ms-ident 0.0.2
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- data/.document +5 -0
- data/Gemfile +31 -0
- data/Gemfile.lock +32 -0
- data/LICENSE +61 -0
- data/README.rdoc +97 -0
- data/Rakefile +54 -0
- data/VERSION +1 -0
- data/lib/merge.rb +7 -0
- data/lib/ms/ident/pepxml/modifications/sequest.rb +237 -0
- data/lib/ms/ident/pepxml/modifications.rb +94 -0
- data/lib/ms/ident/pepxml/msms_pipeline_analysis.rb +70 -0
- data/lib/ms/ident/pepxml/msms_run_summary.rb +81 -0
- data/lib/ms/ident/pepxml/parameters.rb +14 -0
- data/lib/ms/ident/pepxml/pep_summary.rb +104 -0
- data/lib/ms/ident/pepxml/prot_summary.rb +484 -0
- data/lib/ms/ident/pepxml/sample_enzyme.rb +166 -0
- data/lib/ms/ident/pepxml/search_database.rb +42 -0
- data/lib/ms/ident/pepxml/search_hit/modification_info.rb +82 -0
- data/lib/ms/ident/pepxml/search_hit.rb +141 -0
- data/lib/ms/ident/pepxml/search_result.rb +28 -0
- data/lib/ms/ident/pepxml/search_summary.rb +88 -0
- data/lib/ms/ident/pepxml/spectrum_query.rb +83 -0
- data/lib/ms/ident/pepxml.rb +61 -0
- data/lib/ms/ident.rb +11 -0
- data/schema/pepXML_v115.xsd +1458 -0
- data/schema/pepXML_v19.xsd +1337 -0
- data/spec/ms/ident/pepxml/sample_enzyme_spec.rb +181 -0
- data/spec/ms/ident/pepxml_spec.rb +436 -0
- data/spec/spec_helper.rb +40 -0
- metadata +194 -0
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<?xml version="1.0" encoding="UTF-8"?>
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<xs:schema targetNamespace="http://regis-web.systemsbiology.net/pepXML" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:pepx="http://regis-web.systemsbiology.net/pepXML" elementFormDefault="qualified">
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<xs:annotation>
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<xs:documentation xml:lang="en">
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MS/MS pipeline analysis schema. Developed by ISB proteome center.
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</xs:documentation>
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</xs:annotation>
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<xs:element name="msms_pipeline_analysis">
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<xs:complexType>
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<xs:element name="analysis_summary" minOccurs="0" maxOccurs="unbounded">
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<xs:annotation>
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<xs:documentation>Summary of analysis subjected to run(s)</xs:documentation>
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<xs:complexType>
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<xs:any namespace="##any" processContents="lax" minOccurs="0">
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<xs:annotation>
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<xs:documentation>Wildcard for summary info customized for a particular analysis</xs:documentation>
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</xs:any>
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<xs:attribute name="time" type="xs:dateTime" use="required">
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<xs:annotation>
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<xs:documentation>Time analysis complete (unique id)</xs:documentation>
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<xs:attribute name="analysis" type="xs:string" use="required">
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<xs:annotation>
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<xs:documentation>Name of analysis program</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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<xs:attribute name="version" type="xs:string">
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<xs:annotation>
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<xs:documentation>Release</xs:documentation>
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</xs:attribute>
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</xs:complexType>
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</xs:element>
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<xs:element name="dataset_derivation" minOccurs="0">
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<xs:annotation>
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<xs:documentation>Source and filtering criteria used to generate dataset</xs:documentation>
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</xs:annotation>
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<xs:complexType>
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<xs:sequence>
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<xs:element name="data_filter" minOccurs="0" maxOccurs="unbounded">
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<xs:complexType>
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<xs:attribute name="number" type="xs:nonNegativeInteger" use="required"/>
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<xs:attribute name="parent_file" type="xs:string" use="required">
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<xs:annotation>
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<xs:documentation>File from which derived</xs:documentation>
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<xs:attribute name="windows_parent" type="xs:string"/>
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<xs:attribute name="description" type="xs:string" use="required">
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<xs:annotation>
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<xs:documentation>filtering criteria applied to data</xs:documentation>
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</xs:annotation>
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<xs:attribute name="generation_no" type="xs:nonNegativeInteger" use="required">
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<xs:annotation>
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<xs:documentation>number preceding filter generations</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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</xs:complexType>
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</xs:element>
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<xs:element name="msms_run_summary" maxOccurs="unbounded">
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<xs:annotation>
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<xs:documentation>Search results for LC/MS/MS run</xs:documentation>
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</xs:annotation>
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<xs:complexType>
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<xs:sequence>
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<xs:element name="sample_enzyme">
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<xs:annotation>
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<xs:documentation>Defines the net cleavage specificity of an enzyme, chemical reagent, or a mixture of these, for mass spectrometry purposes</xs:documentation>
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</xs:annotation>
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<xs:complexType>
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<xs:sequence>
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<xs:element name="specificity" minOccurs="0" maxOccurs="unbounded">
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<xs:annotation>
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<xs:documentation>Component cleavage specificity. Must be at least one specificity unless enzymeType:fidelity is nonspecific </xs:documentation>
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</xs:annotation>
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<xs:complexType>
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<xs:attribute name="sense" use="required">
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<xs:annotation>
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<xs:documentation>Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut</xs:documentation>
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</xs:annotation>
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<xs:simpleType>
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<xs:restriction base="xs:string">
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<xs:enumeration value="C"/>
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<xs:enumeration value="N"/>
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</xs:restriction>
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</xs:simpleType>
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</xs:attribute>
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<xs:attribute name="min_spacing" type="xs:nonNegativeInteger" default="1">
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<xs:annotation>
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<xs:documentation>minimum separation between adjacent cleavages</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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<xs:attribute name="cut" use="required">
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<xs:annotation>
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<xs:documentation>One or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation>
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</xs:annotation>
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<xs:simpleType>
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<xs:restriction base="xs:string">
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<xs:minLength value="1"/>
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<xs:maxLength value="20"/>
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<xs:pattern value="[A,C-I,K-N,P-T,VWY]+"/>
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</xs:restriction>
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</xs:simpleType>
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</xs:attribute>
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<xs:attribute name="no_cut" use="optional">
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<xs:annotation>
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<xs:documentation>Zero or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation>
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</xs:annotation>
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<xs:simpleType>
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<xs:restriction base="xs:string">
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<xs:minLength value="0"/>
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<xs:maxLength value="20"/>
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</xs:restriction>
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</xs:simpleType>
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</xs:attribute>
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</xs:complexType>
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</xs:element>
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</xs:sequence>
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<xs:attribute name="name" use="required">
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<xs:annotation>
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<xs:documentation>Controlled code name for the enzyme that can be referred to by applications</xs:documentation>
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</xs:annotation>
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<xs:simpleType>
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<xs:restriction base="xs:string">
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<xs:minLength value="1"/>
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</xs:restriction>
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</xs:simpleType>
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</xs:attribute>
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<xs:attribute name="description" type="xs:string" use="optional">
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<xs:annotation>
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<xs:documentation>Free text to describe alternative names, special conditions, etc.</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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<xs:attribute name="fidelity" use="optional" default="specific">
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<xs:annotation>
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<xs:documentation>Semispecific means that at least one end of a pepide must conform to the cleavage specificity, (unless the peptide was at the terminus of the parent sequence). Nonspecific means that neither end of a peptide must conform to the cleavage specificity.</xs:documentation>
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</xs:annotation>
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<xs:simpleType>
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<xs:restriction base="xs:string">
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<xs:enumeration value="specific"/>
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<xs:enumeration value="semispecific"/>
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<xs:enumeration value="nonspecific"/>
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</xs:restriction>
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</xs:simpleType>
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</xs:attribute>
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<xs:attribute name="independent" type="xs:boolean" use="optional" default="1">
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<xs:annotation>
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<xs:documentation>If there are multiple specificities and independent is true, then a single peptide cannot exhibit one specificity at one terminus and a different specificity at the other. If independent is false, then a single peptide can exhibit mixed specificities.</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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</xs:complexType>
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</xs:element>
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<xs:element name="search_summary" maxOccurs="unbounded">
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<xs:annotation>
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<xs:documentation>Database search settings</xs:documentation>
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</xs:annotation>
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<xs:complexType>
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<xs:sequence>
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<xs:element name="search_database" minOccurs="0">
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<xs:complexType>
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<xs:attribute name="local_path" type="xs:string" use="required">
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<xs:annotation>
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<xs:documentation>Full path address of database on local computer</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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<xs:attribute name="URL" type="xs:string"/>
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<xs:attribute name="database_name" type="xs:string"/>
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<xs:attribute name="orig_database_url" type="xs:string"/>
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<xs:attribute name="database_release_date" type="xs:dateTime"/>
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<xs:attribute name="database_release_identifier" type="xs:string"/>
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<xs:attribute name="size_in_db_entries" type="xs:nonNegativeInteger"/>
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<xs:attribute name="size_of_residues" type="xs:nonNegativeInteger"/>
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<xs:attribute name="type" use="required">
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<xs:annotation>
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<xs:documentation>Database type (AA=amino acid, NA=nucleic acid)</xs:documentation>
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</xs:annotation>
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<xs:simpleType>
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<xs:restriction base="xs:string">
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<xs:enumeration value="AA"/>
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<xs:enumeration value="NA"/>
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</xs:restriction>
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</xs:simpleType>
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</xs:attribute>
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</xs:complexType>
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</xs:element>
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<xs:element name="enzymatic_search_constraint" minOccurs="0">
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<xs:annotation>
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<xs:documentation>Required peptide termini</xs:documentation>
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</xs:annotation>
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<xs:complexType>
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<xs:attribute name="enzyme" type="xs:string" use="required"/>
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<xs:attribute name="max_num_internal_cleavages" type="xs:nonNegativeInteger" use="required">
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<xs:annotation>
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<xs:documentation>Maximum number of enzyme cleavage sites allowable within peptide</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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<xs:attribute name="min_number_termini" type="xs:nonNegativeInteger" use="required">
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<xs:annotation>
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<xs:documentation>Minimum number of termini compatible with enzymatic cleavage</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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</xs:complexType>
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</xs:element>
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<xs:element name="sequence_search_constraint" minOccurs="0" maxOccurs="unbounded">
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<xs:annotation>
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<xs:documentation>Required amino acid string</xs:documentation>
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</xs:annotation>
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<xs:complexType>
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<xs:attribute name="sequence" type="xs:string" use="required">
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<xs:annotation>
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<xs:documentation>Required amino acid string</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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</xs:complexType>
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</xs:element>
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<xs:element name="aminoacid_modification" minOccurs="0" maxOccurs="unbounded">
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<xs:annotation>
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<xs:documentation>Modified aminoacid, static or variable</xs:documentation>
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</xs:annotation>
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<xs:complexType>
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<xs:attribute name="aminoacid" type="xs:string" use="required"/>
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<xs:attribute name="massdiff" type="xs:string" use="required">
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<xs:annotation>
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<xs:documentation>Mass difference with respect to unmodified aminoacid, must begin with either + (nonnegative) or - [e.g. +1.05446 or -2.3342]</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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<xs:attribute name="mass" type="xs:float" use="required">
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<xs:annotation>
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<xs:documentation>Mass of modified aminoacid</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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<xs:attribute name="variable" type="xs:string" use="required">
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<xs:annotation>
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<xs:documentation>Y if both modified and unmodified aminoacid could be present in the dataset, N if only modified aminoacid can be present</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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<xs:attribute name="peptide_terminus" type="xs:string">
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<xs:annotation>
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<xs:documentation>whether modification can reside only at protein terminus (specified 'n', 'c', or 'nc')</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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<xs:attribute name="symbol" type="aa_symbolType">
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<xs:annotation>
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<xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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<xs:attribute name="binary" type="xs:string">
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<xs:annotation>
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<xs:documentation>Y if each peptide must have only modified or unmodified aminoacid, N if a peptide may contain both modified and unmodified aminoacid</xs:documentation>
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</xs:annotation>
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</xs:attribute>
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<xs:attribute name="description" type="xs:string"/>
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</xs:complexType>
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</xs:element>
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<xs:element name="terminal_modification" minOccurs="0" maxOccurs="unbounded">
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<xs:annotation>
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+
<xs:documentation>Modification to the N or C terminus, static or variable</xs:documentation>
|
|
270
|
+
</xs:annotation>
|
|
271
|
+
<xs:complexType>
|
|
272
|
+
<xs:attribute name="terminus" type="xs:string" use="required">
|
|
273
|
+
<xs:annotation>
|
|
274
|
+
<xs:documentation>n for N-terminus, c for C-terminus</xs:documentation>
|
|
275
|
+
</xs:annotation>
|
|
276
|
+
</xs:attribute>
|
|
277
|
+
<xs:attribute name="massdiff" type="xs:string" use="required">
|
|
278
|
+
<xs:annotation>
|
|
279
|
+
<xs:documentation>Mass difference with respect to unmodified terminus</xs:documentation>
|
|
280
|
+
</xs:annotation>
|
|
281
|
+
</xs:attribute>
|
|
282
|
+
<xs:attribute name="mass" type="xs:float" use="required">
|
|
283
|
+
<xs:annotation>
|
|
284
|
+
<xs:documentation>Mass of modified terminus</xs:documentation>
|
|
285
|
+
</xs:annotation>
|
|
286
|
+
</xs:attribute>
|
|
287
|
+
<xs:attribute name="variable" type="xs:string" use="required">
|
|
288
|
+
<xs:annotation>
|
|
289
|
+
<xs:documentation>Y if both modified and unmodified terminus could be present in the dataset, N if only modified terminus can be present</xs:documentation>
|
|
290
|
+
</xs:annotation>
|
|
291
|
+
</xs:attribute>
|
|
292
|
+
<xs:attribute name="symbol" type="term_symbolType">
|
|
293
|
+
<xs:annotation>
|
|
294
|
+
<xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation>
|
|
295
|
+
</xs:annotation>
|
|
296
|
+
</xs:attribute>
|
|
297
|
+
<xs:attribute name="protein_terminus" type="xs:string" use="required">
|
|
298
|
+
<xs:annotation>
|
|
299
|
+
<xs:documentation>whether modification can reside only at protein terminus (specified n or c)</xs:documentation>
|
|
300
|
+
</xs:annotation>
|
|
301
|
+
</xs:attribute>
|
|
302
|
+
<xs:attribute name="description" type="xs:string"/>
|
|
303
|
+
</xs:complexType>
|
|
304
|
+
</xs:element>
|
|
305
|
+
|
|
306
|
+
<xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
|
|
307
|
+
</xs:sequence>
|
|
308
|
+
<xs:attribute name="base_name" type="xs:string" use="required">
|
|
309
|
+
<xs:annotation>
|
|
310
|
+
<xs:documentation>Full path location of mzXML file for this search run (without the .mzXML extension)</xs:documentation>
|
|
311
|
+
</xs:annotation>
|
|
312
|
+
</xs:attribute>
|
|
313
|
+
<xs:attribute name="search_engine" type="engineType" use="required">
|
|
314
|
+
<xs:annotation>
|
|
315
|
+
<xs:documentation>SEQUEST, Mascot, COMET, etc</xs:documentation>
|
|
316
|
+
</xs:annotation>
|
|
317
|
+
</xs:attribute>
|
|
318
|
+
<xs:attribute name="precursor_mass_type" type="massType" use="required">
|
|
319
|
+
<xs:annotation>
|
|
320
|
+
<xs:documentation>average or monoisotopic</xs:documentation>
|
|
321
|
+
</xs:annotation>
|
|
322
|
+
</xs:attribute>
|
|
323
|
+
<xs:attribute name="fragment_mass_type" type="massType" use="required">
|
|
324
|
+
<xs:annotation>
|
|
325
|
+
<xs:documentation>average or monoisotopic</xs:documentation>
|
|
326
|
+
</xs:annotation>
|
|
327
|
+
</xs:attribute>
|
|
328
|
+
|
|
329
|
+
<xs:attribute name="out_data_type" type="xs:string" use="optional">
|
|
330
|
+
<xs:annotation>
|
|
331
|
+
<xs:documentation>Format of file storing the runner up peptides (if not present in pepXML)</xs:documentation>
|
|
332
|
+
</xs:annotation>
|
|
333
|
+
</xs:attribute>
|
|
334
|
+
<xs:attribute name="out_data" type="xs:string" use="optional">
|
|
335
|
+
<xs:annotation>
|
|
336
|
+
<xs:documentation>runner up search hit data type extension (e.g. .tgz)</xs:documentation>
|
|
337
|
+
</xs:annotation>
|
|
338
|
+
</xs:attribute>
|
|
339
|
+
|
|
340
|
+
|
|
341
|
+
<xs:attribute name="search_id" type="positiveInt" use="required">
|
|
342
|
+
<xs:annotation>
|
|
343
|
+
<xs:documentation>matches id in search hit</xs:documentation>
|
|
344
|
+
</xs:annotation>
|
|
345
|
+
</xs:attribute>
|
|
346
|
+
</xs:complexType>
|
|
347
|
+
</xs:element>
|
|
348
|
+
<xs:element name="analysis_timestamp" minOccurs="0" maxOccurs="unbounded">
|
|
349
|
+
<xs:annotation>
|
|
350
|
+
<xs:documentation>Reference for analysis applied to current run (time corresponds with analysis_summary/@time, id corresponds with analysis_result/@id)</xs:documentation>
|
|
351
|
+
</xs:annotation>
|
|
352
|
+
<xs:complexType>
|
|
353
|
+
<xs:sequence>
|
|
354
|
+
<xs:any namespace="##any" processContents="lax" minOccurs="0">
|
|
355
|
+
<xs:annotation>
|
|
356
|
+
<xs:documentation>Wildcard for timestamp info customized for a particular analysis</xs:documentation>
|
|
357
|
+
</xs:annotation>
|
|
358
|
+
</xs:any>
|
|
359
|
+
</xs:sequence>
|
|
360
|
+
<xs:attribute name="time" type="xs:dateTime" use="required">
|
|
361
|
+
<xs:annotation>
|
|
362
|
+
<xs:documentation>Date of analysis</xs:documentation>
|
|
363
|
+
</xs:annotation>
|
|
364
|
+
</xs:attribute>
|
|
365
|
+
|
|
366
|
+
<xs:attribute name="analysis" type="xs:string" use="required">
|
|
367
|
+
<xs:annotation>
|
|
368
|
+
<xs:documentation>Analysis name</xs:documentation>
|
|
369
|
+
</xs:annotation>
|
|
370
|
+
</xs:attribute>
|
|
371
|
+
<xs:attribute name="id" type="positiveInt" use="required">
|
|
372
|
+
<xs:annotation>
|
|
373
|
+
<xs:documentation>Unique identifier for each type of analysis</xs:documentation>
|
|
374
|
+
</xs:annotation>
|
|
375
|
+
</xs:attribute>
|
|
376
|
+
</xs:complexType>
|
|
377
|
+
</xs:element>
|
|
378
|
+
|
|
379
|
+
<xs:element name="spectrum_query" minOccurs="0" maxOccurs="unbounded">
|
|
380
|
+
<xs:annotation>
|
|
381
|
+
<xs:documentation>MS/MS spectrum, precursor ion charge and mass</xs:documentation>
|
|
382
|
+
</xs:annotation>
|
|
383
|
+
<xs:complexType>
|
|
384
|
+
<xs:sequence>
|
|
385
|
+
|
|
386
|
+
|
|
387
|
+
<xs:element name="search_result" minOccurs="0" maxOccurs="unbounded">
|
|
388
|
+
<xs:complexType>
|
|
389
|
+
<xs:sequence>
|
|
390
|
+
|
|
391
|
+
|
|
392
|
+
|
|
393
|
+
<xs:element name="search_hit" minOccurs="0" maxOccurs="unbounded">
|
|
394
|
+
<xs:annotation>
|
|
395
|
+
<xs:documentation>Peptide assignment</xs:documentation>
|
|
396
|
+
</xs:annotation>
|
|
397
|
+
<xs:complexType>
|
|
398
|
+
<xs:sequence>
|
|
399
|
+
<xs:element name="alternative_protein" minOccurs="0" maxOccurs="unbounded">
|
|
400
|
+
<xs:annotation>
|
|
401
|
+
<xs:documentation>Other protein in search database that contains peptide</xs:documentation>
|
|
402
|
+
</xs:annotation>
|
|
403
|
+
<xs:complexType>
|
|
404
|
+
<xs:attribute name="protein" type="xs:string" use="required"/>
|
|
405
|
+
<xs:attribute name="protein_descr" type="xs:string"/>
|
|
406
|
+
<xs:attribute name="num_tol_term" type="xs:nonNegativeInteger"/>
|
|
407
|
+
<xs:attribute name="protein_mw" type="xs:double"/>
|
|
408
|
+
<xs:attribute name="peptide_prev_aa" type="xs:string">
|
|
409
|
+
<xs:annotation>
|
|
410
|
+
<xs:documentation>Aminoacid preceding peptide (- if none)</xs:documentation>
|
|
411
|
+
</xs:annotation>
|
|
412
|
+
</xs:attribute>
|
|
413
|
+
<xs:attribute name="peptide_next_aa" type="xs:string">
|
|
414
|
+
<xs:annotation>
|
|
415
|
+
<xs:documentation>Aminoacid following peptide (- if none)</xs:documentation>
|
|
416
|
+
</xs:annotation>
|
|
417
|
+
</xs:attribute>
|
|
418
|
+
</xs:complexType>
|
|
419
|
+
</xs:element>
|
|
420
|
+
<xs:element name="modification_info" minOccurs="0">
|
|
421
|
+
<xs:annotation>
|
|
422
|
+
<xs:documentation>Positions and masses of modifications</xs:documentation>
|
|
423
|
+
</xs:annotation>
|
|
424
|
+
<xs:complexType>
|
|
425
|
+
<xs:sequence>
|
|
426
|
+
<xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
|
|
427
|
+
<xs:complexType>
|
|
428
|
+
<xs:attribute name="position" type="xs:nonNegativeInteger" use="required">
|
|
429
|
+
<xs:annotation>
|
|
430
|
+
<xs:documentation>modified aminoacid position in peptide [ranging from 1 to peptide length]</xs:documentation>
|
|
431
|
+
</xs:annotation>
|
|
432
|
+
</xs:attribute>
|
|
433
|
+
<xs:attribute name="mass" type="xs:double" use="required">
|
|
434
|
+
<xs:annotation>
|
|
435
|
+
<xs:documentation>modified mass of aminoacid</xs:documentation>
|
|
436
|
+
</xs:annotation>
|
|
437
|
+
</xs:attribute>
|
|
438
|
+
</xs:complexType>
|
|
439
|
+
</xs:element>
|
|
440
|
+
</xs:sequence>
|
|
441
|
+
<xs:attribute name="mod_nterm_mass" type="xs:double">
|
|
442
|
+
<xs:annotation>
|
|
443
|
+
<xs:documentation>Mass of modified N terminus</xs:documentation>
|
|
444
|
+
</xs:annotation>
|
|
445
|
+
</xs:attribute>
|
|
446
|
+
<xs:attribute name="mod_cterm_mass" type="xs:double">
|
|
447
|
+
<xs:annotation>
|
|
448
|
+
<xs:documentation>Mass of modified C terminus</xs:documentation>
|
|
449
|
+
</xs:annotation>
|
|
450
|
+
</xs:attribute>
|
|
451
|
+
<xs:attribute name="modified_peptide" type="xs:string">
|
|
452
|
+
<xs:annotation>
|
|
453
|
+
<xs:documentation>Peptide sequence (with indicated modifications)</xs:documentation>
|
|
454
|
+
</xs:annotation>
|
|
455
|
+
</xs:attribute>
|
|
456
|
+
</xs:complexType>
|
|
457
|
+
</xs:element>
|
|
458
|
+
<xs:element name="search_score" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
|
|
459
|
+
<xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">
|
|
460
|
+
<xs:complexType>
|
|
461
|
+
<xs:sequence>
|
|
462
|
+
<xs:any namespace="##any" processContents="lax">
|
|
463
|
+
<xs:annotation>
|
|
464
|
+
<xs:documentation>Wildcard for result info customized for a particular analysis</xs:documentation>
|
|
465
|
+
</xs:annotation>
|
|
466
|
+
</xs:any>
|
|
467
|
+
|
|
468
|
+
</xs:sequence>
|
|
469
|
+
<xs:attribute name="analysis" type="xs:string" use="required"/>
|
|
470
|
+
<xs:attribute name="id" type="positiveInt" default="1"/>
|
|
471
|
+
</xs:complexType>
|
|
472
|
+
</xs:element>
|
|
473
|
+
<xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
|
|
474
|
+
</xs:sequence>
|
|
475
|
+
<xs:attribute name="hit_rank" type="positiveInt" use="required"/>
|
|
476
|
+
<xs:attribute name="peptide" type="xs:string" use="required">
|
|
477
|
+
<xs:annotation>
|
|
478
|
+
<xs:documentation>Peptide aminoacid sequence (with no indicated modifications)</xs:documentation>
|
|
479
|
+
</xs:annotation>
|
|
480
|
+
</xs:attribute>
|
|
481
|
+
<xs:attribute name="peptide_prev_aa" type="xs:string">
|
|
482
|
+
<xs:annotation>
|
|
483
|
+
<xs:documentation>Aminoacid preceding peptide (- if none)</xs:documentation>
|
|
484
|
+
</xs:annotation>
|
|
485
|
+
</xs:attribute>
|
|
486
|
+
<xs:attribute name="peptide_next_aa" type="xs:string">
|
|
487
|
+
<xs:annotation>
|
|
488
|
+
<xs:documentation>Aminoacid following peptide (- if none)</xs:documentation>
|
|
489
|
+
</xs:annotation>
|
|
490
|
+
</xs:attribute>
|
|
491
|
+
<xs:attribute name="protein" type="xs:string" use="required"/>
|
|
492
|
+
<xs:attribute name="num_tot_proteins" type="xs:unsignedInt" use="required">
|
|
493
|
+
<xs:annotation>
|
|
494
|
+
<xs:documentation>Number of unique proteins in search database containing peptide</xs:documentation>
|
|
495
|
+
</xs:annotation>
|
|
496
|
+
</xs:attribute>
|
|
497
|
+
<xs:attribute name="num_matched_ions" type="xs:nonNegativeInteger">
|
|
498
|
+
<xs:annotation>
|
|
499
|
+
<xs:documentation>Number of peptide fragment ions found in spectrum</xs:documentation>
|
|
500
|
+
</xs:annotation>
|
|
501
|
+
</xs:attribute>
|
|
502
|
+
<xs:attribute name="tot_num_ions" type="xs:nonNegativeInteger">
|
|
503
|
+
<xs:annotation>
|
|
504
|
+
<xs:documentation>Number of peptide fragment ions predicted for peptide</xs:documentation>
|
|
505
|
+
</xs:annotation>
|
|
506
|
+
</xs:attribute>
|
|
507
|
+
<xs:attribute name="calc_neutral_pep_mass" type="xs:float" use="required"/>
|
|
508
|
+
<xs:attribute name="massdiff" type="xs:string" use="required">
|
|
509
|
+
<xs:annotation>
|
|
510
|
+
<xs:documentation>Mass(precursor ion) - Mass(peptide)</xs:documentation>
|
|
511
|
+
</xs:annotation>
|
|
512
|
+
</xs:attribute>
|
|
513
|
+
<xs:attribute name="num_tol_term" type="xs:nonNegativeInteger">
|
|
514
|
+
<xs:annotation>
|
|
515
|
+
<xs:documentation>Number of peptide termini consistent with cleavage by sample enzyme</xs:documentation>
|
|
516
|
+
</xs:annotation>
|
|
517
|
+
</xs:attribute>
|
|
518
|
+
<xs:attribute name="num_missed_cleavages" type="xs:integer">
|
|
519
|
+
<xs:annotation>
|
|
520
|
+
<xs:documentation>Number of sample enzyme cleavage sites internal to peptide</xs:documentation>
|
|
521
|
+
</xs:annotation>
|
|
522
|
+
</xs:attribute>
|
|
523
|
+
<xs:attribute name="is_rejected" default="0">
|
|
524
|
+
<xs:annotation>
|
|
525
|
+
<xs:documentation>Potential use in future for user manual validation (0 or 1)</xs:documentation>
|
|
526
|
+
</xs:annotation>
|
|
527
|
+
<xs:simpleType>
|
|
528
|
+
<xs:restriction base="xs:nonNegativeInteger">
|
|
529
|
+
<xs:enumeration value="0"/>
|
|
530
|
+
<xs:enumeration value="1"/>
|
|
531
|
+
</xs:restriction>
|
|
532
|
+
</xs:simpleType>
|
|
533
|
+
|
|
534
|
+
</xs:attribute>
|
|
535
|
+
<xs:attribute name="protein_descr" type="xs:string">
|
|
536
|
+
<xs:annotation>
|
|
537
|
+
<xs:documentation>Extracted from search database</xs:documentation>
|
|
538
|
+
</xs:annotation>
|
|
539
|
+
</xs:attribute>
|
|
540
|
+
<xs:attribute name="calc_pI" type="xs:string"/>
|
|
541
|
+
<xs:attribute name="protein_mw" type="xs:double"/>
|
|
542
|
+
|
|
543
|
+
</xs:complexType>
|
|
544
|
+
|
|
545
|
+
<xs:unique name="unique_result_analysis_id">
|
|
546
|
+
<xs:annotation>
|
|
547
|
+
<xs:documentation>analysis and id must be unique within a search_hit</xs:documentation>
|
|
548
|
+
</xs:annotation>
|
|
549
|
+
<xs:selector xpath="./pepx:analysis_result"/>
|
|
550
|
+
<xs:field xpath="@analysis"/>
|
|
551
|
+
<xs:field xpath="@id"/>
|
|
552
|
+
</xs:unique>
|
|
553
|
+
</xs:element>
|
|
554
|
+
|
|
555
|
+
</xs:sequence>
|
|
556
|
+
|
|
557
|
+
<xs:attribute name="search_id" type="positiveInt" default="1">
|
|
558
|
+
<xs:annotation>
|
|
559
|
+
<xs:documentation>Unique identifier to search summary</xs:documentation>
|
|
560
|
+
</xs:annotation>
|
|
561
|
+
</xs:attribute>
|
|
562
|
+
</xs:complexType>
|
|
563
|
+
</xs:element> <!-- search result -->
|
|
564
|
+
|
|
565
|
+
|
|
566
|
+
|
|
567
|
+
</xs:sequence>
|
|
568
|
+
<xs:attribute name="spectrum" type="xs:string" use="required"/>
|
|
569
|
+
<xs:attribute name="start_scan" type="xs:unsignedInt" use="required">
|
|
570
|
+
<xs:annotation>
|
|
571
|
+
<xs:documentation>first scan number integrated into MS/MS spectrum</xs:documentation>
|
|
572
|
+
</xs:annotation>
|
|
573
|
+
</xs:attribute>
|
|
574
|
+
<xs:attribute name="end_scan" type="xs:unsignedInt" use="required">
|
|
575
|
+
<xs:annotation>
|
|
576
|
+
<xs:documentation>last scan number integrated into MS/MS spectrum</xs:documentation>
|
|
577
|
+
</xs:annotation>
|
|
578
|
+
</xs:attribute>
|
|
579
|
+
<xs:attribute name="retention_time_sec" type="xs:float" use="optional" >
|
|
580
|
+
<xs:annotation>
|
|
581
|
+
<xs:documentation>retention time associated with start_scan</xs:documentation>
|
|
582
|
+
</xs:annotation>
|
|
583
|
+
</xs:attribute>
|
|
584
|
+
<xs:attribute name="activation_method" type="activationMethodType" use="optional" >
|
|
585
|
+
<xs:annotation>
|
|
586
|
+
<xs:documentation>Activation or fragmentation method: ETD, ECD, CID, etc</xs:documentation>
|
|
587
|
+
</xs:annotation>
|
|
588
|
+
</xs:attribute>
|
|
589
|
+
<xs:attribute name="precursor_neutral_mass" type="xs:float" use="required"/>
|
|
590
|
+
<xs:attribute name="assumed_charge" type="xs:nonNegativeInteger" use="required">
|
|
591
|
+
<xs:annotation>
|
|
592
|
+
<xs:documentation>Precursor ion charge used for search</xs:documentation>
|
|
593
|
+
</xs:annotation>
|
|
594
|
+
</xs:attribute>
|
|
595
|
+
<xs:attribute name="search_specification" type="xs:string">
|
|
596
|
+
<xs:annotation>
|
|
597
|
+
<xs:documentation>Search constraint applied specifically to this query</xs:documentation>
|
|
598
|
+
</xs:annotation>
|
|
599
|
+
</xs:attribute>
|
|
600
|
+
<xs:attribute name="index" type="positiveInt" use="required">
|
|
601
|
+
<xs:annotation>
|
|
602
|
+
<xs:documentation>Unique identifier</xs:documentation>
|
|
603
|
+
</xs:annotation>
|
|
604
|
+
</xs:attribute>
|
|
605
|
+
</xs:complexType>
|
|
606
|
+
<xs:unique name="unique_search_id">
|
|
607
|
+
<xs:annotation>
|
|
608
|
+
<xs:documentation>search_id must be unique within each msms_run_summary</xs:documentation>
|
|
609
|
+
</xs:annotation>
|
|
610
|
+
<xs:selector xpath="./pepx:search_result"/>
|
|
611
|
+
<xs:field xpath="@search_id"/>
|
|
612
|
+
</xs:unique>
|
|
613
|
+
|
|
614
|
+
|
|
615
|
+
|
|
616
|
+
</xs:element>
|
|
617
|
+
</xs:sequence>
|
|
618
|
+
<xs:attribute name="base_name" type="xs:string" use="required">
|
|
619
|
+
<xs:annotation>
|
|
620
|
+
<xs:documentation>full path file name of mzXML (minus the .mzXML)</xs:documentation>
|
|
621
|
+
</xs:annotation>
|
|
622
|
+
</xs:attribute>
|
|
623
|
+
<xs:attribute name="raw_data_type" type="xs:string" use="required">
|
|
624
|
+
<xs:annotation>
|
|
625
|
+
<xs:documentation>raw data type extension (e.g. .mzXML)</xs:documentation>
|
|
626
|
+
</xs:annotation>
|
|
627
|
+
</xs:attribute>
|
|
628
|
+
<xs:attribute name="raw_data" type="xs:string" use="required">
|
|
629
|
+
<xs:annotation>
|
|
630
|
+
<xs:documentation>raw data type extension (e.g. .mzXML)</xs:documentation>
|
|
631
|
+
</xs:annotation>
|
|
632
|
+
</xs:attribute>
|
|
633
|
+
<xs:attribute name="msManufacturer" type="xs:string">
|
|
634
|
+
<xs:annotation>
|
|
635
|
+
<xs:documentation>Manufacturer of MS/MS instrument</xs:documentation>
|
|
636
|
+
</xs:annotation>
|
|
637
|
+
</xs:attribute>
|
|
638
|
+
<xs:attribute name="msModel" type="xs:string">
|
|
639
|
+
<xs:annotation>
|
|
640
|
+
<xs:documentation>Instrument model (cf mzXML)</xs:documentation>
|
|
641
|
+
</xs:annotation>
|
|
642
|
+
</xs:attribute>
|
|
643
|
+
<xs:attribute name="msIonization" type="xs:string">
|
|
644
|
+
<xs:annotation>
|
|
645
|
+
<xs:documentation>Instrument model (cf mzXML)</xs:documentation>
|
|
646
|
+
</xs:annotation>
|
|
647
|
+
</xs:attribute>
|
|
648
|
+
<xs:attribute name="msMassAnalyzer" type="xs:string">
|
|
649
|
+
<xs:annotation>
|
|
650
|
+
<xs:documentation>Ion trap, etc (cf mzXML)</xs:documentation>
|
|
651
|
+
</xs:annotation>
|
|
652
|
+
</xs:attribute>
|
|
653
|
+
<xs:attribute name="msDetector" type="xs:string">
|
|
654
|
+
<xs:annotation>
|
|
655
|
+
<xs:documentation>EMT, etc(cf mzXML)</xs:documentation>
|
|
656
|
+
</xs:annotation>
|
|
657
|
+
</xs:attribute>
|
|
658
|
+
|
|
659
|
+
</xs:complexType>
|
|
660
|
+
<xs:unique name="unique_timestamp_analysis_time">
|
|
661
|
+
<xs:annotation>
|
|
662
|
+
<xs:documentation>analysis_timestamp analysis and time must be unique within each msms_run_summary</xs:documentation>
|
|
663
|
+
</xs:annotation>
|
|
664
|
+
<xs:selector xpath="./pepx:analysis_timestamp"/>
|
|
665
|
+
<xs:field xpath="@analysis"/>
|
|
666
|
+
<xs:field xpath="@time"/>
|
|
667
|
+
</xs:unique>
|
|
668
|
+
<xs:key name="search_summary_id">
|
|
669
|
+
<xs:selector xpath="./pepx:search_summary"/>
|
|
670
|
+
<xs:field xpath="@search_id"/>
|
|
671
|
+
</xs:key>
|
|
672
|
+
<xs:keyref name="search_result_id" refer="search_summary_id">
|
|
673
|
+
<xs:annotation>
|
|
674
|
+
<xs:documentation>search_id within each search_hit must correspond with that of a search_summary</xs:documentation>
|
|
675
|
+
</xs:annotation>
|
|
676
|
+
<xs:selector xpath="./pepx:spectrum_query/pepx:search_result"/>
|
|
677
|
+
<xs:field xpath="@search_id"/>
|
|
678
|
+
</xs:keyref>
|
|
679
|
+
<xs:key name="timestamp_analysis_id">
|
|
680
|
+
<xs:selector xpath="./pepx:analysis_timestamp"/>
|
|
681
|
+
<xs:field xpath="@analysis"/>
|
|
682
|
+
<xs:field xpath="@id"/>
|
|
683
|
+
</xs:key>
|
|
684
|
+
<xs:keyref name="result_analysis_id" refer="timestamp_analysis_id">
|
|
685
|
+
<xs:annotation>
|
|
686
|
+
<xs:documentation>analysis and id in analysis_result must correspond with those in an analysis_timestamp element</xs:documentation>
|
|
687
|
+
</xs:annotation>
|
|
688
|
+
<xs:selector xpath="./pepx:spectrum_query/pepx:search_result/pepx:search_hit/pepx:analysis_result"/>
|
|
689
|
+
<xs:field xpath="@analysis"/>
|
|
690
|
+
<xs:field xpath="@id"/>
|
|
691
|
+
</xs:keyref>
|
|
692
|
+
|
|
693
|
+
|
|
694
|
+
</xs:element>
|
|
695
|
+
</xs:sequence>
|
|
696
|
+
<xs:attribute name="name" type="xs:string">
|
|
697
|
+
<xs:annotation>
|
|
698
|
+
<xs:documentation>Summary name (currently not used)</xs:documentation>
|
|
699
|
+
</xs:annotation>
|
|
700
|
+
</xs:attribute>
|
|
701
|
+
<xs:attribute name="date" type="xs:dateTime" use="required">
|
|
702
|
+
<xs:annotation>
|
|
703
|
+
<xs:documentation>Date pepXML file was written</xs:documentation>
|
|
704
|
+
</xs:annotation>
|
|
705
|
+
</xs:attribute>
|
|
706
|
+
<xs:attribute name="summary_xml" type="xs:string" use="required">
|
|
707
|
+
<xs:annotation>
|
|
708
|
+
<xs:documentation>Full path self reference</xs:documentation>
|
|
709
|
+
</xs:annotation>
|
|
710
|
+
</xs:attribute>
|
|
711
|
+
</xs:complexType>
|
|
712
|
+
<xs:key name="summary_analysis_time">
|
|
713
|
+
<xs:selector xpath="./pepx:analysis_summary"/>
|
|
714
|
+
<xs:field xpath="@time"/>
|
|
715
|
+
<xs:field xpath="@analysis"/>
|
|
716
|
+
</xs:key>
|
|
717
|
+
<xs:keyref name="timestamp_analysis_time" refer="summary_analysis_time">
|
|
718
|
+
<xs:annotation>
|
|
719
|
+
<xs:documentation>time and analysis within timestamp must correspond with those within analysis_summary element</xs:documentation>
|
|
720
|
+
</xs:annotation>
|
|
721
|
+
<xs:selector xpath="./pepx:msms_run_summary/pepx:analysis_timestamp"/>
|
|
722
|
+
<xs:field xpath="@time"/>
|
|
723
|
+
<xs:field xpath="@analysis"/>
|
|
724
|
+
</xs:keyref>
|
|
725
|
+
<xs:unique name="unique_search_summary_basename">
|
|
726
|
+
<xs:annotation>
|
|
727
|
+
<xs:documentation>search_summary base_name (mzXML file) must be unique within document</xs:documentation>
|
|
728
|
+
</xs:annotation>
|
|
729
|
+
<xs:selector xpath="./pepx:msms_run_summary/pepx:search_summary"/>
|
|
730
|
+
<xs:field xpath="@base_name"/>
|
|
731
|
+
</xs:unique>
|
|
732
|
+
<xs:unique name="unique_query_index">
|
|
733
|
+
<xs:annotation>
|
|
734
|
+
<xs:documentation>spectrum_query index must be unique in document</xs:documentation>
|
|
735
|
+
</xs:annotation>
|
|
736
|
+
<xs:selector xpath="./pepx:msms_run_summary/pepx:spectrum_query"/>
|
|
737
|
+
<xs:field xpath="@index"/>
|
|
738
|
+
</xs:unique>
|
|
739
|
+
</xs:element>
|
|
740
|
+
|
|
741
|
+
<xs:element name="peptideprophet_summary">
|
|
742
|
+
<xs:annotation>
|
|
743
|
+
<xs:documentation>Summary information for PeptideProphet analysis</xs:documentation>
|
|
744
|
+
</xs:annotation>
|
|
745
|
+
<xs:complexType>
|
|
746
|
+
<xs:sequence>
|
|
747
|
+
<xs:element name="inputfile" minOccurs="1" maxOccurs="unbounded">
|
|
748
|
+
<xs:complexType>
|
|
749
|
+
<xs:attribute name="name" type="xs:string" use="required">
|
|
750
|
+
<xs:annotation>
|
|
751
|
+
<xs:documentation>Input file</xs:documentation>
|
|
752
|
+
</xs:annotation>
|
|
753
|
+
</xs:attribute>
|
|
754
|
+
</xs:complexType>
|
|
755
|
+
</xs:element>
|
|
756
|
+
|
|
757
|
+
|
|
758
|
+
<xs:element name="roc_data_point" minOccurs="0" maxOccurs="unbounded">
|
|
759
|
+
<xs:complexType>
|
|
760
|
+
<xs:attribute name="min_prob" type="xs:float" use="required">
|
|
761
|
+
<xs:annotation>
|
|
762
|
+
<xs:documentation>Filter threshold</xs:documentation>
|
|
763
|
+
</xs:annotation>
|
|
764
|
+
</xs:attribute>
|
|
765
|
+
<xs:attribute name="sensitivity" type="xs:float" use="required">
|
|
766
|
+
<xs:annotation>
|
|
767
|
+
<xs:documentation>Predicted sensitivity</xs:documentation>
|
|
768
|
+
</xs:annotation>
|
|
769
|
+
</xs:attribute>
|
|
770
|
+
<xs:attribute name="error" type="xs:float" use="required">
|
|
771
|
+
<xs:annotation>
|
|
772
|
+
<xs:documentation>Predicted false positive error rate</xs:documentation>
|
|
773
|
+
</xs:annotation>
|
|
774
|
+
</xs:attribute>
|
|
775
|
+
<xs:attribute name="num_corr" type="xs:unsignedInt" use="required">
|
|
776
|
+
<xs:annotation>
|
|
777
|
+
<xs:documentation>Predicted number of correct results passing filter</xs:documentation>
|
|
778
|
+
</xs:annotation>
|
|
779
|
+
</xs:attribute>
|
|
780
|
+
<xs:attribute name="num_incorr" type="xs:unsignedInt" use="required">
|
|
781
|
+
<xs:annotation>
|
|
782
|
+
<xs:documentation>Predicted number of incorrect results passing filter</xs:documentation>
|
|
783
|
+
</xs:annotation>
|
|
784
|
+
</xs:attribute>
|
|
785
|
+
</xs:complexType>
|
|
786
|
+
</xs:element>
|
|
787
|
+
<xs:element name="error_point" minOccurs="0" maxOccurs="unbounded">
|
|
788
|
+
<xs:complexType>
|
|
789
|
+
<xs:attribute name="error" type="xs:float" use="required">
|
|
790
|
+
<xs:annotation>
|
|
791
|
+
<xs:documentation>Predicted false positive error rate</xs:documentation>
|
|
792
|
+
</xs:annotation>
|
|
793
|
+
</xs:attribute>
|
|
794
|
+
<xs:attribute name="min_prob" type="xs:float" use="required">
|
|
795
|
+
<xs:annotation>
|
|
796
|
+
<xs:documentation>Filter threshold</xs:documentation>
|
|
797
|
+
</xs:annotation>
|
|
798
|
+
</xs:attribute>
|
|
799
|
+
<xs:attribute name="num_corr" type="xs:unsignedInt" use="required">
|
|
800
|
+
<xs:annotation>
|
|
801
|
+
<xs:documentation>Predicted number of correct results passing filter</xs:documentation>
|
|
802
|
+
</xs:annotation>
|
|
803
|
+
</xs:attribute>
|
|
804
|
+
<xs:attribute name="num_incorr" type="xs:unsignedInt" use="required">
|
|
805
|
+
<xs:annotation>
|
|
806
|
+
<xs:documentation>Predicted number of incorrect results passing filter</xs:documentation>
|
|
807
|
+
</xs:annotation>
|
|
808
|
+
</xs:attribute>
|
|
809
|
+
</xs:complexType>
|
|
810
|
+
</xs:element>
|
|
811
|
+
<xs:element name="distribution_point" minOccurs="0" maxOccurs="unbounded">
|
|
812
|
+
<xs:complexType>
|
|
813
|
+
<xs:attribute name="fvalue" type="xs:float" use="required">
|
|
814
|
+
<xs:annotation>
|
|
815
|
+
<xs:documentation>Discriminant Score (fval) bin</xs:documentation>
|
|
816
|
+
</xs:annotation>
|
|
817
|
+
</xs:attribute>
|
|
818
|
+
<xs:attribute name="obs_1_distr" type="xs:nonNegativeInteger" use="required">
|
|
819
|
+
<xs:annotation>
|
|
820
|
+
<xs:documentation>Number of 1+ spectra</xs:documentation>
|
|
821
|
+
</xs:annotation>
|
|
822
|
+
</xs:attribute>
|
|
823
|
+
<xs:attribute name="model_1_pos_distr" type="xs:float" use="required">
|
|
824
|
+
<xs:annotation>
|
|
825
|
+
<xs:documentation>Inferred number of correct 1+ spectra</xs:documentation>
|
|
826
|
+
</xs:annotation>
|
|
827
|
+
</xs:attribute>
|
|
828
|
+
<xs:attribute name="model_1_neg_distr" type="xs:float" use="required">
|
|
829
|
+
<xs:annotation>
|
|
830
|
+
<xs:documentation>Inferred number of incorrect 1+ spectra</xs:documentation>
|
|
831
|
+
</xs:annotation>
|
|
832
|
+
</xs:attribute>
|
|
833
|
+
<xs:attribute name="obs_2_distr" type="xs:nonNegativeInteger" use="required">
|
|
834
|
+
<xs:annotation>
|
|
835
|
+
<xs:documentation>Number of 2+ spectra</xs:documentation>
|
|
836
|
+
</xs:annotation>
|
|
837
|
+
</xs:attribute>
|
|
838
|
+
<xs:attribute name="model_2_pos_distr" type="xs:float" use="required">
|
|
839
|
+
<xs:annotation>
|
|
840
|
+
<xs:documentation>Inferred number of correct 2+ spectra</xs:documentation>
|
|
841
|
+
</xs:annotation>
|
|
842
|
+
</xs:attribute>
|
|
843
|
+
<xs:attribute name="model_2_neg_distr" type="xs:float" use="required">
|
|
844
|
+
<xs:annotation>
|
|
845
|
+
<xs:documentation>Inferred number of incorrect 2+ spectra</xs:documentation>
|
|
846
|
+
</xs:annotation>
|
|
847
|
+
</xs:attribute>
|
|
848
|
+
<xs:attribute name="obs_3_distr" type="xs:nonNegativeInteger" use="required">
|
|
849
|
+
<xs:annotation>
|
|
850
|
+
<xs:documentation>Number of 3+ spectra</xs:documentation>
|
|
851
|
+
</xs:annotation>
|
|
852
|
+
</xs:attribute>
|
|
853
|
+
<xs:attribute name="model_3_pos_distr" type="xs:float" use="required">
|
|
854
|
+
<xs:annotation>
|
|
855
|
+
<xs:documentation>Inferred number of correct 3+ spectra</xs:documentation>
|
|
856
|
+
</xs:annotation>
|
|
857
|
+
</xs:attribute>
|
|
858
|
+
<xs:attribute name="model_3_neg_distr" type="xs:float" use="required">
|
|
859
|
+
<xs:annotation>
|
|
860
|
+
<xs:documentation>Inferred number of incorrect 3+ spectra</xs:documentation>
|
|
861
|
+
</xs:annotation>
|
|
862
|
+
</xs:attribute>
|
|
863
|
+
<xs:attribute name="obs_4_distr" type="xs:nonNegativeInteger" use="required">
|
|
864
|
+
<xs:annotation>
|
|
865
|
+
<xs:documentation>Number of 4+ spectra</xs:documentation>
|
|
866
|
+
</xs:annotation>
|
|
867
|
+
</xs:attribute>
|
|
868
|
+
<xs:attribute name="model_4_pos_distr" type="xs:float" use="required">
|
|
869
|
+
<xs:annotation>
|
|
870
|
+
<xs:documentation>Inferred number of correct 4+ spectra</xs:documentation>
|
|
871
|
+
</xs:annotation>
|
|
872
|
+
</xs:attribute>
|
|
873
|
+
<xs:attribute name="model_4_neg_distr" type="xs:float" use="required">
|
|
874
|
+
<xs:annotation>
|
|
875
|
+
<xs:documentation>Inferred number of incorrect 4+ spectra</xs:documentation>
|
|
876
|
+
</xs:annotation>
|
|
877
|
+
</xs:attribute>
|
|
878
|
+
<xs:attribute name="obs_5_distr" type="xs:nonNegativeInteger" use="required">
|
|
879
|
+
<xs:annotation>
|
|
880
|
+
<xs:documentation>Number of 5+ spectra</xs:documentation>
|
|
881
|
+
</xs:annotation>
|
|
882
|
+
</xs:attribute>
|
|
883
|
+
<xs:attribute name="model_5_pos_distr" type="xs:float" use="required">
|
|
884
|
+
<xs:annotation>
|
|
885
|
+
<xs:documentation>Inferred number of correct 5+ spectra</xs:documentation>
|
|
886
|
+
</xs:annotation>
|
|
887
|
+
</xs:attribute>
|
|
888
|
+
<xs:attribute name="model_5_neg_distr" type="xs:float" use="required">
|
|
889
|
+
<xs:annotation>
|
|
890
|
+
<xs:documentation>Inferred number of incorrect 5+ spectra</xs:documentation>
|
|
891
|
+
</xs:annotation>
|
|
892
|
+
</xs:attribute>
|
|
893
|
+
<xs:attribute name="obs_6_distr" type="xs:nonNegativeInteger" use="required">
|
|
894
|
+
<xs:annotation>
|
|
895
|
+
<xs:documentation>Number of 6+ spectra</xs:documentation>
|
|
896
|
+
</xs:annotation>
|
|
897
|
+
</xs:attribute>
|
|
898
|
+
<xs:attribute name="model_6_pos_distr" type="xs:float" use="required">
|
|
899
|
+
<xs:annotation>
|
|
900
|
+
<xs:documentation>Inferred number of correct 6+ spectra</xs:documentation>
|
|
901
|
+
</xs:annotation>
|
|
902
|
+
</xs:attribute>
|
|
903
|
+
<xs:attribute name="model_6_neg_distr" type="xs:float" use="required">
|
|
904
|
+
<xs:annotation>
|
|
905
|
+
<xs:documentation>Inferred number of incorrect 6+ spectra</xs:documentation>
|
|
906
|
+
</xs:annotation>
|
|
907
|
+
</xs:attribute>
|
|
908
|
+
<xs:attribute name="obs_7_distr" type="xs:nonNegativeInteger" use="required">
|
|
909
|
+
<xs:annotation>
|
|
910
|
+
<xs:documentation>Number of 7+ spectra</xs:documentation>
|
|
911
|
+
</xs:annotation>
|
|
912
|
+
</xs:attribute>
|
|
913
|
+
<xs:attribute name="model_7_pos_distr" type="xs:float" use="required">
|
|
914
|
+
<xs:annotation>
|
|
915
|
+
<xs:documentation>Inferred number of correct 7+ spectra</xs:documentation>
|
|
916
|
+
</xs:annotation>
|
|
917
|
+
</xs:attribute>
|
|
918
|
+
<xs:attribute name="model_7_neg_distr" type="xs:float" use="required">
|
|
919
|
+
<xs:annotation>
|
|
920
|
+
<xs:documentation>Inferred number of incorrect 7+ spectra</xs:documentation>
|
|
921
|
+
</xs:annotation>
|
|
922
|
+
</xs:attribute>
|
|
923
|
+
</xs:complexType>
|
|
924
|
+
</xs:element>
|
|
925
|
+
<xs:element name="mixture_model" minOccurs="0" maxOccurs="unbounded">
|
|
926
|
+
<xs:complexType>
|
|
927
|
+
<xs:choice maxOccurs="unbounded">
|
|
928
|
+
<!-- mixturemodel_distribution -->
|
|
929
|
+
<xs:element name="mixturemodel_distribution" maxOccurs="unbounded">
|
|
930
|
+
<xs:complexType>
|
|
931
|
+
<xs:sequence>
|
|
932
|
+
<xs:element name="posmodel_distribution">
|
|
933
|
+
<xs:complexType>
|
|
934
|
+
<xs:sequence>
|
|
935
|
+
<xs:element name="parameter" type="nameValueType" maxOccurs="unbounded"/>
|
|
936
|
+
</xs:sequence>
|
|
937
|
+
<xs:attribute name="type" type="model_dis_type"/>
|
|
938
|
+
</xs:complexType>
|
|
939
|
+
</xs:element>
|
|
940
|
+
<xs:element name="negmodel_distribution">
|
|
941
|
+
<xs:complexType>
|
|
942
|
+
<xs:sequence>
|
|
943
|
+
<xs:element name="parameter" type="nameValueType" maxOccurs="unbounded"/>
|
|
944
|
+
</xs:sequence>
|
|
945
|
+
<xs:attribute name="type" type="model_dis_type"/>
|
|
946
|
+
</xs:complexType>
|
|
947
|
+
</xs:element>
|
|
948
|
+
</xs:sequence>
|
|
949
|
+
<xs:attribute name="name" type="xs:string" use="required"/>
|
|
950
|
+
</xs:complexType>
|
|
951
|
+
</xs:element>
|
|
952
|
+
<!-- mixturemodel_distribution -->
|
|
953
|
+
|
|
954
|
+
<!-- mixturemodel -->
|
|
955
|
+
<xs:element name="mixturemodel" maxOccurs="unbounded">
|
|
956
|
+
<xs:complexType>
|
|
957
|
+
<xs:sequence>
|
|
958
|
+
<xs:element name="point" maxOccurs="unbounded">
|
|
959
|
+
<xs:complexType>
|
|
960
|
+
<xs:attribute name="value" type="xs:float"/>
|
|
961
|
+
<xs:attribute name="pos_dens" type="xs:float"/>
|
|
962
|
+
<xs:attribute name="neg_dens" type="xs:float"/>
|
|
963
|
+
</xs:complexType>
|
|
964
|
+
</xs:element>
|
|
965
|
+
</xs:sequence>
|
|
966
|
+
<xs:attribute name="name" type="xs:string" use="required"/>
|
|
967
|
+
<xs:attribute name="pos_bandwidth" type="xs:float" use="required"/>
|
|
968
|
+
<xs:attribute name="neg_bandwidth" type="xs:float" use="required"/>
|
|
969
|
+
</xs:complexType>
|
|
970
|
+
</xs:element>
|
|
971
|
+
<!-- mixturemodel -->
|
|
972
|
+
|
|
973
|
+
|
|
974
|
+
</xs:choice>
|
|
975
|
+
<xs:attribute name="precursor_ion_charge" type="xs:nonNegativeInteger" use="required"/>
|
|
976
|
+
<xs:attribute name="comments" type="xs:string" use="required"/>
|
|
977
|
+
<xs:attribute name="prior_probability" type="xs:float" use="required">
|
|
978
|
+
<xs:annotation>
|
|
979
|
+
<xs:documentation>Fraction of results inferred to be correct</xs:documentation>
|
|
980
|
+
</xs:annotation>
|
|
981
|
+
</xs:attribute>
|
|
982
|
+
<xs:attribute name="est_tot_correct" type="xs:float" use="required"/>
|
|
983
|
+
<xs:attribute name="tot_num_spectra" type="xs:nonNegativeInteger" use="required">
|
|
984
|
+
<xs:annotation>
|
|
985
|
+
<xs:documentation>Number of input spectra</xs:documentation>
|
|
986
|
+
</xs:annotation>
|
|
987
|
+
</xs:attribute>
|
|
988
|
+
<xs:attribute name="num_iterations" type="xs:nonNegativeInteger" use="required">
|
|
989
|
+
<xs:annotation>
|
|
990
|
+
<xs:documentation>Number of EM interations prior to convergence</xs:documentation>
|
|
991
|
+
</xs:annotation>
|
|
992
|
+
</xs:attribute>
|
|
993
|
+
</xs:complexType>
|
|
994
|
+
</xs:element>
|
|
995
|
+
</xs:sequence>
|
|
996
|
+
<xs:attribute name="version" type="xs:string" use="required"/>
|
|
997
|
+
<xs:attribute name="author" type="xs:string" use="required"/>
|
|
998
|
+
<xs:attribute name="min_prob" type="xs:float" use="required">
|
|
999
|
+
<xs:annotation>
|
|
1000
|
+
<xs:documentation>Min probability to be included in output</xs:documentation>
|
|
1001
|
+
</xs:annotation>
|
|
1002
|
+
</xs:attribute>
|
|
1003
|
+
<xs:attribute name="options" type="xs:string">
|
|
1004
|
+
<xs:annotation>
|
|
1005
|
+
<xs:documentation>User specified run options</xs:documentation>
|
|
1006
|
+
</xs:annotation>
|
|
1007
|
+
</xs:attribute>
|
|
1008
|
+
<xs:attribute name="est_tot_num_correct" type="xs:float">
|
|
1009
|
+
<xs:annotation>
|
|
1010
|
+
<xs:documentation>Total inferred number of correct results</xs:documentation>
|
|
1011
|
+
</xs:annotation>
|
|
1012
|
+
</xs:attribute>
|
|
1013
|
+
</xs:complexType>
|
|
1014
|
+
</xs:element>
|
|
1015
|
+
<xs:element name="asapratio_summary">
|
|
1016
|
+
<xs:annotation>
|
|
1017
|
+
<xs:documentation>Quantitation</xs:documentation>
|
|
1018
|
+
</xs:annotation>
|
|
1019
|
+
<xs:complexType>
|
|
1020
|
+
<xs:attribute name="version" type="xs:string" use="required"/>
|
|
1021
|
+
<xs:attribute name="author" type="xs:string" use="required"/>
|
|
1022
|
+
<xs:attribute name="elution" type="xs:integer" use="required">
|
|
1023
|
+
<xs:annotation>
|
|
1024
|
+
<xs:documentation>Elution order of light vs heavy labeled peptide</xs:documentation>
|
|
1025
|
+
</xs:annotation>
|
|
1026
|
+
</xs:attribute>
|
|
1027
|
+
<xs:attribute name="labeled_residues" type="xs:string" use="required">
|
|
1028
|
+
<xs:annotation>
|
|
1029
|
+
<xs:documentation>Aminoacids and termini that are differentially labeled for quantitaiton</xs:documentation>
|
|
1030
|
+
</xs:annotation>
|
|
1031
|
+
</xs:attribute>
|
|
1032
|
+
<xs:attribute name="area_flag" type="xs:nonNegativeInteger" use="required"/>
|
|
1033
|
+
<xs:attribute name="static_quant" type="xs:string" use="required">
|
|
1034
|
+
<xs:annotation>
|
|
1035
|
+
<xs:documentation>Y if dataset is all light or heavy labeled, N if dataset is mixed heavy and light labeled</xs:documentation>
|
|
1036
|
+
</xs:annotation>
|
|
1037
|
+
</xs:attribute>
|
|
1038
|
+
</xs:complexType>
|
|
1039
|
+
</xs:element>
|
|
1040
|
+
<xs:element name="xpressratio_summary">
|
|
1041
|
+
<xs:annotation>
|
|
1042
|
+
<xs:documentation>Quantitation</xs:documentation>
|
|
1043
|
+
</xs:annotation>
|
|
1044
|
+
<xs:complexType>
|
|
1045
|
+
<xs:attribute name="version" type="xs:string" use="required"/>
|
|
1046
|
+
<xs:attribute name="author" type="xs:string" use="required"/>
|
|
1047
|
+
<xs:attribute name="same_scan_range" type="xs:string" use="required"/>
|
|
1048
|
+
<xs:attribute name="labeled_residues" type="xs:string" use="required"/>
|
|
1049
|
+
<xs:attribute name="xpress_light" type="xs:unsignedInt" use="required"/>
|
|
1050
|
+
<xs:attribute name="massdiff" type="xs:string" use="required"/>
|
|
1051
|
+
<xs:attribute name="masstol" type="xs:float" use="required"/>
|
|
1052
|
+
</xs:complexType>
|
|
1053
|
+
</xs:element>
|
|
1054
|
+
<xs:element name="peptideprophet_result">
|
|
1055
|
+
<xs:annotation>
|
|
1056
|
+
<xs:documentation>PeptideProphet validation results for search hit</xs:documentation>
|
|
1057
|
+
</xs:annotation>
|
|
1058
|
+
<xs:complexType>
|
|
1059
|
+
<xs:sequence>
|
|
1060
|
+
<xs:element name="search_score_summary" minOccurs="0">
|
|
1061
|
+
<xs:complexType>
|
|
1062
|
+
<xs:sequence>
|
|
1063
|
+
<xs:element name="parameter" type="nameValueType" minOccurs="2" maxOccurs="unbounded"/>
|
|
1064
|
+
</xs:sequence>
|
|
1065
|
+
</xs:complexType>
|
|
1066
|
+
</xs:element>
|
|
1067
|
+
</xs:sequence>
|
|
1068
|
+
<xs:attribute name="probability" type="xs:float" use="required"/>
|
|
1069
|
+
<xs:attribute name="all_ntt_prob" type="xs:string"/>
|
|
1070
|
+
<xs:attribute name="analysis" type="xs:string"/>
|
|
1071
|
+
</xs:complexType>
|
|
1072
|
+
</xs:element>
|
|
1073
|
+
<xs:element name="asapratio_result">
|
|
1074
|
+
<xs:annotation>
|
|
1075
|
+
<xs:documentation>ASAPRatio quantitation results for search hit</xs:documentation>
|
|
1076
|
+
</xs:annotation>
|
|
1077
|
+
<xs:complexType>
|
|
1078
|
+
<xs:sequence>
|
|
1079
|
+
<xs:element ref="asapratio_peptide_data"/>
|
|
1080
|
+
</xs:sequence>
|
|
1081
|
+
<xs:attribute name="mean" type="xs:float" use="required"/>
|
|
1082
|
+
<xs:attribute name="error" type="xs:float" use="required"/>
|
|
1083
|
+
<xs:attribute name="heavy2light_mean" type="xs:float" use="required"/>
|
|
1084
|
+
<xs:attribute name="heavy2light_error" type="xs:float" use="required"/>
|
|
1085
|
+
</xs:complexType>
|
|
1086
|
+
</xs:element>
|
|
1087
|
+
<xs:element name="asapratio_peptide_data">
|
|
1088
|
+
<xs:complexType>
|
|
1089
|
+
<xs:sequence>
|
|
1090
|
+
<xs:element ref="asapratio_contribution" maxOccurs="unbounded"/>
|
|
1091
|
+
</xs:sequence>
|
|
1092
|
+
<xs:attribute name="status" type="xs:byte" use="required"/>
|
|
1093
|
+
<xs:attribute name="cidIndex" type="xs:int" use="required"/>
|
|
1094
|
+
<xs:attribute name="light_mass" type="xs:float" use="required"/>
|
|
1095
|
+
<xs:attribute name="heavy_mass" type="xs:float" use="required"/>
|
|
1096
|
+
<xs:attribute name="area_flag" type="xs:unsignedInt" use="required"/>
|
|
1097
|
+
</xs:complexType>
|
|
1098
|
+
</xs:element>
|
|
1099
|
+
<xs:element name="asapratio_contribution">
|
|
1100
|
+
<xs:complexType>
|
|
1101
|
+
<xs:sequence>
|
|
1102
|
+
<xs:element ref="asapratio_lc_lightpeak"/>
|
|
1103
|
+
<xs:element ref="asapratio_lc_heavypeak"/>
|
|
1104
|
+
</xs:sequence>
|
|
1105
|
+
<xs:attribute name="ratio" type="xs:float" use="required"/>
|
|
1106
|
+
<xs:attribute name="error" type="xs:float" use="required"/>
|
|
1107
|
+
<xs:attribute name="charge" type="xs:nonNegativeInteger" use="required"/>
|
|
1108
|
+
<xs:attribute name="use" type="xs:unsignedByte" use="required"/>
|
|
1109
|
+
</xs:complexType>
|
|
1110
|
+
</xs:element>
|
|
1111
|
+
<xs:element name="asapratio_lc_lightpeak">
|
|
1112
|
+
<xs:complexType>
|
|
1113
|
+
<xs:attribute name="status" type="xs:byte" use="required"/>
|
|
1114
|
+
<xs:attribute name="left_valley" type="xs:int" use="required"/>
|
|
1115
|
+
<xs:attribute name="right_valley" type="xs:int" use="required"/>
|
|
1116
|
+
<xs:attribute name="background" type="xs:float" use="required"/>
|
|
1117
|
+
<xs:attribute name="area" type="xs:float" use="required"/>
|
|
1118
|
+
<xs:attribute name="area_error" type="xs:float" use="required"/>
|
|
1119
|
+
<xs:attribute name="time" type="xs:float" use="required"/>
|
|
1120
|
+
<xs:attribute name="time_width" type="xs:float" use="required"/>
|
|
1121
|
+
<xs:attribute name="is_heavy" type="xs:string" use="required"/>
|
|
1122
|
+
</xs:complexType>
|
|
1123
|
+
</xs:element>
|
|
1124
|
+
<xs:element name="asapratio_lc_heavypeak">
|
|
1125
|
+
<xs:complexType>
|
|
1126
|
+
<xs:attribute name="status" type="xs:byte" use="required"/>
|
|
1127
|
+
<xs:attribute name="left_valley" type="xs:int" use="required"/>
|
|
1128
|
+
<xs:attribute name="right_valley" type="xs:int" use="required"/>
|
|
1129
|
+
<xs:attribute name="background" type="xs:float" use="required"/>
|
|
1130
|
+
<xs:attribute name="area" type="xs:float" use="required"/>
|
|
1131
|
+
<xs:attribute name="area_error" type="xs:float" use="required"/>
|
|
1132
|
+
<xs:attribute name="time" type="xs:float" use="required"/>
|
|
1133
|
+
<xs:attribute name="time_width" type="xs:float" use="required"/>
|
|
1134
|
+
<xs:attribute name="is_heavy" type="xs:string" use="required"/>
|
|
1135
|
+
</xs:complexType>
|
|
1136
|
+
</xs:element>
|
|
1137
|
+
<xs:element name="database_refresh_timestamp">
|
|
1138
|
+
<xs:complexType>
|
|
1139
|
+
<xs:attribute name="database" type="xs:string" use="required"/>
|
|
1140
|
+
<xs:attribute name="min_num_enz_term" type="xs:nonNegativeInteger">
|
|
1141
|
+
<xs:annotation>
|
|
1142
|
+
<xs:documentation>minimum number of termini compaitble with enzyme used (should correspond with search enzyme constraint)</xs:documentation>
|
|
1143
|
+
</xs:annotation>
|
|
1144
|
+
</xs:attribute>
|
|
1145
|
+
</xs:complexType>
|
|
1146
|
+
</xs:element>
|
|
1147
|
+
<xs:element name="xpressratio_timestamp">
|
|
1148
|
+
<xs:complexType>
|
|
1149
|
+
<xs:attribute name="xpress_light" type="xs:integer" use="required"/>
|
|
1150
|
+
</xs:complexType>
|
|
1151
|
+
</xs:element>
|
|
1152
|
+
<xs:element name="asapratio_timestamp">
|
|
1153
|
+
<xs:complexType>
|
|
1154
|
+
<xs:attribute name="quant_label_masses" type="xs:string"/>
|
|
1155
|
+
<xs:attribute name="static_quant_label" type="xs:string"/>
|
|
1156
|
+
</xs:complexType>
|
|
1157
|
+
</xs:element>
|
|
1158
|
+
<xs:element name="xpressratio_result">
|
|
1159
|
+
<xs:annotation>
|
|
1160
|
+
<xs:documentation>Quantitation</xs:documentation>
|
|
1161
|
+
</xs:annotation>
|
|
1162
|
+
<xs:complexType>
|
|
1163
|
+
<xs:attribute name="light_firstscan" type="xs:unsignedInt" use="required"/>
|
|
1164
|
+
<xs:attribute name="light_lastscan" type="xs:unsignedInt" use="required"/>
|
|
1165
|
+
<xs:attribute name="light_mass" type="xs:float" use="required"/>
|
|
1166
|
+
<xs:attribute name="heavy_firstscan" type="xs:unsignedInt" use="required"/>
|
|
1167
|
+
<xs:attribute name="heavy_lastscan" type="xs:unsignedInt" use="required"/>
|
|
1168
|
+
<xs:attribute name="heavy_mass" type="xs:float" use="required"/>
|
|
1169
|
+
<xs:attribute name="mass_tol" type="xs:float" use="required"/>
|
|
1170
|
+
<xs:attribute name="ratio" type="xs:string" use="required"/>
|
|
1171
|
+
<xs:attribute name="heavy2light_ratio" type="xs:string" use="required"/>
|
|
1172
|
+
<xs:attribute name="light_area" type="xs:float" use="required"/>
|
|
1173
|
+
<xs:attribute name="heavy_area" type="xs:float" use="required"/>
|
|
1174
|
+
<xs:attribute name="decimal_ratio" type="xs:decimal" use="required"/>
|
|
1175
|
+
</xs:complexType>
|
|
1176
|
+
</xs:element>
|
|
1177
|
+
<!--the types used by above elements.-->
|
|
1178
|
+
|
|
1179
|
+
<xs:simpleType name="engineType">
|
|
1180
|
+
<xs:restriction base="xs:string">
|
|
1181
|
+
<xs:enumeration value="SEQUEST"/>
|
|
1182
|
+
<xs:enumeration value="MASCOT"/>
|
|
1183
|
+
<xs:enumeration value="COMET"/>
|
|
1184
|
+
<xs:enumeration value="PROBID"/>
|
|
1185
|
+
<xs:enumeration value="OMSSA"/>
|
|
1186
|
+
<xs:enumeration value="MyriMatch"/>
|
|
1187
|
+
<xs:enumeration value="X! Tandem (k-score)"/>
|
|
1188
|
+
<xs:enumeration value="X! Tandem"/>
|
|
1189
|
+
<xs:enumeration value="InsPecT"/>
|
|
1190
|
+
<xs:enumeration value="ProteinPilot"/>
|
|
1191
|
+
<xs:enumeration value="ProteinLynx"/>
|
|
1192
|
+
<xs:enumeration value="Spectrum Mill"/>
|
|
1193
|
+
<xs:enumeration value="greylag"/>
|
|
1194
|
+
<xs:enumeration value="Phenyx"/>
|
|
1195
|
+
<xs:enumeration value="Proteios"/>
|
|
1196
|
+
<xs:enumeration value="Crux"/>
|
|
1197
|
+
<xs:enumeration value="Tide"/>
|
|
1198
|
+
</xs:restriction>
|
|
1199
|
+
</xs:simpleType>
|
|
1200
|
+
<xs:simpleType name="activationMethodType">
|
|
1201
|
+
<xs:restriction base="xs:string">
|
|
1202
|
+
<xs:enumeration value="ETD"/>
|
|
1203
|
+
<xs:enumeration value="ECD"/>
|
|
1204
|
+
<xs:enumeration value="CID"/>
|
|
1205
|
+
<xs:enumeration value="ETD/CID"/>
|
|
1206
|
+
<xs:enumeration value="HCD"/>
|
|
1207
|
+
</xs:restriction>
|
|
1208
|
+
</xs:simpleType>
|
|
1209
|
+
<xs:simpleType name="model_dis_type">
|
|
1210
|
+
<xs:restriction base="xs:string">
|
|
1211
|
+
<xs:enumeration value="discrete"/>
|
|
1212
|
+
<xs:enumeration value="gaussian"/>
|
|
1213
|
+
<xs:enumeration value="extremevalue"/>
|
|
1214
|
+
<xs:enumeration value="gamma"/>
|
|
1215
|
+
<xs:enumeration value="evd"/>
|
|
1216
|
+
<xs:enumeration value="non-parametric"/>
|
|
1217
|
+
</xs:restriction>
|
|
1218
|
+
</xs:simpleType>
|
|
1219
|
+
<xs:simpleType name="massType">
|
|
1220
|
+
<xs:restriction base="xs:string">
|
|
1221
|
+
<xs:enumeration value="monoisotopic"/>
|
|
1222
|
+
<xs:enumeration value="average"/>
|
|
1223
|
+
</xs:restriction>
|
|
1224
|
+
</xs:simpleType>
|
|
1225
|
+
<xs:simpleType name="aa_symbolType">
|
|
1226
|
+
<xs:restriction base="xs:string">
|
|
1227
|
+
<xs:enumeration value="1"/>
|
|
1228
|
+
<xs:enumeration value="2"/>
|
|
1229
|
+
<xs:enumeration value="3"/>
|
|
1230
|
+
<xs:enumeration value="4"/>
|
|
1231
|
+
<xs:enumeration value="5"/>
|
|
1232
|
+
<xs:enumeration value="6"/>
|
|
1233
|
+
<xs:enumeration value="7"/>
|
|
1234
|
+
<xs:enumeration value="8"/>
|
|
1235
|
+
<xs:enumeration value="9"/>
|
|
1236
|
+
<xs:enumeration value="#"/>
|
|
1237
|
+
<xs:enumeration value="@"/>
|
|
1238
|
+
<xs:enumeration value="*"/>
|
|
1239
|
+
<xs:enumeration value="~"/>
|
|
1240
|
+
<xs:enumeration value="'"/>
|
|
1241
|
+
<xs:enumeration value="''"/>
|
|
1242
|
+
<xs:enumeration value="$"/>
|
|
1243
|
+
<xs:enumeration value="!"/>
|
|
1244
|
+
<xs:enumeration value="^"/>
|
|
1245
|
+
<xs:enumeration value="?"/>
|
|
1246
|
+
</xs:restriction>
|
|
1247
|
+
</xs:simpleType>
|
|
1248
|
+
<xs:simpleType name="term_symbolType">
|
|
1249
|
+
<xs:restriction base="xs:string">
|
|
1250
|
+
<xs:enumeration value=","/>
|
|
1251
|
+
<xs:enumeration value=";"/>
|
|
1252
|
+
<xs:enumeration value=":"/>
|
|
1253
|
+
</xs:restriction>
|
|
1254
|
+
</xs:simpleType>
|
|
1255
|
+
<xs:simpleType name="positiveInt">
|
|
1256
|
+
<xs:restriction base="xs:unsignedInt">
|
|
1257
|
+
<xs:minInclusive value="1"/>
|
|
1258
|
+
</xs:restriction>
|
|
1259
|
+
</xs:simpleType>
|
|
1260
|
+
<xs:complexType name="nameValueType">
|
|
1261
|
+
<xs:simpleContent>
|
|
1262
|
+
<xs:extension base="xs:anySimpleType">
|
|
1263
|
+
<xs:attribute name="name" type="xs:string" use="required"/>
|
|
1264
|
+
<xs:attribute name="value" type="xs:anySimpleType" use="required"/>
|
|
1265
|
+
<xs:attribute name="type" type="xs:anySimpleType"/>
|
|
1266
|
+
</xs:extension>
|
|
1267
|
+
</xs:simpleContent>
|
|
1268
|
+
</xs:complexType>
|
|
1269
|
+
<xs:element name="interact_summary">
|
|
1270
|
+
<xs:annotation>
|
|
1271
|
+
<xs:documentation>Combined datasets</xs:documentation>
|
|
1272
|
+
</xs:annotation>
|
|
1273
|
+
<xs:complexType>
|
|
1274
|
+
<xs:sequence>
|
|
1275
|
+
<xs:element name="inputfile" minOccurs="1" maxOccurs="unbounded">
|
|
1276
|
+
<xs:annotation>
|
|
1277
|
+
<xs:documentation>Input file</xs:documentation>
|
|
1278
|
+
</xs:annotation>
|
|
1279
|
+
<xs:complexType>
|
|
1280
|
+
<xs:attribute name="name" type="xs:string" use="required"/>
|
|
1281
|
+
</xs:complexType>
|
|
1282
|
+
</xs:element>
|
|
1283
|
+
</xs:sequence>
|
|
1284
|
+
<xs:attribute name="filename" type="xs:string" use="required">
|
|
1285
|
+
<xs:annotation>
|
|
1286
|
+
<xs:documentation>Self reference</xs:documentation>
|
|
1287
|
+
</xs:annotation>
|
|
1288
|
+
</xs:attribute>
|
|
1289
|
+
<xs:attribute name="directory" type="xs:string" use="required">
|
|
1290
|
+
<xs:annotation>
|
|
1291
|
+
<xs:documentation>Directory of self</xs:documentation>
|
|
1292
|
+
</xs:annotation>
|
|
1293
|
+
</xs:attribute>
|
|
1294
|
+
</xs:complexType>
|
|
1295
|
+
</xs:element>
|
|
1296
|
+
<xs:element name="libra_result">
|
|
1297
|
+
<xs:annotation>
|
|
1298
|
+
<xs:documentation>libra quantitation for search hit</xs:documentation>
|
|
1299
|
+
</xs:annotation>
|
|
1300
|
+
<xs:complexType>
|
|
1301
|
+
<xs:sequence>
|
|
1302
|
+
<xs:element name="intensity" maxOccurs="unbounded">
|
|
1303
|
+
<xs:annotation>
|
|
1304
|
+
<xs:documentation>integrated mass intensity</xs:documentation>
|
|
1305
|
+
</xs:annotation>
|
|
1306
|
+
<xs:complexType>
|
|
1307
|
+
<xs:attribute name="channel" type="positiveInt" use="required">
|
|
1308
|
+
<xs:annotation>
|
|
1309
|
+
<xs:documentation>mass channel number</xs:documentation>
|
|
1310
|
+
</xs:annotation>
|
|
1311
|
+
</xs:attribute>
|
|
1312
|
+
<xs:attribute name="target_mass" type="xs:float" use="required">
|
|
1313
|
+
<xs:annotation>
|
|
1314
|
+
<xs:documentation>mass of channel</xs:documentation>
|
|
1315
|
+
</xs:annotation>
|
|
1316
|
+
</xs:attribute>
|
|
1317
|
+
<xs:attribute name="absolute" type="xs:float" use="required">
|
|
1318
|
+
<xs:annotation>
|
|
1319
|
+
<xs:documentation>absolute integrated intensity</xs:documentation>
|
|
1320
|
+
</xs:annotation>
|
|
1321
|
+
</xs:attribute>
|
|
1322
|
+
<xs:attribute name="normalized" type="xs:float" use="required">
|
|
1323
|
+
<xs:annotation>
|
|
1324
|
+
<xs:documentation>normalized integrated intensity (normalization channel stored in libra_summary)</xs:documentation>
|
|
1325
|
+
</xs:annotation>
|
|
1326
|
+
</xs:attribute>
|
|
1327
|
+
<xs:attribute name="reject" type="xs:boolean" use="optional" default="0">
|
|
1328
|
+
<xs:annotation>
|
|
1329
|
+
<xs:documentation>whether or not to reject this ratio as valid</xs:documentation>
|
|
1330
|
+
</xs:annotation>
|
|
1331
|
+
</xs:attribute>
|
|
1332
|
+
</xs:complexType>
|
|
1333
|
+
</xs:element>
|
|
1334
|
+
</xs:sequence>
|
|
1335
|
+
<xs:attribute name="is_rejected" type="xs:boolean" use="optional" default="0">
|
|
1336
|
+
<xs:annotation>
|
|
1337
|
+
<xs:documentation>whether or not to reject this ratio as valid</xs:documentation>
|
|
1338
|
+
</xs:annotation>
|
|
1339
|
+
</xs:attribute>
|
|
1340
|
+
</xs:complexType>
|
|
1341
|
+
<xs:unique name="libra_result_channel_index">
|
|
1342
|
+
<xs:annotation>
|
|
1343
|
+
<xs:documentation>channel number must be unique</xs:documentation>
|
|
1344
|
+
</xs:annotation>
|
|
1345
|
+
<xs:selector xpath="."/>
|
|
1346
|
+
<xs:field xpath="@channel"/>
|
|
1347
|
+
</xs:unique>
|
|
1348
|
+
</xs:element>
|
|
1349
|
+
<xs:element name="libra_summary">
|
|
1350
|
+
<xs:annotation>
|
|
1351
|
+
<xs:documentation>summary info for libra quantitation analysis</xs:documentation>
|
|
1352
|
+
</xs:annotation>
|
|
1353
|
+
<xs:complexType>
|
|
1354
|
+
<xs:sequence>
|
|
1355
|
+
<xs:element name="fragment_masses" maxOccurs="unbounded">
|
|
1356
|
+
<xs:annotation>
|
|
1357
|
+
<xs:documentation>quantitation channel</xs:documentation>
|
|
1358
|
+
</xs:annotation>
|
|
1359
|
+
<xs:complexType>
|
|
1360
|
+
<xs:attribute name="channel" type="positiveInt" use="required">
|
|
1361
|
+
<xs:annotation>
|
|
1362
|
+
<xs:documentation>channel number</xs:documentation>
|
|
1363
|
+
</xs:annotation>
|
|
1364
|
+
</xs:attribute>
|
|
1365
|
+
<xs:attribute name="mz" type="xs:float" use="required">
|
|
1366
|
+
<xs:annotation>
|
|
1367
|
+
<xs:documentation>channel mass</xs:documentation>
|
|
1368
|
+
</xs:annotation>
|
|
1369
|
+
</xs:attribute>
|
|
1370
|
+
<xs:attribute name="offset" type="xs:float">
|
|
1371
|
+
<xs:annotation>
|
|
1372
|
+
<xs:documentation>mass offset from mz value</xs:documentation>
|
|
1373
|
+
</xs:annotation>
|
|
1374
|
+
</xs:attribute>
|
|
1375
|
+
</xs:complexType>
|
|
1376
|
+
</xs:element>
|
|
1377
|
+
<xs:element name="isotopic_contributions" minOccurs="0">
|
|
1378
|
+
<xs:annotation>
|
|
1379
|
+
<xs:documentation>isotopic contributions from one channel to others</xs:documentation>
|
|
1380
|
+
</xs:annotation>
|
|
1381
|
+
<xs:complexType>
|
|
1382
|
+
<xs:sequence>
|
|
1383
|
+
<xs:element name="contributing_channel" maxOccurs="unbounded">
|
|
1384
|
+
<xs:annotation>
|
|
1385
|
+
<xs:documentation>channel donor</xs:documentation>
|
|
1386
|
+
</xs:annotation>
|
|
1387
|
+
<xs:complexType>
|
|
1388
|
+
<xs:sequence>
|
|
1389
|
+
<xs:element name="affected_channel" maxOccurs="unbounded">
|
|
1390
|
+
<xs:annotation>
|
|
1391
|
+
<xs:documentation>channel recipient</xs:documentation>
|
|
1392
|
+
</xs:annotation>
|
|
1393
|
+
<xs:complexType>
|
|
1394
|
+
<xs:attribute name="channel" type="positiveInt" use="required">
|
|
1395
|
+
<xs:annotation>
|
|
1396
|
+
<xs:documentation>channel number</xs:documentation>
|
|
1397
|
+
</xs:annotation>
|
|
1398
|
+
</xs:attribute>
|
|
1399
|
+
<xs:attribute name="correction" type="xs:float" use="required">
|
|
1400
|
+
<xs:annotation>
|
|
1401
|
+
<xs:documentation>fraction of affected channel due to contributing</xs:documentation>
|
|
1402
|
+
</xs:annotation>
|
|
1403
|
+
</xs:attribute>
|
|
1404
|
+
</xs:complexType>
|
|
1405
|
+
</xs:element>
|
|
1406
|
+
</xs:sequence>
|
|
1407
|
+
<xs:attribute name="channel" type="positiveInt" use="required">
|
|
1408
|
+
<xs:annotation>
|
|
1409
|
+
<xs:documentation>channel number</xs:documentation>
|
|
1410
|
+
</xs:annotation>
|
|
1411
|
+
</xs:attribute>
|
|
1412
|
+
</xs:complexType>
|
|
1413
|
+
</xs:element>
|
|
1414
|
+
</xs:sequence>
|
|
1415
|
+
</xs:complexType>
|
|
1416
|
+
</xs:element>
|
|
1417
|
+
</xs:sequence>
|
|
1418
|
+
<xs:attribute name="mass_tolerance" type="xs:float" use="required">
|
|
1419
|
+
<xs:annotation>
|
|
1420
|
+
<xs:documentation>channel mass width</xs:documentation>
|
|
1421
|
+
</xs:annotation>
|
|
1422
|
+
</xs:attribute>
|
|
1423
|
+
<xs:attribute name="centroiding_preference" type="xs:int" use="required"/>
|
|
1424
|
+
<xs:attribute name="normalization" type="xs:int" use="required">
|
|
1425
|
+
<xs:annotation>
|
|
1426
|
+
<xs:documentation>channel used as denominator for normalized integrated intensities (0 means use channel with strongest absolute integrated intensity)</xs:documentation>
|
|
1427
|
+
</xs:annotation>
|
|
1428
|
+
</xs:attribute>
|
|
1429
|
+
<xs:attribute name="output_type" type="xs:int" use="required"/>
|
|
1430
|
+
<xs:attribute name="channel_code" type="xs:string">
|
|
1431
|
+
<xs:annotation>
|
|
1432
|
+
<xs:documentation>concatenated channel masses (used as signature for defined channel masses)</xs:documentation>
|
|
1433
|
+
</xs:annotation>
|
|
1434
|
+
</xs:attribute>
|
|
1435
|
+
</xs:complexType>
|
|
1436
|
+
|
|
1437
|
+
<xs:key name="libra_channel_index">
|
|
1438
|
+
<xs:selector xpath="./pepx:fragment_masses"/>
|
|
1439
|
+
<xs:field xpath="@channel"/>
|
|
1440
|
+
</xs:key>
|
|
1441
|
+
<xs:keyref name="libra_contr_channel_index_ref" refer="libra_channel_index">
|
|
1442
|
+
<xs:annotation>
|
|
1443
|
+
<xs:documentation>contributing channel numbers must correspond with defined channels</xs:documentation>
|
|
1444
|
+
</xs:annotation>
|
|
1445
|
+
<xs:selector xpath="./pepx:isotopic_contributions/pepx:contributing_channel"/>
|
|
1446
|
+
<xs:field xpath="@channel"/>
|
|
1447
|
+
</xs:keyref>
|
|
1448
|
+
<xs:keyref name="libra_aff_channel_index_ref" refer="libra_channel_index">
|
|
1449
|
+
<xs:annotation>
|
|
1450
|
+
<xs:documentation>contributing channel numbers must correspond with defined channels</xs:documentation>
|
|
1451
|
+
</xs:annotation>
|
|
1452
|
+
<xs:selector xpath="./pepx:isotopic_contributions/pepx:contributing_channel/pepx:affected_channel"/>
|
|
1453
|
+
<xs:field xpath="@channel"/>
|
|
1454
|
+
</xs:keyref>
|
|
1455
|
+
|
|
1456
|
+
</xs:element>
|
|
1457
|
+
|
|
1458
|
+
</xs:schema>
|