_stripped_peptides" type="xs:string"/>
    <xs:attribute name="group_sibling_id" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>protein group id</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="total_number_peptides" type="xs:integer">
      <xs:annotation>
        <xs:documentation>total number of corresponding peptides that contributed to protein probability</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="subsuming_protein_entry" type="xs:string">
      <xs:annotation>
        <xs:documentation>name of portein containing all corresponding peptides, and more</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="pct_spectrum_ids" type="xs:string">
      <xs:annotation>
        <xs:documentation>fraction of correct dataset peptide identifications corresponding to protein</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
  <xs:unique name="unique_result_analysis_id">
    <xs:annotation>
      <xs:documentation>can only have one analysis/id combination within each protein element</xs:documentation>
    </xs:annotation>
    <xs:selector xpath="./protx:analysis_result"/>
    <xs:field xpath="@analysis"/>
    <xs:field xpath="@id"/>
  </xs:unique>
</xs:element>

element protein_summary/protein_group/protein/parameter
diagram
namespace http://regis-web.systemsbiology.net/protXML
type extension of xs:anySimpleType
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" minOccurs="0" maxOccurs="unbounded">
  <xs:complexType>
    <xs:simpleContent>
      <xs:extension base="xs:anySimpleType">
        <xs:attribute name="name" type="xs:string" use="required"/>
        <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
        <xs:attribute name="type" type="xs:anySimpleType"/>
      </xs:extension>
    </xs:simpleContent>
  </xs:complexType>
</xs:element>

element protein_summary/protein_group/protein/analysis_result
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
analysis  xs:stringrequired      
documentation 
name of protein level analysis
id  xs:nonNegativeInteger  1    
documentation 
unique identifier to analysis_summary element
source 
<xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">
  <xs:complexType>
    <xs:sequence>
      <xs:any namespace="##any" processContents="lax">
        <xs:annotation>
          <xs:documentation>wildcard to be substituted with element storing analysis-specific result info</xs:documentation>
        </xs:annotation>
      </xs:any>
    </xs:sequence>
    <xs:attribute name="analysis" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>name of protein level analysis</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="id" type="xs:nonNegativeInteger" default="1">
      <xs:annotation>
        <xs:documentation>unique identifier to analysis_summary element</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element protein_summary/protein_group/protein/annotation
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
protein_description  xs:stringrequired      
ipi_name  xs:string      
refseq_name  xs:string      
swissprot_name  xs:string      
ensembl_name  xs:string      
trembl_name  xs:string      
locus_link_name  xs:string      
flybase  xs:string      
source 
<xs:element name="annotation" minOccurs="0">
  <xs:complexType>
    <xs:attribute name="protein_description" type="xs:string" use="required"/>
    <xs:attribute name="ipi_name" type="xs:string"/>
    <xs:attribute name="refseq_name" type="xs:string"/>
    <xs:attribute name="swissprot_name" type="xs:string"/>
    <xs:attribute name="ensembl_name" type="xs:string"/>
    <xs:attribute name="trembl_name" type="xs:string"/>
    <xs:attribute name="locus_link_name" type="xs:string"/>
    <xs:attribute name="flybase" type="xs:string"/>
  </xs:complexType>
</xs:element>

element protein_summary/protein_group/protein/indistinguishable_protein
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
children annotation
attributes
Name  Type  Use  Default  Fixed  Annotation
protein_name  xs:stringrequired      
annotation
documentation 
other protein sharing corresponding peptides
source 
<xs:element name="indistinguishable_protein" minOccurs="0" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>other protein sharing corresponding peptides</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="annotation" minOccurs="0">
        <xs:annotation>
          <xs:documentation>protein description</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="protein_description" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>description</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="ipi_name" type="xs:string"/>
          <xs:attribute name="refseq_name" type="xs:string"/>
          <xs:attribute name="swissprot_name" type="xs:string"/>
          <xs:attribute name="ensembl_name" type="xs:string"/>
          <xs:attribute name="trembl_name" type="xs:string"/>
          <xs:attribute name="locus_link_name" type="xs:string"/>
          <xs:attribute name="flybase" type="xs:string"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="protein_name" type="xs:string" use="required"/>
  </xs:complexType>
</xs:element>

element protein_summary/protein_group/protein/indistinguishable_protein/annotation
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
protein_description  xs:stringrequired      
documentation 
description
ipi_name  xs:string      
refseq_name  xs:string      
swissprot_name  xs:string      
ensembl_name  xs:string      
trembl_name  xs:string      
locus_link_name  xs:string      
flybase  xs:string      
annotation
documentation 
protein description
source 
<xs:element name="annotation" minOccurs="0">
  <xs:annotation>
    <xs:documentation>protein description</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="protein_description" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>description</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="ipi_name" type="xs:string"/>
    <xs:attribute name="refseq_name" type="xs:string"/>
    <xs:attribute name="swissprot_name" type="xs:string"/>
    <xs:attribute name="ensembl_name" type="xs:string"/>
    <xs:attribute name="trembl_name" type="xs:string"/>
    <xs:attribute name="locus_link_name" type="xs:string"/>
    <xs:attribute name="flybase" type="xs:string"/>
  </xs:complexType>
</xs:element>

element protein_summary/protein_group/protein/peptide
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
children parameter modification_info peptide_parent_protein indistinguishable_peptide
attributes
Name  Type  Use  Default  Fixed  Annotation
peptide_sequence  xs:stringrequired      
documentation 
unmodified aa sequence
charge  xs:positiveIntegerrequired      
documentation 
precursor ion charge
initial_probability  xs:doublerequired      
documentation 
prior to nsp adjustment
nsp_adjusted_probability  xs:doubleoptional      
documentation 
after nsp adjustment
peptide_group_designator  xs:string      
documentation 
link to spectra with other precursor ion charges assigned to same peptide
weight  xs:double  1.0    
is_nondegenerate_evidence  xs:stringrequired      
documentation 
confidence that peptide corresponds with this protein (rather than others in which it occurs)
n_enzymatic_termini  xs:nonNegativeIntegerrequired      
documentation 
number of termini consistent with proteolytic cleavage
n_sibling_peptides  xs:double      
documentation 
estimated number of sibling peptides (other identified peptides corresponding to same protein)
n_sibling_peptides_bin  xs:integer  0    
documentation 
discretized nsp value
n_instances  xs:integerrequired      
documentation 
number of times peptide assigned to spectrum of precursor ion charge in dataset
calc_neutral_pep_mass  xs:double      
is_contributing_evidence  xs:stringrequired      
source 
<xs:element name="peptide" maxOccurs="unbounded">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="parameter" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:simpleContent>
            <xs:extension base="xs:anySimpleType">
              <xs:attribute name="name" type="xs:string" use="required"/>
              <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
              <xs:attribute name="type" type="xs:anySimpleType"/>
            </xs:extension>
          </xs:simpleContent>
        </xs:complexType>
      </xs:element>
      <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:attribute name="position" type="xs:string" use="required"/>
                <xs:attribute name="mass" type="xs:string" use="required"/>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="mod_nterm_mass" type="xs:string"/>
          <xs:attribute name="mod_cterm_mass" type="xs:string"/>
          <xs:attribute name="modified_peptide" type="xs:string"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="peptide_parent_protein" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:attribute name="protein_name" type="xs:string" use="required"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="indistinguishable_peptide" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
                    <xs:complexType>
                      <xs:attribute name="position" type="xs:string" use="required"/>
                      <xs:attribute name="mass" type="xs:string" use="required"/>
                    </xs:complexType>
                  </xs:element>
                </xs:sequence>
                <xs:attribute name="mod_nterm_mass" type="xs:string"/>
                <xs:attribute name="mod_cterm_mass" type="xs:string"/>
                <xs:attribute name="modified_peptide" type="xs:string"/>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="peptide_sequence" type="xs:string" use="required"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="peptide_sequence" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>unmodified aa sequence</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="charge" type="xs:positiveInteger" use="required">
      <xs:annotation>
        <xs:documentation>precursor ion charge</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="initial_probability" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>prior to nsp adjustment</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="nsp_adjusted_probability" type="xs:double" use="optional">
      <xs:annotation>
        <xs:documentation>after nsp adjustment</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="peptide_group_designator" type="xs:string">
      <xs:annotation>
        <xs:documentation>link to spectra with other precursor ion charges assigned to same peptide</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="weight" type="xs:double" default="1.0"/>
    <xs:attribute name="is_nondegenerate_evidence" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>confidence that peptide corresponds with this protein (rather than others in which it occurs)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="n_enzymatic_termini" type="xs:nonNegativeInteger" use="required">
      <xs:annotation>
        <xs:documentation>number of termini consistent with proteolytic cleavage</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="n_sibling_peptides" type="xs:double">
      <xs:annotation>
        <xs:documentation>estimated number of sibling peptides (other identified peptides corresponding to same protein)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="n_sibling_peptides_bin" type="xs:integer" default="0">
      <xs:annotation>
        <xs:documentation>discretized nsp value</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="n_instances" type="xs:integer" use="required">
      <xs:annotation>
        <xs:documentation>number of times peptide assigned to spectrum of precursor ion charge in dataset</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="calc_neutral_pep_mass" type="xs:double"/>
    <xs:attribute name="is_contributing_evidence" type="xs:string" use="required"/>
  </xs:complexType>
</xs:element>

element protein_summary/protein_group/protein/peptide/parameter
diagram
namespace http://regis-web.systemsbiology.net/protXML
type extension of xs:anySimpleType
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" minOccurs="0" maxOccurs="unbounded">
  <xs:complexType>
    <xs:simpleContent>
      <xs:extension base="xs:anySimpleType">
        <xs:attribute name="name" type="xs:string" use="required"/>
        <xs:attribute name="value" type="xs:anySimpleType" use="required"/>
        <xs:attribute name="type" type="xs:anySimpleType"/>
      </xs:extension>
    </xs:simpleContent>
  </xs:complexType>
</xs:element>

element protein_summary/protein_group/protein/peptide/modification_info
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
children mod_aminoacid_mass
attributes
Name  Type  Use  Default  Fixed  Annotation
mod_nterm_mass  xs:string      
mod_cterm_mass  xs:string      
modified_peptide  xs:string      
source 
<xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:attribute name="position" type="xs:string" use="required"/>
          <xs:attribute name="mass" type="xs:string" use="required"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="mod_nterm_mass" type="xs:string"/>
    <xs:attribute name="mod_cterm_mass" type="xs:string"/>
    <xs:attribute name="modified_peptide" type="xs:string"/>
  </xs:complexType>
</xs:element>

element protein_summary/protein_group/protein/peptide/modification_info/mod_aminoacid_mass
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
position  xs:stringrequired      
mass  xs:stringrequired      
source 
<xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
  <xs:complexType>
    <xs:attribute name="position" type="xs:string" use="required"/>
    <xs:attribute name="mass" type="xs:string" use="required"/>
  </xs:complexType>
</xs:element>

element protein_summary/protein_group/protein/peptide/peptide_parent_protein
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
protein_name  xs:stringrequired      
source 
<xs:element name="peptide_parent_protein" minOccurs="0" maxOccurs="unbounded">
  <xs:complexType>
    <xs:attribute name="protein_name" type="xs:string" use="required"/>
  </xs:complexType>
</xs:element>

element protein_summary/protein_group/protein/peptide/indistinguishable_peptide
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
children modification_info
attributes
Name  Type  Use  Default  Fixed  Annotation
peptide_sequence  xs:stringrequired      
source 
<xs:element name="indistinguishable_peptide" minOccurs="0" maxOccurs="unbounded">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:attribute name="position" type="xs:string" use="required"/>
                <xs:attribute name="mass" type="xs:string" use="required"/>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="mod_nterm_mass" type="xs:string"/>
          <xs:attribute name="mod_cterm_mass" type="xs:string"/>
          <xs:attribute name="modified_peptide" type="xs:string"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="peptide_sequence" type="xs:string" use="required"/>
  </xs:complexType>
</xs:element>

element protein_summary/protein_group/protein/peptide/indistinguishable_peptide/modification_info
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
children mod_aminoacid_mass
attributes
Name  Type  Use  Default  Fixed  Annotation
mod_nterm_mass  xs:string      
mod_cterm_mass  xs:string      
modified_peptide  xs:string      
source 
<xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
  <xs:complexType>
    <xs:sequence>
      <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
        <xs:complexType>
          <xs:attribute name="position" type="xs:string" use="required"/>
          <xs:attribute name="mass" type="xs:string" use="required"/>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="mod_nterm_mass" type="xs:string"/>
    <xs:attribute name="mod_cterm_mass" type="xs:string"/>
    <xs:attribute name="modified_peptide" type="xs:string"/>
  </xs:complexType>
</xs:element>

element protein_summary/protein_group/protein/peptide/indistinguishable_peptide/modification_info/mod_aminoacid_mass
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
position  xs:stringrequired      
mass  xs:stringrequired      
source 
<xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
  <xs:complexType>
    <xs:attribute name="position" type="xs:string" use="required"/>
    <xs:attribute name="mass" type="xs:string" use="required"/>
  </xs:complexType>
</xs:element>

element proteinprophet_details
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
content complex
children nsp_information protein_summary_data_filter
attributes
Name  Type  Use  Default  Fixed  Annotation
occam_flag  xs:stringrequired      
documentation 
whether or not occams razor was used to apportion peptides corresponding to multiple proteins
groups_flag  xs:stringrequired      
documentation 
whether or not related proteins are organized together in common protein groups
degen_flag  xs:stringrequired      
documentation 
whether or not all proteins corresponding to each identified peptide were used in analysis
nsp_flag  xs:stringrequired      
documentation 
whether or not peptide probabilities were adjusted for estimated number of sibling peptides
initial_peptide_wt_iters  xs:stringrequired      
documentation 
proteinprophet number of initial iterations to compute peptide weights
nsp_distribution_iters  xs:stringrequired      
documentation 
proteinprophet number of interations used to compute nsp distributions
final_peptide_wt_iters  xs:stringrequired      
documentation 
proteinprophet number of final interations used to compute final peptide weights
run_options  xs:string      
documentation 
special run options
annotation
documentation 
ProteinProphet analysis details
source 
<xs:element name="proteinprophet_details">
  <xs:annotation>
    <xs:documentation>ProteinProphet analysis details</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="nsp_information">
        <xs:annotation>
          <xs:documentation>learned distributions of estimated number of sibling peptides</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="nsp_distribution" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>histogram slice of estimated number of sibling peptides</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:attribute name="bin_no" type="xs:integer" use="required">
                  <xs:annotation>
                    <xs:documentation>discretized bin number</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="nsp_lower_bound_incl" type="xs:double" use="required">
                  <xs:annotation>
                    <xs:documentation>lower bound nsp value (inclusive)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="nsp_upper_bound_excl" type="xs:string" use="required">
                  <xs:annotation>
                    <xs:documentation>upper bound nsp value (exclusive)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="pos_freq" type="xs:double" use="required">
                  <xs:annotation>
                    <xs:documentation>fraction of correct peptides in bin</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="neg_freq" type="xs:double" use="required">
                  <xs:annotation>
                    <xs:documentation>fraction of incorrect peptides in bin</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="pos_to_neg_ratio" type="xs:double" use="required">
                  <xs:annotation>
                    <xs:documentation>fraction of correct / fraction of incorrect</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
                <xs:attribute name="alt_pos_to_neg_ratio" type="xs:double">
                  <xs:annotation>
                    <xs:documentation>pos_to_neg_ratio of preceding bin (if greater than that of current bin)</xs:documentation>
                  </xs:annotation>
                </xs:attribute>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
          <xs:attribute name="neighboring_bin_smoothing" type="xs:string" use="required"/>
        </xs:complexType>
      </xs:element>
      <xs:element name="protein_summary_data_filter" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>predicted error/sensitivity for filtering at minimum probability</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="min_probability" type="xs:double" use="required">
            <xs:annotation>
              <xs:documentation>filter setting</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="sensitivity" type="xs:double" use="required">
            <xs:annotation>
              <xs:documentation>predicted sensitivity (fraction of correct results passing filter)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="false_positive_error_rate" type="xs:double" use="required">
            <xs:annotation>
              <xs:documentation>predicted error rate (fraction of results passing filter than are incorrect)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="predicted_num_correct" type="xs:double">
            <xs:annotation>
              <xs:documentation>predicted number of correct results passing filter</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="predicted_num_incorrect" type="xs:double">
            <xs:annotation>
              <xs:documentation>predicted number of incorrect results passing filter</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="occam_flag" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>whether or not occams razor was used to apportion peptides corresponding to multiple proteins</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="groups_flag" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>whether or not related proteins are organized together in common protein groups</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="degen_flag" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>whether or not all proteins corresponding to each identified peptide were used in analysis</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="nsp_flag" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>whether or not peptide probabilities were adjusted for estimated number of sibling peptides</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="initial_peptide_wt_iters" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>proteinprophet number of initial iterations to compute peptide weights</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="nsp_distribution_iters" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>proteinprophet number of interations used to compute nsp distributions</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="final_peptide_wt_iters" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>proteinprophet number of final interations used to compute final peptide weights</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="run_options" type="xs:string">
      <xs:annotation>
        <xs:documentation>special run options</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element proteinprophet_details/nsp_information
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
children nsp_distribution
attributes
Name  Type  Use  Default  Fixed  Annotation
neighboring_bin_smoothing  xs:stringrequired      
annotation
documentation 
learned distributions of estimated number of sibling peptides
source 
<xs:element name="nsp_information">
  <xs:annotation>
    <xs:documentation>learned distributions of estimated number of sibling peptides</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="nsp_distribution" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>histogram slice of estimated number of sibling peptides</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:attribute name="bin_no" type="xs:integer" use="required">
            <xs:annotation>
              <xs:documentation>discretized bin number</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="nsp_lower_bound_incl" type="xs:double" use="required">
            <xs:annotation>
              <xs:documentation>lower bound nsp value (inclusive)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="nsp_upper_bound_excl" type="xs:string" use="required">
            <xs:annotation>
              <xs:documentation>upper bound nsp value (exclusive)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="pos_freq" type="xs:double" use="required">
            <xs:annotation>
              <xs:documentation>fraction of correct peptides in bin</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="neg_freq" type="xs:double" use="required">
            <xs:annotation>
              <xs:documentation>fraction of incorrect peptides in bin</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="pos_to_neg_ratio" type="xs:double" use="required">
            <xs:annotation>
              <xs:documentation>fraction of correct / fraction of incorrect</xs:documentation>
            </xs:annotation>
          </xs:attribute>
          <xs:attribute name="alt_pos_to_neg_ratio" type="xs:double">
            <xs:annotation>
              <xs:documentation>pos_to_neg_ratio of preceding bin (if greater than that of current bin)</xs:documentation>
            </xs:annotation>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
    <xs:attribute name="neighboring_bin_smoothing" type="xs:string" use="required"/>
  </xs:complexType>
</xs:element>

element proteinprophet_details/nsp_information/nsp_distribution
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
bin_no  xs:integerrequired      
documentation 
discretized bin number
nsp_lower_bound_incl  xs:doublerequired      
documentation 
lower bound nsp value (inclusive)
nsp_upper_bound_excl  xs:stringrequired      
documentation 
upper bound nsp value (exclusive)
pos_freq  xs:doublerequired      
documentation 
fraction of correct peptides in bin
neg_freq  xs:doublerequired      
documentation 
fraction of incorrect peptides in bin
pos_to_neg_ratio  xs:doublerequired      
documentation 
fraction of correct / fraction of incorrect
alt_pos_to_neg_ratio  xs:double      
documentation 
pos_to_neg_ratio of preceding bin (if greater than that of current bin)
annotation
documentation 
histogram slice of estimated number of sibling peptides
source 
<xs:element name="nsp_distribution" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>histogram slice of estimated number of sibling peptides</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="bin_no" type="xs:integer" use="required">
      <xs:annotation>
        <xs:documentation>discretized bin number</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="nsp_lower_bound_incl" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>lower bound nsp value (inclusive)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="nsp_upper_bound_excl" type="xs:string" use="required">
      <xs:annotation>
        <xs:documentation>upper bound nsp value (exclusive)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="pos_freq" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>fraction of correct peptides in bin</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="neg_freq" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>fraction of incorrect peptides in bin</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="pos_to_neg_ratio" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>fraction of correct / fraction of incorrect</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="alt_pos_to_neg_ratio" type="xs:double">
      <xs:annotation>
        <xs:documentation>pos_to_neg_ratio of preceding bin (if greater than that of current bin)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element proteinprophet_details/protein_summary_data_filter
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
min_probability  xs:doublerequired      
documentation 
filter setting
sensitivity  xs:doublerequired      
documentation 
predicted sensitivity (fraction of correct results passing filter)
false_positive_error_rate  xs:doublerequired      
documentation 
predicted error rate (fraction of results passing filter than are incorrect)
predicted_num_correct  xs:double      
documentation 
predicted number of correct results passing filter
predicted_num_incorrect  xs:double      
documentation 
predicted number of incorrect results passing filter
annotation
documentation 
predicted error/sensitivity for filtering at minimum probability
source 
<xs:element name="protein_summary_data_filter" maxOccurs="unbounded">
  <xs:annotation>
    <xs:documentation>predicted error/sensitivity for filtering at minimum probability</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="min_probability" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>filter setting</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="sensitivity" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>predicted sensitivity (fraction of correct results passing filter)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="false_positive_error_rate" type="xs:double" use="required">
      <xs:annotation>
        <xs:documentation>predicted error rate (fraction of results passing filter than are incorrect)</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="predicted_num_correct" type="xs:double">
      <xs:annotation>
        <xs:documentation>predicted number of correct results passing filter</xs:documentation>
      </xs:annotation>
    </xs:attribute>
    <xs:attribute name="predicted_num_incorrect" type="xs:double">
      <xs:annotation>
        <xs:documentation>predicted number of incorrect results passing filter</xs:documentation>
      </xs:annotation>
    </xs:attribute>
  </xs:complexType>
</xs:element>

element XPress_analysis_summary
diagram
namespace http://regis-web.systemsbiology.net/protXML
properties
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
min_peptide_probability  xs:doublerequired      
min_peptide_weight  xs:doublerequired      
min_protein_probability  xs:doublerequired      
reference_isotope  xs:string      
source 
<xs:element name="XPress_analysis_summary">
  <xs:complexType>
    <xs:attribute name="min_peptide_probability" type="xs:double" use="required"/>
    <xs:attribute name="min_peptide_weight" type="xs:double" use="required"/>
    <xs:attribute name="min_protein_probability" type="xs:double" use="required"/>
    <xs:attribute name="reference_isotope" type="xs:string"/>
  </xs:complexType>
</xs:element>

simpleType positiveInt
namespace http://regis-web.systemsbiology.net/protXML
type restriction of xs:unsignedInt
used by
attributes libra_summary/fragment_masses/@channel libra_summary/isotopic_contributions/contributing_channel/affected_channel/@channel libra_summary/isotopic_contributions/contributing_channel/@channel
facets
minInclusive 1
source 
<xs:simpleType name="positiveInt">
  <xs:restriction base="xs:unsignedInt">
    <xs:minInclusive value="1"/>
  </xs:restriction>
</xs:simpleType>


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