ms-ident 0.0.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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: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: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: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:complexType>
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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: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:complexType>
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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 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>
|
|
269
|
+
<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="required">
|
|
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="required">
|
|
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:complexType>
|
|
409
|
+
</xs:element>
|
|
410
|
+
<xs:element name="modification_info" minOccurs="0">
|
|
411
|
+
<xs:annotation>
|
|
412
|
+
<xs:documentation>Positions and masses of modifications</xs:documentation>
|
|
413
|
+
</xs:annotation>
|
|
414
|
+
<xs:complexType>
|
|
415
|
+
<xs:sequence>
|
|
416
|
+
<xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
|
|
417
|
+
<xs:complexType>
|
|
418
|
+
<xs:attribute name="position" type="xs:nonNegativeInteger" use="required">
|
|
419
|
+
<xs:annotation>
|
|
420
|
+
<xs:documentation>modified aminoacid position in peptide [ranging from 1 to peptide length]</xs:documentation>
|
|
421
|
+
</xs:annotation>
|
|
422
|
+
</xs:attribute>
|
|
423
|
+
<xs:attribute name="mass" type="xs:double" use="required">
|
|
424
|
+
<xs:annotation>
|
|
425
|
+
<xs:documentation>modified mass of aminoacid</xs:documentation>
|
|
426
|
+
</xs:annotation>
|
|
427
|
+
</xs:attribute>
|
|
428
|
+
</xs:complexType>
|
|
429
|
+
</xs:element>
|
|
430
|
+
</xs:sequence>
|
|
431
|
+
<xs:attribute name="mod_nterm_mass" type="xs:double">
|
|
432
|
+
<xs:annotation>
|
|
433
|
+
<xs:documentation>Mass of modified N terminus</xs:documentation>
|
|
434
|
+
</xs:annotation>
|
|
435
|
+
</xs:attribute>
|
|
436
|
+
<xs:attribute name="mod_cterm_mass" type="xs:double">
|
|
437
|
+
<xs:annotation>
|
|
438
|
+
<xs:documentation>Mass of modified C terminus</xs:documentation>
|
|
439
|
+
</xs:annotation>
|
|
440
|
+
</xs:attribute>
|
|
441
|
+
<xs:attribute name="modified_peptide" type="xs:string">
|
|
442
|
+
<xs:annotation>
|
|
443
|
+
<xs:documentation>Peptide sequence (with indicated modifications)</xs:documentation>
|
|
444
|
+
</xs:annotation>
|
|
445
|
+
</xs:attribute>
|
|
446
|
+
</xs:complexType>
|
|
447
|
+
</xs:element>
|
|
448
|
+
<xs:element name="search_score" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
|
|
449
|
+
<xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">
|
|
450
|
+
<xs:complexType>
|
|
451
|
+
<xs:sequence>
|
|
452
|
+
<xs:any namespace="##any" processContents="lax">
|
|
453
|
+
<xs:annotation>
|
|
454
|
+
<xs:documentation>Wildcard for result info customized for a particular analysis</xs:documentation>
|
|
455
|
+
</xs:annotation>
|
|
456
|
+
</xs:any>
|
|
457
|
+
|
|
458
|
+
</xs:sequence>
|
|
459
|
+
<xs:attribute name="analysis" type="xs:string" use="required"/>
|
|
460
|
+
<xs:attribute name="id" type="positiveInt" default="1"/>
|
|
461
|
+
</xs:complexType>
|
|
462
|
+
</xs:element>
|
|
463
|
+
<xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
|
|
464
|
+
</xs:sequence>
|
|
465
|
+
<xs:attribute name="hit_rank" type="positiveInt" use="required"/>
|
|
466
|
+
<xs:attribute name="peptide" type="xs:string" use="required">
|
|
467
|
+
<xs:annotation>
|
|
468
|
+
<xs:documentation>Peptide aminoacid sequence (with no indicated modifications)</xs:documentation>
|
|
469
|
+
</xs:annotation>
|
|
470
|
+
</xs:attribute>
|
|
471
|
+
<xs:attribute name="peptide_prev_aa" type="xs:string">
|
|
472
|
+
<xs:annotation>
|
|
473
|
+
<xs:documentation>Aminoacid preceding peptide (- if none)</xs:documentation>
|
|
474
|
+
</xs:annotation>
|
|
475
|
+
</xs:attribute>
|
|
476
|
+
<xs:attribute name="peptide_next_aa" type="xs:string">
|
|
477
|
+
<xs:annotation>
|
|
478
|
+
<xs:documentation>Aminoacid following peptide (- if none)</xs:documentation>
|
|
479
|
+
</xs:annotation>
|
|
480
|
+
</xs:attribute>
|
|
481
|
+
<xs:attribute name="protein" type="xs:string" use="required"/>
|
|
482
|
+
<xs:attribute name="num_tot_proteins" type="xs:unsignedInt" use="required">
|
|
483
|
+
<xs:annotation>
|
|
484
|
+
<xs:documentation>Number of unique proteins in search database containing peptide</xs:documentation>
|
|
485
|
+
</xs:annotation>
|
|
486
|
+
</xs:attribute>
|
|
487
|
+
<xs:attribute name="num_matched_ions" type="xs:nonNegativeInteger">
|
|
488
|
+
<xs:annotation>
|
|
489
|
+
<xs:documentation>Number of peptide fragment ions found in spectrum</xs:documentation>
|
|
490
|
+
</xs:annotation>
|
|
491
|
+
</xs:attribute>
|
|
492
|
+
<xs:attribute name="tot_num_ions" type="xs:nonNegativeInteger">
|
|
493
|
+
<xs:annotation>
|
|
494
|
+
<xs:documentation>Number of peptide fragment ions predicted for peptide</xs:documentation>
|
|
495
|
+
</xs:annotation>
|
|
496
|
+
</xs:attribute>
|
|
497
|
+
<xs:attribute name="calc_neutral_pep_mass" type="xs:float" use="required"/>
|
|
498
|
+
<xs:attribute name="massdiff" type="xs:string" use="required">
|
|
499
|
+
<xs:annotation>
|
|
500
|
+
<xs:documentation>Mass(precursor ion) - Mass(peptide)</xs:documentation>
|
|
501
|
+
</xs:annotation>
|
|
502
|
+
</xs:attribute>
|
|
503
|
+
<xs:attribute name="num_tol_term" type="xs:nonNegativeInteger">
|
|
504
|
+
<xs:annotation>
|
|
505
|
+
<xs:documentation>Number of peptide termini consistent with cleavage by sample enzyme</xs:documentation>
|
|
506
|
+
</xs:annotation>
|
|
507
|
+
</xs:attribute>
|
|
508
|
+
<xs:attribute name="num_missed_cleavages" type="xs:integer">
|
|
509
|
+
<xs:annotation>
|
|
510
|
+
<xs:documentation>Number of sample enzyme cleavage sites internal to peptide</xs:documentation>
|
|
511
|
+
</xs:annotation>
|
|
512
|
+
</xs:attribute>
|
|
513
|
+
<xs:attribute name="is_rejected" default="0">
|
|
514
|
+
<xs:annotation>
|
|
515
|
+
<xs:documentation>Potential use in future for user manual validation (0 or 1)</xs:documentation>
|
|
516
|
+
</xs:annotation>
|
|
517
|
+
<xs:simpleType>
|
|
518
|
+
<xs:restriction base="xs:nonNegativeInteger">
|
|
519
|
+
<xs:enumeration value="0"/>
|
|
520
|
+
<xs:enumeration value="1"/>
|
|
521
|
+
</xs:restriction>
|
|
522
|
+
</xs:simpleType>
|
|
523
|
+
|
|
524
|
+
</xs:attribute>
|
|
525
|
+
<xs:attribute name="protein_descr" type="xs:string">
|
|
526
|
+
<xs:annotation>
|
|
527
|
+
<xs:documentation>Extracted from search database</xs:documentation>
|
|
528
|
+
</xs:annotation>
|
|
529
|
+
</xs:attribute>
|
|
530
|
+
<xs:attribute name="calc_pI" type="xs:string"/>
|
|
531
|
+
<xs:attribute name="protein_mw" type="xs:double"/>
|
|
532
|
+
|
|
533
|
+
</xs:complexType>
|
|
534
|
+
|
|
535
|
+
<xs:unique name="unique_result_analysis_id">
|
|
536
|
+
<xs:annotation>
|
|
537
|
+
<xs:documentation>analysis and id must be unique within a search_hit</xs:documentation>
|
|
538
|
+
</xs:annotation>
|
|
539
|
+
<xs:selector xpath="./pepx:analysis_result"/>
|
|
540
|
+
<xs:field xpath="@analysis"/>
|
|
541
|
+
<xs:field xpath="@id"/>
|
|
542
|
+
</xs:unique>
|
|
543
|
+
</xs:element>
|
|
544
|
+
|
|
545
|
+
</xs:sequence>
|
|
546
|
+
|
|
547
|
+
<xs:attribute name="search_id" type="positiveInt" default="1">
|
|
548
|
+
<xs:annotation>
|
|
549
|
+
<xs:documentation>Unique identifier to search summary</xs:documentation>
|
|
550
|
+
</xs:annotation>
|
|
551
|
+
</xs:attribute>
|
|
552
|
+
</xs:complexType>
|
|
553
|
+
</xs:element> <!-- search result -->
|
|
554
|
+
|
|
555
|
+
|
|
556
|
+
|
|
557
|
+
</xs:sequence>
|
|
558
|
+
<xs:attribute name="spectrum" type="xs:string" use="required"/>
|
|
559
|
+
<xs:attribute name="start_scan" type="xs:unsignedInt" use="required">
|
|
560
|
+
<xs:annotation>
|
|
561
|
+
<xs:documentation>first scan number integrated into MS/MS spectrum</xs:documentation>
|
|
562
|
+
</xs:annotation>
|
|
563
|
+
</xs:attribute>
|
|
564
|
+
<xs:attribute name="end_scan" type="xs:unsignedInt" use="required">
|
|
565
|
+
<xs:annotation>
|
|
566
|
+
<xs:documentation>last scan number integrated into MS/MS spectrum</xs:documentation>
|
|
567
|
+
</xs:annotation>
|
|
568
|
+
</xs:attribute>
|
|
569
|
+
<xs:attribute name="retention_time_sec" type="xs:float" use="optional" >
|
|
570
|
+
<xs:annotation>
|
|
571
|
+
<xs:documentation>retention time associated with start_scan</xs:documentation>
|
|
572
|
+
</xs:annotation>
|
|
573
|
+
</xs:attribute>
|
|
574
|
+
<xs:attribute name="precursor_neutral_mass" type="xs:float" use="required"/>
|
|
575
|
+
<xs:attribute name="assumed_charge" type="xs:nonNegativeInteger" use="required">
|
|
576
|
+
<xs:annotation>
|
|
577
|
+
<xs:documentation>Precursor ion charge used for search</xs:documentation>
|
|
578
|
+
</xs:annotation>
|
|
579
|
+
</xs:attribute>
|
|
580
|
+
<xs:attribute name="search_specification" type="xs:string">
|
|
581
|
+
<xs:annotation>
|
|
582
|
+
<xs:documentation>Search constraint applied specifically to this query</xs:documentation>
|
|
583
|
+
</xs:annotation>
|
|
584
|
+
</xs:attribute>
|
|
585
|
+
<xs:attribute name="index" type="positiveInt" use="required">
|
|
586
|
+
<xs:annotation>
|
|
587
|
+
<xs:documentation>Unique identifier</xs:documentation>
|
|
588
|
+
</xs:annotation>
|
|
589
|
+
</xs:attribute>
|
|
590
|
+
</xs:complexType>
|
|
591
|
+
<xs:unique name="unique_search_id">
|
|
592
|
+
<xs:annotation>
|
|
593
|
+
<xs:documentation>search_id must be unique within each msms_run_summary</xs:documentation>
|
|
594
|
+
</xs:annotation>
|
|
595
|
+
<xs:selector xpath="./pepx:search_result"/>
|
|
596
|
+
<xs:field xpath="@search_id"/>
|
|
597
|
+
</xs:unique>
|
|
598
|
+
|
|
599
|
+
|
|
600
|
+
|
|
601
|
+
</xs:element>
|
|
602
|
+
</xs:sequence>
|
|
603
|
+
<xs:attribute name="base_name" type="xs:string" use="required">
|
|
604
|
+
<xs:annotation>
|
|
605
|
+
<xs:documentation>full path file name of mzXML (minus the .mzXML)</xs:documentation>
|
|
606
|
+
</xs:annotation>
|
|
607
|
+
</xs:attribute>
|
|
608
|
+
<xs:attribute name="raw_data_type" type="xs:string" use="required">
|
|
609
|
+
<xs:annotation>
|
|
610
|
+
<xs:documentation>raw data type extension (e.g. .mzXML)</xs:documentation>
|
|
611
|
+
</xs:annotation>
|
|
612
|
+
</xs:attribute>
|
|
613
|
+
<xs:attribute name="raw_data" type="xs:string" use="required">
|
|
614
|
+
<xs:annotation>
|
|
615
|
+
<xs:documentation>raw data type extension (e.g. .mzXML)</xs:documentation>
|
|
616
|
+
</xs:annotation>
|
|
617
|
+
</xs:attribute>
|
|
618
|
+
<xs:attribute name="msManufacturer" type="xs:string">
|
|
619
|
+
<xs:annotation>
|
|
620
|
+
<xs:documentation>Manufacturer of MS/MS instrument</xs:documentation>
|
|
621
|
+
</xs:annotation>
|
|
622
|
+
</xs:attribute>
|
|
623
|
+
<xs:attribute name="msModel" type="xs:string">
|
|
624
|
+
<xs:annotation>
|
|
625
|
+
<xs:documentation>Instrument model (cf mzXML)</xs:documentation>
|
|
626
|
+
</xs:annotation>
|
|
627
|
+
</xs:attribute>
|
|
628
|
+
<xs:attribute name="msIonization" type="xs:string">
|
|
629
|
+
<xs:annotation>
|
|
630
|
+
<xs:documentation>Instrument model (cf mzXML)</xs:documentation>
|
|
631
|
+
</xs:annotation>
|
|
632
|
+
</xs:attribute>
|
|
633
|
+
<xs:attribute name="msMassAnalyzer" type="xs:string">
|
|
634
|
+
<xs:annotation>
|
|
635
|
+
<xs:documentation>Ion trap, etc (cf mzXML)</xs:documentation>
|
|
636
|
+
</xs:annotation>
|
|
637
|
+
</xs:attribute>
|
|
638
|
+
<xs:attribute name="msDetector" type="xs:string">
|
|
639
|
+
<xs:annotation>
|
|
640
|
+
<xs:documentation>EMT, etc(cf mzXML)</xs:documentation>
|
|
641
|
+
</xs:annotation>
|
|
642
|
+
</xs:attribute>
|
|
643
|
+
|
|
644
|
+
</xs:complexType>
|
|
645
|
+
<xs:unique name="unique_timestamp_analysis_time">
|
|
646
|
+
<xs:annotation>
|
|
647
|
+
<xs:documentation>analysis_timestamp analysis and time must be unique within each msms_run_summary</xs:documentation>
|
|
648
|
+
</xs:annotation>
|
|
649
|
+
<xs:selector xpath="./pepx:analysis_timestamp"/>
|
|
650
|
+
<xs:field xpath="@analysis"/>
|
|
651
|
+
<xs:field xpath="@time"/>
|
|
652
|
+
</xs:unique>
|
|
653
|
+
<xs:key name="search_summary_id">
|
|
654
|
+
<xs:selector xpath="./pepx:search_summary"/>
|
|
655
|
+
<xs:field xpath="@search_id"/>
|
|
656
|
+
</xs:key>
|
|
657
|
+
<xs:keyref name="search_result_id" refer="search_summary_id">
|
|
658
|
+
<xs:annotation>
|
|
659
|
+
<xs:documentation>search_id within each search_hit must correspond with that of a search_summary</xs:documentation>
|
|
660
|
+
</xs:annotation>
|
|
661
|
+
<xs:selector xpath="./pepx:spectrum_query/pepx:search_result"/>
|
|
662
|
+
<xs:field xpath="@search_id"/>
|
|
663
|
+
</xs:keyref>
|
|
664
|
+
<xs:key name="timestamp_analysis_id">
|
|
665
|
+
<xs:selector xpath="./pepx:analysis_timestamp"/>
|
|
666
|
+
<xs:field xpath="@analysis"/>
|
|
667
|
+
<xs:field xpath="@id"/>
|
|
668
|
+
</xs:key>
|
|
669
|
+
<xs:keyref name="result_analysis_id" refer="timestamp_analysis_id">
|
|
670
|
+
<xs:annotation>
|
|
671
|
+
<xs:documentation>analysis and id in analysis_result must correspond with those in an analysis_timestamp element</xs:documentation>
|
|
672
|
+
</xs:annotation>
|
|
673
|
+
<xs:selector xpath="./pepx:spectrum_query/pepx:search_result/pepx:search_hit/pepx:analysis_result"/>
|
|
674
|
+
<xs:field xpath="@analysis"/>
|
|
675
|
+
<xs:field xpath="@id"/>
|
|
676
|
+
</xs:keyref>
|
|
677
|
+
|
|
678
|
+
|
|
679
|
+
</xs:element>
|
|
680
|
+
</xs:sequence>
|
|
681
|
+
<xs:attribute name="name" type="xs:string">
|
|
682
|
+
<xs:annotation>
|
|
683
|
+
<xs:documentation>Summary name (currently not used)</xs:documentation>
|
|
684
|
+
</xs:annotation>
|
|
685
|
+
</xs:attribute>
|
|
686
|
+
<xs:attribute name="date" type="xs:dateTime" use="required">
|
|
687
|
+
<xs:annotation>
|
|
688
|
+
<xs:documentation>Date pepXML file was written</xs:documentation>
|
|
689
|
+
</xs:annotation>
|
|
690
|
+
</xs:attribute>
|
|
691
|
+
<xs:attribute name="summary_xml" type="xs:string" use="required">
|
|
692
|
+
<xs:annotation>
|
|
693
|
+
<xs:documentation>Full path self reference</xs:documentation>
|
|
694
|
+
</xs:annotation>
|
|
695
|
+
</xs:attribute>
|
|
696
|
+
</xs:complexType>
|
|
697
|
+
<xs:key name="summary_analysis_time">
|
|
698
|
+
<xs:selector xpath="./pepx:analysis_summary"/>
|
|
699
|
+
<xs:field xpath="@time"/>
|
|
700
|
+
<xs:field xpath="@analysis"/>
|
|
701
|
+
</xs:key>
|
|
702
|
+
<xs:keyref name="timestamp_analysis_time" refer="summary_analysis_time">
|
|
703
|
+
<xs:annotation>
|
|
704
|
+
<xs:documentation>time and analysis within timestamp must correspond with those within analysis_summary element</xs:documentation>
|
|
705
|
+
</xs:annotation>
|
|
706
|
+
<xs:selector xpath="./pepx:msms_run_summary/pepx:analysis_timestamp"/>
|
|
707
|
+
<xs:field xpath="@time"/>
|
|
708
|
+
<xs:field xpath="@analysis"/>
|
|
709
|
+
</xs:keyref>
|
|
710
|
+
<xs:unique name="unique_search_summary_basename">
|
|
711
|
+
<xs:annotation>
|
|
712
|
+
<xs:documentation>search_summary base_name (mzXML file) must be unique within document</xs:documentation>
|
|
713
|
+
</xs:annotation>
|
|
714
|
+
<xs:selector xpath="./pepx:msms_run_summary/pepx:search_summary"/>
|
|
715
|
+
<xs:field xpath="@base_name"/>
|
|
716
|
+
</xs:unique>
|
|
717
|
+
<xs:unique name="unique_query_index">
|
|
718
|
+
<xs:annotation>
|
|
719
|
+
<xs:documentation>spectrum_query index must be unique in document</xs:documentation>
|
|
720
|
+
</xs:annotation>
|
|
721
|
+
<xs:selector xpath="./pepx:msms_run_summary/pepx:spectrum_query"/>
|
|
722
|
+
<xs:field xpath="@index"/>
|
|
723
|
+
</xs:unique>
|
|
724
|
+
</xs:element>
|
|
725
|
+
|
|
726
|
+
<xs:element name="peptideprophet_summary">
|
|
727
|
+
<xs:annotation>
|
|
728
|
+
<xs:documentation>Summary information for PeptideProphet analysis</xs:documentation>
|
|
729
|
+
</xs:annotation>
|
|
730
|
+
<xs:complexType>
|
|
731
|
+
<xs:sequence>
|
|
732
|
+
<xs:element name="inputfile" minOccurs="1" maxOccurs="unbounded">
|
|
733
|
+
<xs:complexType>
|
|
734
|
+
<xs:attribute name="name" type="xs:string" use="required">
|
|
735
|
+
<xs:annotation>
|
|
736
|
+
<xs:documentation>Input file</xs:documentation>
|
|
737
|
+
</xs:annotation>
|
|
738
|
+
</xs:attribute>
|
|
739
|
+
</xs:complexType>
|
|
740
|
+
</xs:element>
|
|
741
|
+
|
|
742
|
+
|
|
743
|
+
<xs:element name="roc_data_point" minOccurs="0" maxOccurs="unbounded">
|
|
744
|
+
<xs:complexType>
|
|
745
|
+
<xs:attribute name="min_prob" type="xs:float" use="required">
|
|
746
|
+
<xs:annotation>
|
|
747
|
+
<xs:documentation>Filter threshold</xs:documentation>
|
|
748
|
+
</xs:annotation>
|
|
749
|
+
</xs:attribute>
|
|
750
|
+
<xs:attribute name="sensitivity" type="xs:float" use="required">
|
|
751
|
+
<xs:annotation>
|
|
752
|
+
<xs:documentation>Predicted sensitivity</xs:documentation>
|
|
753
|
+
</xs:annotation>
|
|
754
|
+
</xs:attribute>
|
|
755
|
+
<xs:attribute name="error" type="xs:float" use="required">
|
|
756
|
+
<xs:annotation>
|
|
757
|
+
<xs:documentation>Predicted false positive error rate</xs:documentation>
|
|
758
|
+
</xs:annotation>
|
|
759
|
+
</xs:attribute>
|
|
760
|
+
<xs:attribute name="num_corr" type="xs:unsignedInt" use="required">
|
|
761
|
+
<xs:annotation>
|
|
762
|
+
<xs:documentation>Predicted number of correct results passing filter</xs:documentation>
|
|
763
|
+
</xs:annotation>
|
|
764
|
+
</xs:attribute>
|
|
765
|
+
<xs:attribute name="num_incorr" type="xs:unsignedInt" use="required">
|
|
766
|
+
<xs:annotation>
|
|
767
|
+
<xs:documentation>Predicted number of incorrect results passing filter</xs:documentation>
|
|
768
|
+
</xs:annotation>
|
|
769
|
+
</xs:attribute>
|
|
770
|
+
</xs:complexType>
|
|
771
|
+
</xs:element>
|
|
772
|
+
<xs:element name="error_point" minOccurs="0" maxOccurs="unbounded">
|
|
773
|
+
<xs:complexType>
|
|
774
|
+
<xs:attribute name="error" type="xs:float" use="required">
|
|
775
|
+
<xs:annotation>
|
|
776
|
+
<xs:documentation>Predicted false positive error rate</xs:documentation>
|
|
777
|
+
</xs:annotation>
|
|
778
|
+
</xs:attribute>
|
|
779
|
+
<xs:attribute name="min_prob" type="xs:float" use="required">
|
|
780
|
+
<xs:annotation>
|
|
781
|
+
<xs:documentation>Filter threshold</xs:documentation>
|
|
782
|
+
</xs:annotation>
|
|
783
|
+
</xs:attribute>
|
|
784
|
+
<xs:attribute name="num_corr" type="xs:unsignedInt" use="required">
|
|
785
|
+
<xs:annotation>
|
|
786
|
+
<xs:documentation>Predicted number of correct results passing filter</xs:documentation>
|
|
787
|
+
</xs:annotation>
|
|
788
|
+
</xs:attribute>
|
|
789
|
+
<xs:attribute name="num_incorr" type="xs:unsignedInt" use="required">
|
|
790
|
+
<xs:annotation>
|
|
791
|
+
<xs:documentation>Predicted number of incorrect results passing filter</xs:documentation>
|
|
792
|
+
</xs:annotation>
|
|
793
|
+
</xs:attribute>
|
|
794
|
+
</xs:complexType>
|
|
795
|
+
</xs:element>
|
|
796
|
+
<xs:element name="distribution_point" minOccurs="0" maxOccurs="unbounded">
|
|
797
|
+
<xs:complexType>
|
|
798
|
+
<xs:attribute name="fvalue" type="xs:float" use="required">
|
|
799
|
+
<xs:annotation>
|
|
800
|
+
<xs:documentation>Discriminant Score (fval) bin</xs:documentation>
|
|
801
|
+
</xs:annotation>
|
|
802
|
+
</xs:attribute>
|
|
803
|
+
<xs:attribute name="obs_1_distr" type="xs:nonNegativeInteger" use="required">
|
|
804
|
+
<xs:annotation>
|
|
805
|
+
<xs:documentation>Number of 1+ spectra</xs:documentation>
|
|
806
|
+
</xs:annotation>
|
|
807
|
+
</xs:attribute>
|
|
808
|
+
<xs:attribute name="model_1_pos_distr" type="xs:float" use="required">
|
|
809
|
+
<xs:annotation>
|
|
810
|
+
<xs:documentation>Inferred number of correct 1+ spectra</xs:documentation>
|
|
811
|
+
</xs:annotation>
|
|
812
|
+
</xs:attribute>
|
|
813
|
+
<xs:attribute name="model_1_neg_distr" type="xs:float" use="required">
|
|
814
|
+
<xs:annotation>
|
|
815
|
+
<xs:documentation>Inferred number of incorrect 1+ spectra</xs:documentation>
|
|
816
|
+
</xs:annotation>
|
|
817
|
+
</xs:attribute>
|
|
818
|
+
<xs:attribute name="obs_2_distr" type="xs:nonNegativeInteger" use="required">
|
|
819
|
+
<xs:annotation>
|
|
820
|
+
<xs:documentation>Number of 2+ spectra</xs:documentation>
|
|
821
|
+
</xs:annotation>
|
|
822
|
+
</xs:attribute>
|
|
823
|
+
<xs:attribute name="model_2_pos_distr" type="xs:float" use="required">
|
|
824
|
+
<xs:annotation>
|
|
825
|
+
<xs:documentation>Inferred number of correct 2+ spectra</xs:documentation>
|
|
826
|
+
</xs:annotation>
|
|
827
|
+
</xs:attribute>
|
|
828
|
+
<xs:attribute name="model_2_neg_distr" type="xs:float" use="required">
|
|
829
|
+
<xs:annotation>
|
|
830
|
+
<xs:documentation>Inferred number of incorrect 2+ spectra</xs:documentation>
|
|
831
|
+
</xs:annotation>
|
|
832
|
+
</xs:attribute>
|
|
833
|
+
<xs:attribute name="obs_3_distr" type="xs:nonNegativeInteger" use="required">
|
|
834
|
+
<xs:annotation>
|
|
835
|
+
<xs:documentation>Number of 3+ spectra</xs:documentation>
|
|
836
|
+
</xs:annotation>
|
|
837
|
+
</xs:attribute>
|
|
838
|
+
<xs:attribute name="model_3_pos_distr" type="xs:float" use="required">
|
|
839
|
+
<xs:annotation>
|
|
840
|
+
<xs:documentation>Inferred number of correct 3+ spectra</xs:documentation>
|
|
841
|
+
</xs:annotation>
|
|
842
|
+
</xs:attribute>
|
|
843
|
+
<xs:attribute name="model_3_neg_distr" type="xs:float" use="required">
|
|
844
|
+
<xs:annotation>
|
|
845
|
+
<xs:documentation>Inferred number of incorrect 3+ spectra</xs:documentation>
|
|
846
|
+
</xs:annotation>
|
|
847
|
+
</xs:attribute>
|
|
848
|
+
</xs:complexType>
|
|
849
|
+
</xs:element>
|
|
850
|
+
<xs:element name="mixture_model" minOccurs="0" maxOccurs="unbounded">
|
|
851
|
+
<xs:complexType>
|
|
852
|
+
<xs:sequence>
|
|
853
|
+
<xs:element name="mixturemodel_distribution" maxOccurs="unbounded">
|
|
854
|
+
<xs:complexType>
|
|
855
|
+
<xs:sequence>
|
|
856
|
+
<xs:element name="posmodel_distribution">
|
|
857
|
+
<xs:complexType>
|
|
858
|
+
<xs:sequence>
|
|
859
|
+
<xs:element name="parameter" type="nameValueType" maxOccurs="unbounded"/>
|
|
860
|
+
</xs:sequence>
|
|
861
|
+
<xs:attribute name="type" type="model_dis_type"/>
|
|
862
|
+
</xs:complexType>
|
|
863
|
+
</xs:element>
|
|
864
|
+
<xs:element name="negmodel_distribution">
|
|
865
|
+
<xs:complexType>
|
|
866
|
+
<xs:sequence>
|
|
867
|
+
<xs:element name="parameter" type="nameValueType" maxOccurs="unbounded"/>
|
|
868
|
+
</xs:sequence>
|
|
869
|
+
<xs:attribute name="type" type="model_dis_type"/>
|
|
870
|
+
</xs:complexType>
|
|
871
|
+
</xs:element>
|
|
872
|
+
</xs:sequence>
|
|
873
|
+
<xs:attribute name="name" type="xs:string" use="required"/>
|
|
874
|
+
</xs:complexType>
|
|
875
|
+
</xs:element>
|
|
876
|
+
</xs:sequence>
|
|
877
|
+
<xs:attribute name="precursor_ion_charge" type="xs:nonNegativeInteger" use="required"/>
|
|
878
|
+
<xs:attribute name="comments" type="xs:string" use="required"/>
|
|
879
|
+
<xs:attribute name="prior_probability" type="xs:float" use="required">
|
|
880
|
+
<xs:annotation>
|
|
881
|
+
<xs:documentation>Fraction of results inferred to be correct</xs:documentation>
|
|
882
|
+
</xs:annotation>
|
|
883
|
+
</xs:attribute>
|
|
884
|
+
<xs:attribute name="est_tot_correct" type="xs:float" use="required"/>
|
|
885
|
+
<xs:attribute name="tot_num_spectra" type="xs:nonNegativeInteger" use="required">
|
|
886
|
+
<xs:annotation>
|
|
887
|
+
<xs:documentation>Number of input spectra</xs:documentation>
|
|
888
|
+
</xs:annotation>
|
|
889
|
+
</xs:attribute>
|
|
890
|
+
<xs:attribute name="num_iterations" type="xs:nonNegativeInteger" use="required">
|
|
891
|
+
<xs:annotation>
|
|
892
|
+
<xs:documentation>Number of EM interations prior to convergence</xs:documentation>
|
|
893
|
+
</xs:annotation>
|
|
894
|
+
</xs:attribute>
|
|
895
|
+
</xs:complexType>
|
|
896
|
+
</xs:element>
|
|
897
|
+
</xs:sequence>
|
|
898
|
+
<xs:attribute name="version" type="xs:string" use="required"/>
|
|
899
|
+
<xs:attribute name="author" type="xs:string" use="required"/>
|
|
900
|
+
<xs:attribute name="min_prob" type="xs:float" use="required">
|
|
901
|
+
<xs:annotation>
|
|
902
|
+
<xs:documentation>Min probability to be included in output</xs:documentation>
|
|
903
|
+
</xs:annotation>
|
|
904
|
+
</xs:attribute>
|
|
905
|
+
<xs:attribute name="options" type="xs:string">
|
|
906
|
+
<xs:annotation>
|
|
907
|
+
<xs:documentation>User specified run options</xs:documentation>
|
|
908
|
+
</xs:annotation>
|
|
909
|
+
</xs:attribute>
|
|
910
|
+
<xs:attribute name="est_tot_num_correct" type="xs:float">
|
|
911
|
+
<xs:annotation>
|
|
912
|
+
<xs:documentation>Total inferred number of correct results</xs:documentation>
|
|
913
|
+
</xs:annotation>
|
|
914
|
+
</xs:attribute>
|
|
915
|
+
</xs:complexType>
|
|
916
|
+
</xs:element>
|
|
917
|
+
<xs:element name="asapratio_summary">
|
|
918
|
+
<xs:annotation>
|
|
919
|
+
<xs:documentation>Quantitation</xs:documentation>
|
|
920
|
+
</xs:annotation>
|
|
921
|
+
<xs:complexType>
|
|
922
|
+
<xs:attribute name="version" type="xs:string" use="required"/>
|
|
923
|
+
<xs:attribute name="author" type="xs:string" use="required"/>
|
|
924
|
+
<xs:attribute name="elution" type="xs:integer" use="required">
|
|
925
|
+
<xs:annotation>
|
|
926
|
+
<xs:documentation>Elution order of light vs heavy labeled peptide</xs:documentation>
|
|
927
|
+
</xs:annotation>
|
|
928
|
+
</xs:attribute>
|
|
929
|
+
<xs:attribute name="labeled_residues" type="xs:string" use="required">
|
|
930
|
+
<xs:annotation>
|
|
931
|
+
<xs:documentation>Aminoacids and termini that are differentially labeled for quantitaiton</xs:documentation>
|
|
932
|
+
</xs:annotation>
|
|
933
|
+
</xs:attribute>
|
|
934
|
+
<xs:attribute name="area_flag" type="xs:nonNegativeInteger" use="required"/>
|
|
935
|
+
<xs:attribute name="static_quant" type="xs:string" use="required">
|
|
936
|
+
<xs:annotation>
|
|
937
|
+
<xs:documentation>Y if dataset is all light or heavy labeled, N if dataset is mixed heavy and light labeled</xs:documentation>
|
|
938
|
+
</xs:annotation>
|
|
939
|
+
</xs:attribute>
|
|
940
|
+
</xs:complexType>
|
|
941
|
+
</xs:element>
|
|
942
|
+
<xs:element name="xpressratio_summary">
|
|
943
|
+
<xs:annotation>
|
|
944
|
+
<xs:documentation>Quantitation</xs:documentation>
|
|
945
|
+
</xs:annotation>
|
|
946
|
+
<xs:complexType>
|
|
947
|
+
<xs:attribute name="version" type="xs:string" use="required"/>
|
|
948
|
+
<xs:attribute name="author" type="xs:string" use="required"/>
|
|
949
|
+
<xs:attribute name="same_scan_range" type="xs:string" use="required"/>
|
|
950
|
+
<xs:attribute name="labeled_residues" type="xs:string" use="required"/>
|
|
951
|
+
<xs:attribute name="xpress_light" type="xs:unsignedInt" use="required"/>
|
|
952
|
+
<xs:attribute name="massdiff" type="xs:string" use="required"/>
|
|
953
|
+
<xs:attribute name="masstol" type="xs:float" use="required"/>
|
|
954
|
+
</xs:complexType>
|
|
955
|
+
</xs:element>
|
|
956
|
+
<xs:element name="peptideprophet_result">
|
|
957
|
+
<xs:annotation>
|
|
958
|
+
<xs:documentation>PeptideProphet validation results for search hit</xs:documentation>
|
|
959
|
+
</xs:annotation>
|
|
960
|
+
<xs:complexType>
|
|
961
|
+
<xs:sequence>
|
|
962
|
+
<xs:element name="search_score_summary" minOccurs="0">
|
|
963
|
+
<xs:complexType>
|
|
964
|
+
<xs:sequence>
|
|
965
|
+
<xs:element name="parameter" type="nameValueType" minOccurs="2" maxOccurs="unbounded"/>
|
|
966
|
+
</xs:sequence>
|
|
967
|
+
</xs:complexType>
|
|
968
|
+
</xs:element>
|
|
969
|
+
</xs:sequence>
|
|
970
|
+
<xs:attribute name="probability" type="xs:float" use="required"/>
|
|
971
|
+
<xs:attribute name="all_ntt_prob" type="xs:string"/>
|
|
972
|
+
<xs:attribute name="analysis" type="xs:string"/>
|
|
973
|
+
</xs:complexType>
|
|
974
|
+
</xs:element>
|
|
975
|
+
<xs:element name="asapratio_result">
|
|
976
|
+
<xs:annotation>
|
|
977
|
+
<xs:documentation>ASAPRatio quantitation results for search hit</xs:documentation>
|
|
978
|
+
</xs:annotation>
|
|
979
|
+
<xs:complexType>
|
|
980
|
+
<xs:sequence>
|
|
981
|
+
<xs:element ref="asapratio_peptide_data"/>
|
|
982
|
+
</xs:sequence>
|
|
983
|
+
<xs:attribute name="mean" type="xs:float" use="required"/>
|
|
984
|
+
<xs:attribute name="error" type="xs:float" use="required"/>
|
|
985
|
+
<xs:attribute name="heavy2light_mean" type="xs:float" use="required"/>
|
|
986
|
+
<xs:attribute name="heavy2light_error" type="xs:float" use="required"/>
|
|
987
|
+
</xs:complexType>
|
|
988
|
+
</xs:element>
|
|
989
|
+
<xs:element name="asapratio_peptide_data">
|
|
990
|
+
<xs:complexType>
|
|
991
|
+
<xs:sequence>
|
|
992
|
+
<xs:element ref="asapratio_contribution" maxOccurs="unbounded"/>
|
|
993
|
+
</xs:sequence>
|
|
994
|
+
<xs:attribute name="status" type="xs:byte" use="required"/>
|
|
995
|
+
<xs:attribute name="cidIndex" type="xs:int" use="required"/>
|
|
996
|
+
<xs:attribute name="light_mass" type="xs:float" use="required"/>
|
|
997
|
+
<xs:attribute name="heavy_mass" type="xs:float" use="required"/>
|
|
998
|
+
<xs:attribute name="area_flag" type="xs:unsignedInt" use="required"/>
|
|
999
|
+
</xs:complexType>
|
|
1000
|
+
</xs:element>
|
|
1001
|
+
<xs:element name="asapratio_contribution">
|
|
1002
|
+
<xs:complexType>
|
|
1003
|
+
<xs:sequence>
|
|
1004
|
+
<xs:element ref="asapratio_lc_lightpeak"/>
|
|
1005
|
+
<xs:element ref="asapratio_lc_heavypeak"/>
|
|
1006
|
+
</xs:sequence>
|
|
1007
|
+
<xs:attribute name="ratio" type="xs:float" use="required"/>
|
|
1008
|
+
<xs:attribute name="error" type="xs:float" use="required"/>
|
|
1009
|
+
<xs:attribute name="charge" type="xs:nonNegativeInteger" use="required"/>
|
|
1010
|
+
<xs:attribute name="use" type="xs:unsignedByte" use="required"/>
|
|
1011
|
+
</xs:complexType>
|
|
1012
|
+
</xs:element>
|
|
1013
|
+
<xs:element name="asapratio_lc_lightpeak">
|
|
1014
|
+
<xs:complexType>
|
|
1015
|
+
<xs:attribute name="status" type="xs:byte" use="required"/>
|
|
1016
|
+
<xs:attribute name="left_valley" type="xs:int" use="required"/>
|
|
1017
|
+
<xs:attribute name="right_valley" type="xs:int" use="required"/>
|
|
1018
|
+
<xs:attribute name="background" type="xs:float" use="required"/>
|
|
1019
|
+
<xs:attribute name="area" type="xs:float" use="required"/>
|
|
1020
|
+
<xs:attribute name="area_error" type="xs:float" use="required"/>
|
|
1021
|
+
<xs:attribute name="time" type="xs:float" use="required"/>
|
|
1022
|
+
<xs:attribute name="time_width" type="xs:float" use="required"/>
|
|
1023
|
+
<xs:attribute name="is_heavy" type="xs:string" use="required"/>
|
|
1024
|
+
</xs:complexType>
|
|
1025
|
+
</xs:element>
|
|
1026
|
+
<xs:element name="asapratio_lc_heavypeak">
|
|
1027
|
+
<xs:complexType>
|
|
1028
|
+
<xs:attribute name="status" type="xs:byte" use="required"/>
|
|
1029
|
+
<xs:attribute name="left_valley" type="xs:int" use="required"/>
|
|
1030
|
+
<xs:attribute name="right_valley" type="xs:int" use="required"/>
|
|
1031
|
+
<xs:attribute name="background" type="xs:float" use="required"/>
|
|
1032
|
+
<xs:attribute name="area" type="xs:float" use="required"/>
|
|
1033
|
+
<xs:attribute name="area_error" type="xs:float" use="required"/>
|
|
1034
|
+
<xs:attribute name="time" type="xs:float" use="required"/>
|
|
1035
|
+
<xs:attribute name="time_width" type="xs:float" use="required"/>
|
|
1036
|
+
<xs:attribute name="is_heavy" type="xs:string" use="required"/>
|
|
1037
|
+
</xs:complexType>
|
|
1038
|
+
</xs:element>
|
|
1039
|
+
<xs:element name="database_refresh_timestamp">
|
|
1040
|
+
<xs:complexType>
|
|
1041
|
+
<xs:attribute name="database" type="xs:string" use="required"/>
|
|
1042
|
+
<xs:attribute name="min_num_enz_term" type="xs:nonNegativeInteger">
|
|
1043
|
+
<xs:annotation>
|
|
1044
|
+
<xs:documentation>minimum number of termini compaitble with enzyme used (should correspond with search enzyme constraint)</xs:documentation>
|
|
1045
|
+
</xs:annotation>
|
|
1046
|
+
</xs:attribute>
|
|
1047
|
+
</xs:complexType>
|
|
1048
|
+
</xs:element>
|
|
1049
|
+
<xs:element name="xpressratio_timestamp">
|
|
1050
|
+
<xs:complexType>
|
|
1051
|
+
<xs:attribute name="xpress_light" type="xs:integer" use="required"/>
|
|
1052
|
+
</xs:complexType>
|
|
1053
|
+
</xs:element>
|
|
1054
|
+
<xs:element name="asapratio_timestamp">
|
|
1055
|
+
<xs:complexType>
|
|
1056
|
+
<xs:attribute name="quant_label_masses" type="xs:string"/>
|
|
1057
|
+
<xs:attribute name="static_quant_label" type="xs:string"/>
|
|
1058
|
+
</xs:complexType>
|
|
1059
|
+
</xs:element>
|
|
1060
|
+
<xs:element name="xpressratio_result">
|
|
1061
|
+
<xs:annotation>
|
|
1062
|
+
<xs:documentation>Quantitation</xs:documentation>
|
|
1063
|
+
</xs:annotation>
|
|
1064
|
+
<xs:complexType>
|
|
1065
|
+
<xs:attribute name="light_firstscan" type="xs:unsignedInt" use="required"/>
|
|
1066
|
+
<xs:attribute name="light_lastscan" type="xs:unsignedInt" use="required"/>
|
|
1067
|
+
<xs:attribute name="light_mass" type="xs:float" use="required"/>
|
|
1068
|
+
<xs:attribute name="heavy_firstscan" type="xs:unsignedInt" use="required"/>
|
|
1069
|
+
<xs:attribute name="heavy_lastscan" type="xs:unsignedInt" use="required"/>
|
|
1070
|
+
<xs:attribute name="heavy_mass" type="xs:float" use="required"/>
|
|
1071
|
+
<xs:attribute name="mass_tol" type="xs:float" use="required"/>
|
|
1072
|
+
<xs:attribute name="ratio" type="xs:string" use="required"/>
|
|
1073
|
+
<xs:attribute name="heavy2light_ratio" type="xs:string" use="required"/>
|
|
1074
|
+
<xs:attribute name="light_area" type="xs:float" use="required"/>
|
|
1075
|
+
<xs:attribute name="heavy_area" type="xs:float" use="required"/>
|
|
1076
|
+
<xs:attribute name="decimal_ratio" type="xs:decimal" use="required"/>
|
|
1077
|
+
</xs:complexType>
|
|
1078
|
+
</xs:element>
|
|
1079
|
+
<!--the types used by above elements.-->
|
|
1080
|
+
|
|
1081
|
+
<xs:simpleType name="engineType">
|
|
1082
|
+
<xs:restriction base="xs:string">
|
|
1083
|
+
<xs:enumeration value="SEQUEST"/>
|
|
1084
|
+
<xs:enumeration value="MASCOT"/>
|
|
1085
|
+
<xs:enumeration value="COMET"/>
|
|
1086
|
+
<xs:enumeration value="PROBID"/>
|
|
1087
|
+
</xs:restriction>
|
|
1088
|
+
</xs:simpleType>
|
|
1089
|
+
<xs:simpleType name="model_dis_type">
|
|
1090
|
+
<xs:restriction base="xs:string">
|
|
1091
|
+
<xs:enumeration value="discrete"/>
|
|
1092
|
+
<xs:enumeration value="gaussian"/>
|
|
1093
|
+
<xs:enumeration value="extremevalue"/>
|
|
1094
|
+
<xs:enumeration value="gamma"/>
|
|
1095
|
+
<xs:enumeration value="evd"/>
|
|
1096
|
+
</xs:restriction>
|
|
1097
|
+
</xs:simpleType>
|
|
1098
|
+
<xs:simpleType name="massType">
|
|
1099
|
+
<xs:restriction base="xs:string">
|
|
1100
|
+
<xs:enumeration value="monoisotopic"/>
|
|
1101
|
+
<xs:enumeration value="average"/>
|
|
1102
|
+
</xs:restriction>
|
|
1103
|
+
</xs:simpleType>
|
|
1104
|
+
<xs:simpleType name="aa_symbolType">
|
|
1105
|
+
<xs:restriction base="xs:string">
|
|
1106
|
+
<xs:enumeration value="1"/>
|
|
1107
|
+
<xs:enumeration value="2"/>
|
|
1108
|
+
<xs:enumeration value="3"/>
|
|
1109
|
+
<xs:enumeration value="4"/>
|
|
1110
|
+
<xs:enumeration value="5"/>
|
|
1111
|
+
<xs:enumeration value="6"/>
|
|
1112
|
+
<xs:enumeration value="7"/>
|
|
1113
|
+
<xs:enumeration value="8"/>
|
|
1114
|
+
<xs:enumeration value="9"/>
|
|
1115
|
+
<xs:enumeration value="#"/>
|
|
1116
|
+
<xs:enumeration value="@"/>
|
|
1117
|
+
<xs:enumeration value="*"/>
|
|
1118
|
+
<xs:enumeration value="~"/>
|
|
1119
|
+
<xs:enumeration value="'"/>
|
|
1120
|
+
<xs:enumeration value="''"/>
|
|
1121
|
+
<xs:enumeration value="$"/>
|
|
1122
|
+
<xs:enumeration value="!"/>
|
|
1123
|
+
<xs:enumeration value="^"/>
|
|
1124
|
+
<xs:enumeration value="?"/>
|
|
1125
|
+
</xs:restriction>
|
|
1126
|
+
</xs:simpleType>
|
|
1127
|
+
<xs:simpleType name="term_symbolType">
|
|
1128
|
+
<xs:restriction base="xs:string">
|
|
1129
|
+
<xs:enumeration value=","/>
|
|
1130
|
+
<xs:enumeration value=";"/>
|
|
1131
|
+
<xs:enumeration value=":"/>
|
|
1132
|
+
</xs:restriction>
|
|
1133
|
+
</xs:simpleType>
|
|
1134
|
+
<xs:simpleType name="positiveInt">
|
|
1135
|
+
<xs:restriction base="xs:unsignedInt">
|
|
1136
|
+
<xs:minInclusive value="1"/>
|
|
1137
|
+
</xs:restriction>
|
|
1138
|
+
</xs:simpleType>
|
|
1139
|
+
<xs:complexType name="nameValueType">
|
|
1140
|
+
<xs:simpleContent>
|
|
1141
|
+
<xs:extension base="xs:anySimpleType">
|
|
1142
|
+
<xs:attribute name="name" type="xs:string" use="required"/>
|
|
1143
|
+
<xs:attribute name="value" type="xs:anySimpleType" use="required"/>
|
|
1144
|
+
<xs:attribute name="type" type="xs:anySimpleType"/>
|
|
1145
|
+
</xs:extension>
|
|
1146
|
+
</xs:simpleContent>
|
|
1147
|
+
</xs:complexType>
|
|
1148
|
+
<xs:element name="interact_summary">
|
|
1149
|
+
<xs:annotation>
|
|
1150
|
+
<xs:documentation>Combined datasets</xs:documentation>
|
|
1151
|
+
</xs:annotation>
|
|
1152
|
+
<xs:complexType>
|
|
1153
|
+
<xs:sequence>
|
|
1154
|
+
<xs:element name="inputfile" minOccurs="1" maxOccurs="unbounded">
|
|
1155
|
+
<xs:annotation>
|
|
1156
|
+
<xs:documentation>Input file</xs:documentation>
|
|
1157
|
+
</xs:annotation>
|
|
1158
|
+
<xs:complexType>
|
|
1159
|
+
<xs:attribute name="name" type="xs:string" use="required"/>
|
|
1160
|
+
</xs:complexType>
|
|
1161
|
+
</xs:element>
|
|
1162
|
+
</xs:sequence>
|
|
1163
|
+
<xs:attribute name="filename" type="xs:string" use="required">
|
|
1164
|
+
<xs:annotation>
|
|
1165
|
+
<xs:documentation>Self reference</xs:documentation>
|
|
1166
|
+
</xs:annotation>
|
|
1167
|
+
</xs:attribute>
|
|
1168
|
+
<xs:attribute name="directory" type="xs:string" use="required">
|
|
1169
|
+
<xs:annotation>
|
|
1170
|
+
<xs:documentation>Directory of self</xs:documentation>
|
|
1171
|
+
</xs:annotation>
|
|
1172
|
+
</xs:attribute>
|
|
1173
|
+
</xs:complexType>
|
|
1174
|
+
</xs:element>
|
|
1175
|
+
<xs:element name="libra_result">
|
|
1176
|
+
<xs:annotation>
|
|
1177
|
+
<xs:documentation>libra quantitation for search hit</xs:documentation>
|
|
1178
|
+
</xs:annotation>
|
|
1179
|
+
<xs:complexType>
|
|
1180
|
+
<xs:sequence>
|
|
1181
|
+
<xs:element name="intensity" maxOccurs="unbounded">
|
|
1182
|
+
<xs:annotation>
|
|
1183
|
+
<xs:documentation>integrated mass intensity</xs:documentation>
|
|
1184
|
+
</xs:annotation>
|
|
1185
|
+
<xs:complexType>
|
|
1186
|
+
<xs:attribute name="channel" type="positiveInt" use="required">
|
|
1187
|
+
<xs:annotation>
|
|
1188
|
+
<xs:documentation>mass channel number</xs:documentation>
|
|
1189
|
+
</xs:annotation>
|
|
1190
|
+
</xs:attribute>
|
|
1191
|
+
<xs:attribute name="target_mass" type="xs:float" use="required">
|
|
1192
|
+
<xs:annotation>
|
|
1193
|
+
<xs:documentation>mass of channel</xs:documentation>
|
|
1194
|
+
</xs:annotation>
|
|
1195
|
+
</xs:attribute>
|
|
1196
|
+
<xs:attribute name="absolute" type="xs:float" use="required">
|
|
1197
|
+
<xs:annotation>
|
|
1198
|
+
<xs:documentation>absolute integrated intensity</xs:documentation>
|
|
1199
|
+
</xs:annotation>
|
|
1200
|
+
</xs:attribute>
|
|
1201
|
+
<xs:attribute name="normalized" type="xs:float" use="required">
|
|
1202
|
+
<xs:annotation>
|
|
1203
|
+
<xs:documentation>normalized integrated intensity (normalization channel stored in libra_summary)</xs:documentation>
|
|
1204
|
+
</xs:annotation>
|
|
1205
|
+
</xs:attribute>
|
|
1206
|
+
<xs:attribute name="reject" type="xs:boolean" use="optional" default="0">
|
|
1207
|
+
<xs:annotation>
|
|
1208
|
+
<xs:documentation>whether or not to reject this ratio as valid</xs:documentation>
|
|
1209
|
+
</xs:annotation>
|
|
1210
|
+
</xs:attribute>
|
|
1211
|
+
</xs:complexType>
|
|
1212
|
+
</xs:element>
|
|
1213
|
+
</xs:sequence>
|
|
1214
|
+
<xs:attribute name="is_rejected" type="xs:boolean" use="optional" default="0">
|
|
1215
|
+
<xs:annotation>
|
|
1216
|
+
<xs:documentation>whether or not to reject this ratio as valid</xs:documentation>
|
|
1217
|
+
</xs:annotation>
|
|
1218
|
+
</xs:attribute>
|
|
1219
|
+
</xs:complexType>
|
|
1220
|
+
<xs:unique name="libra_result_channel_index">
|
|
1221
|
+
<xs:annotation>
|
|
1222
|
+
<xs:documentation>channel number must be unique</xs:documentation>
|
|
1223
|
+
</xs:annotation>
|
|
1224
|
+
<xs:selector xpath="."/>
|
|
1225
|
+
<xs:field xpath="@channel"/>
|
|
1226
|
+
</xs:unique>
|
|
1227
|
+
</xs:element>
|
|
1228
|
+
<xs:element name="libra_summary">
|
|
1229
|
+
<xs:annotation>
|
|
1230
|
+
<xs:documentation>summary info for libra quantitation analysis</xs:documentation>
|
|
1231
|
+
</xs:annotation>
|
|
1232
|
+
<xs:complexType>
|
|
1233
|
+
<xs:sequence>
|
|
1234
|
+
<xs:element name="fragment_masses" maxOccurs="unbounded">
|
|
1235
|
+
<xs:annotation>
|
|
1236
|
+
<xs:documentation>quantitation channel</xs:documentation>
|
|
1237
|
+
</xs:annotation>
|
|
1238
|
+
<xs:complexType>
|
|
1239
|
+
<xs:attribute name="channel" type="positiveInt" use="required">
|
|
1240
|
+
<xs:annotation>
|
|
1241
|
+
<xs:documentation>channel number</xs:documentation>
|
|
1242
|
+
</xs:annotation>
|
|
1243
|
+
</xs:attribute>
|
|
1244
|
+
<xs:attribute name="mz" type="xs:float" use="required">
|
|
1245
|
+
<xs:annotation>
|
|
1246
|
+
<xs:documentation>channel mass</xs:documentation>
|
|
1247
|
+
</xs:annotation>
|
|
1248
|
+
</xs:attribute>
|
|
1249
|
+
<xs:attribute name="offset" type="xs:float">
|
|
1250
|
+
<xs:annotation>
|
|
1251
|
+
<xs:documentation>mass offset from mz value</xs:documentation>
|
|
1252
|
+
</xs:annotation>
|
|
1253
|
+
</xs:attribute>
|
|
1254
|
+
</xs:complexType>
|
|
1255
|
+
</xs:element>
|
|
1256
|
+
<xs:element name="isotopic_contributions" minOccurs="0">
|
|
1257
|
+
<xs:annotation>
|
|
1258
|
+
<xs:documentation>isotopic contributions from one channel to others</xs:documentation>
|
|
1259
|
+
</xs:annotation>
|
|
1260
|
+
<xs:complexType>
|
|
1261
|
+
<xs:sequence>
|
|
1262
|
+
<xs:element name="contributing_channel" maxOccurs="unbounded">
|
|
1263
|
+
<xs:annotation>
|
|
1264
|
+
<xs:documentation>channel donor</xs:documentation>
|
|
1265
|
+
</xs:annotation>
|
|
1266
|
+
<xs:complexType>
|
|
1267
|
+
<xs:sequence>
|
|
1268
|
+
<xs:element name="affected_channel" maxOccurs="unbounded">
|
|
1269
|
+
<xs:annotation>
|
|
1270
|
+
<xs:documentation>channel recipient</xs:documentation>
|
|
1271
|
+
</xs:annotation>
|
|
1272
|
+
<xs:complexType>
|
|
1273
|
+
<xs:attribute name="channel" type="positiveInt" use="required">
|
|
1274
|
+
<xs:annotation>
|
|
1275
|
+
<xs:documentation>channel number</xs:documentation>
|
|
1276
|
+
</xs:annotation>
|
|
1277
|
+
</xs:attribute>
|
|
1278
|
+
<xs:attribute name="correction" type="xs:float" use="required">
|
|
1279
|
+
<xs:annotation>
|
|
1280
|
+
<xs:documentation>fraction of affected channel due to contributing</xs:documentation>
|
|
1281
|
+
</xs:annotation>
|
|
1282
|
+
</xs:attribute>
|
|
1283
|
+
</xs:complexType>
|
|
1284
|
+
</xs:element>
|
|
1285
|
+
</xs:sequence>
|
|
1286
|
+
<xs:attribute name="channel" type="positiveInt" use="required">
|
|
1287
|
+
<xs:annotation>
|
|
1288
|
+
<xs:documentation>channel number</xs:documentation>
|
|
1289
|
+
</xs:annotation>
|
|
1290
|
+
</xs:attribute>
|
|
1291
|
+
</xs:complexType>
|
|
1292
|
+
</xs:element>
|
|
1293
|
+
</xs:sequence>
|
|
1294
|
+
</xs:complexType>
|
|
1295
|
+
</xs:element>
|
|
1296
|
+
</xs:sequence>
|
|
1297
|
+
<xs:attribute name="mass_tolerance" type="xs:float" use="required">
|
|
1298
|
+
<xs:annotation>
|
|
1299
|
+
<xs:documentation>channel mass width</xs:documentation>
|
|
1300
|
+
</xs:annotation>
|
|
1301
|
+
</xs:attribute>
|
|
1302
|
+
<xs:attribute name="centroiding_preference" type="xs:int" use="required"/>
|
|
1303
|
+
<xs:attribute name="normalization" type="xs:int" use="required">
|
|
1304
|
+
<xs:annotation>
|
|
1305
|
+
<xs:documentation>channel used as denominator for normalized integrated intensities (0 means use channel with strongest absolute integrated intensity)</xs:documentation>
|
|
1306
|
+
</xs:annotation>
|
|
1307
|
+
</xs:attribute>
|
|
1308
|
+
<xs:attribute name="output_type" type="xs:int" use="required"/>
|
|
1309
|
+
<xs:attribute name="channel_code" type="xs:string">
|
|
1310
|
+
<xs:annotation>
|
|
1311
|
+
<xs:documentation>concatenated channel masses (used as signature for defined channel masses)</xs:documentation>
|
|
1312
|
+
</xs:annotation>
|
|
1313
|
+
</xs:attribute>
|
|
1314
|
+
</xs:complexType>
|
|
1315
|
+
|
|
1316
|
+
<xs:key name="libra_channel_index">
|
|
1317
|
+
<xs:selector xpath="./pepx:fragment_masses"/>
|
|
1318
|
+
<xs:field xpath="@channel"/>
|
|
1319
|
+
</xs:key>
|
|
1320
|
+
<xs:keyref name="libra_contr_channel_index_ref" refer="libra_channel_index">
|
|
1321
|
+
<xs:annotation>
|
|
1322
|
+
<xs:documentation>contributing channel numbers must correspond with defined channels</xs:documentation>
|
|
1323
|
+
</xs:annotation>
|
|
1324
|
+
<xs:selector xpath="./pepx:isotopic_contributions/pepx:contributing_channel"/>
|
|
1325
|
+
<xs:field xpath="@channel"/>
|
|
1326
|
+
</xs:keyref>
|
|
1327
|
+
<xs:keyref name="libra_aff_channel_index_ref" refer="libra_channel_index">
|
|
1328
|
+
<xs:annotation>
|
|
1329
|
+
<xs:documentation>contributing channel numbers must correspond with defined channels</xs:documentation>
|
|
1330
|
+
</xs:annotation>
|
|
1331
|
+
<xs:selector xpath="./pepx:isotopic_contributions/pepx:contributing_channel/pepx:affected_channel"/>
|
|
1332
|
+
<xs:field xpath="@channel"/>
|
|
1333
|
+
</xs:keyref>
|
|
1334
|
+
|
|
1335
|
+
</xs:element>
|
|
1336
|
+
|
|
1337
|
+
</xs:schema>
|