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<?xml version="1.0" encoding="UTF-8"?>
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns="http://per-colator.com/percolator_out/15"
targetNamespace="http://per-colator.com/percolator_out/15"
elementFormDefault="qualified" attributeFormDefault="unqualified">
<!-- define some general types -->
<xsd:simpleType name="probability_t">
<xsd:annotation>
<xsd:documentation>Probability (Double in [0-1] or NaN)</xsd:documentation>
</xsd:annotation>
<xsd:union memberTypes="xsd:double">
<xsd:simpleType>
<xsd:restriction base="xsd:double">
<xsd:enumeration value="NaN"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="xsd:double">
<xsd:maxInclusive value="1.0"/>
<xsd:minInclusive value="0.0"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType name="aa_seq_t">
<xsd:restriction base="xsd:string">
<xsd:pattern value="([A-Z]*(\[[^\]]+\])*[A-Z]*)*"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="aa_term_t">
<xsd:restriction base="xsd:string">
<xsd:pattern value="[A-Z\-]"/>
</xsd:restriction>
</xsd:simpleType>
<!-- end general types -->
<!-- define process_info-->
<xsd:element name="process_info">
<xsd:complexType>
<xsd:sequence>
<xsd:element name="command_line" type="xsd:string"/>
<xsd:element name="other_command_line" type="xsd:string"/>
<xsd:element name="pi_0_psms" type="probability_t" minOccurs="0" maxOccurs="1"/>
<xsd:element name="pi_0_peptides" type="probability_t" minOccurs="0" maxOccurs="1"/>
<xsd:element name="pi_0_proteins" type="probability_t" minOccurs="0" maxOccurs="1"/>
<xsd:element name="fdr_proteins" type="probability_t" minOccurs="0" maxOccurs="1"/>
<xsd:element name="alpha" type="probability_t" minOccurs="0" maxOccurs="1"/>
<xsd:element name="beta" type="probability_t" minOccurs="0" maxOccurs="1"/>
<xsd:element name="gamma" type="probability_t" minOccurs="0" maxOccurs="1"/>
<xsd:element name="psms_qlevel" type="xsd:double" minOccurs="0" maxOccurs="1"/>
<xsd:element name="peptides_qlevel" type="xsd:double" minOccurs="0" maxOccurs="1"/>
<xsd:element name="proteins_qlevel" type="xsd:double" minOccurs="0" maxOccurs="1"/>
<xsd:element minOccurs="0" name="average_delta_mass" type="xsd:double"/>
<xsd:element minOccurs="0" name="average_pi" type="xsd:double"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" name="comment">
<xsd:complexType>
<xsd:attribute name="name" type="xsd:string" use="required"/>
<xsd:attribute name="value" type="xsd:string" use="required"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:complexType>
</xsd:element><!-- end process_info-->
<!-- define elements for psm and peptide-->
<xsd:element name="svm_score" type="xsd:double">
<xsd:annotation>
<xsd:documentation xml:lang="en">The score stemming from the SVM. Higher score corresponds to a better PSM than a lower score.</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="q_value" type="probability_t">
<xsd:annotation>
<xsd:documentation xml:lang="en">The PSMs q-value, i.e. the expected fraction of incorrect identifications up to this PSM score</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="q_value_emp" type="probability_t">
<xsd:annotation>
<xsd:documentation xml:lang="en">The Protein empirical q-value, i.e. the expected fraction of incorrect identifications up to this Protein score</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="pep" type="probability_t">
<xsd:annotation>
<xsd:documentation xml:lang="en">The PSMs posterior error probability, i.e. the probability that this PSM is incorrect.</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="exp_mass" type="xsd:double">
<xsd:annotation>
<xsd:documentation xml:lang="en">The experimental (observed) mass of the PSM</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="calc_mass" type="xsd:double">
<xsd:annotation>
<xsd:documentation xml:lang="en">The calculated mass of the PSM</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="retentionTime">
<xsd:annotation>
<xsd:documentation xml:lang="en">This field contains the observed and predicted retention time in minutes</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:attribute name="predicted" type="xsd:double"/>
<xsd:attribute name="observed" type="xsd:double"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="peptide_seq">
<xsd:annotation>
<xsd:documentation xml:lang="en">Peptide sequence of this PSM including the amino acids N- and C-terminal of the peptide in the proteins sequence.</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:attribute name="n" type="aa_term_t"/>
<xsd:attribute name="c" type="aa_term_t"/>
<xsd:attribute name="seq" type="aa_seq_t" use="required"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="protein_id" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">Protein identifier.</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="psm_ids">
<xsd:annotation>
<xsd:documentation xml:lang="en">List of Psm for a particular peptide.</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element name="psm_id" maxOccurs="unbounded" type="xsd:string"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="p_value" type="probability_t">
<xsd:annotation>
<xsd:documentation xml:lang="en">The PSMs p-value</xsd:documentation>
</xsd:annotation>
</xsd:element>
<!-- end elements for psm and peptide-->
<!-- define attributes for psm, peptide and protein-->
<xsd:attribute name="psm_id" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">Unique PSM identifier</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="peptide_id" type="aa_seq_t">
<xsd:annotation>
<xsd:documentation xml:lang="en">Unique peptiude identifier</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="decoy" type="xsd:boolean"/>
<xsd:attribute name="protein_id" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">Unique protein identifier</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<!-- define attributes for psm, peptide and protein-->
<!-- define psm-->
<xsd:element name="psm">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="svm_score"/>
<xsd:element ref="q_value"/>
<xsd:element ref="pep"/>
<xsd:element ref="exp_mass" minOccurs="0"/>
<xsd:element ref="calc_mass" minOccurs="0"/>
<xsd:element ref="retentionTime" minOccurs="0"/>
<xsd:element ref="peptide_seq"/>
<xsd:element ref="protein_id" maxOccurs="unbounded"/>
<xsd:element ref="p_value"/>
</xsd:sequence>
<xsd:attribute ref="psm_id" use="required"/>
<xsd:attribute ref="decoy"/>
</xsd:complexType>
</xsd:element> <!-- end psm-->
<!-- define psms-->
<xsd:element name="psms">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="psm" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element><!-- end psms-->
<!-- define peptide-->
<xsd:element name="peptide">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="svm_score"/>
<xsd:element ref="q_value"/>
<xsd:element ref="pep"/>
<xsd:element ref="exp_mass" minOccurs="0"/>
<xsd:element ref="calc_mass" minOccurs="0"/>
<xsd:element ref="retentionTime" minOccurs="0"/>
<xsd:element ref="protein_id" maxOccurs="unbounded"/>
<xsd:element ref="p_value"/>
<xsd:element ref="psm_ids" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
<xsd:attribute ref="peptide_id" use="required"/>
<xsd:attribute ref="decoy"/>
</xsd:complexType>
</xsd:element><!-- end peptide-->
<!-- define peptides-->
<xsd:element name="peptides">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="peptide" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<!-- define protein-->
<xsd:element name="protein">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="pep" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="q_value" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="q_value_emp" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="p_value" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="peptide_seq" maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute ref="protein_id" use="required"/>
<xsd:attribute ref="decoy"/>
</xsd:complexType>
</xsd:element><!-- end protein-->
<!-- define proteins-->
<xsd:element name="proteins">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="protein" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<!-- define attributes of percolator_output-->
<xsd:attribute name="percolator_version" type="xsd:string">
<xsd:annotation>
<xsd:documentation>Version of percolator</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="majorVersion" type="xsd:unsignedShort">
<xsd:annotation>
<xsd:documentation>Major version number</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="minorVersion" type="xsd:unsignedShort">
<xsd:annotation>
<xsd:documentation>Minor version number</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<!-- end attributes of percolator_output-->
<!-- define percolator_output-->
<xsd:element name="percolator_output">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="process_info" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="psms" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="peptides" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="proteins" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
<xsd:attribute ref="percolator_version" use="required" />
<xsd:attribute ref="majorVersion" use="required" fixed="2"/>
<xsd:attribute ref="minorVersion" use="required" />
</xsd:complexType>
</xsd:element><!-- end percolator_output-->
</xsd:schema>