XML Schema Documentation

Table of Contents

Schema Document Properties
Global Declarations
Global Definitions

Legend

Glossary

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Schema Document Properties

Target Namespace	http://regis-web.systemsbiology.net/pepXML
Element and Attribute Namespaces	Global element and attribute declarations belong to this schema's target namespace. By default, local element declarations belong to this schema's target namespace. By default, local attribute declarations have no namespace.
Documentation	MS/MS pipeline analysis schema. Developed by ISB proteome center.

Declared Namespaces

Prefix	Namespace
Default namespace	http://regis-web.systemsbiology.net/pepXML
xml	http://www.w3.org/XML/1998/namespace
xs	http://www.w3.org/2001/XMLSchema
pepx	http://regis-web.systemsbiology.net/pepXML

Schema Component Representation

<xs:schema targetNamespace="http://regis-web.systemsbiology.net/pepXML" elementFormDefault="qualified">

...

</xs:schema>

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Global Declarations

Element: asapratio_contribution

Name	asapratio_contribution
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<asapratio_contribution
ratio=" xs:float [1]"
error=" xs:float [1]"
charge=" xs:nonNegativeInteger [1]"
use=" xs:unsignedByte [1]">

<asapratio_lc_lightpeak> ... </asapratio_lc_lightpeak> [1]

<asapratio_lc_heavypeak> ... </asapratio_lc_heavypeak> [1]

</asapratio_contribution>

Schema Component Representation

<xs:element name="asapratio_contribution">

<xs:complexType>

<xs:sequence>

<xs:element ref=" asapratio_lc_lightpeak "/>

<xs:element ref=" asapratio_lc_heavypeak "/>

</xs:sequence>

<xs:attribute name="ratio" type=" xs:float " use="required"/>

<xs:attribute name="error" type=" xs:float " use="required"/>

<xs:attribute name="charge" type=" xs:nonNegativeInteger " use="required"/>

<xs:attribute name="use" type=" xs:unsignedByte " use="required"/>

</xs:complexType>

</xs:element>

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Element: asapratio_lc_heavypeak

Name	asapratio_lc_heavypeak
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<asapratio_lc_heavypeak
status=" xs:byte [1]"
left_valley=" xs:int [1]"
right_valley=" xs:int [1]"
background=" xs:float [1]"
area=" xs:float [1]"
area_error=" xs:float [1]"
time=" xs:float [1]"
time_width=" xs:float [1]"
is_heavy=" xs:string [1]"/>

Schema Component Representation

<xs:element name="asapratio_lc_heavypeak">

<xs:complexType>

<xs:attribute name="status" type=" xs:byte " use="required"/>

<xs:attribute name="left_valley" type=" xs:int " use="required"/>

<xs:attribute name="right_valley" type=" xs:int " use="required"/>

<xs:attribute name="background" type=" xs:float " use="required"/>

<xs:attribute name="area" type=" xs:float " use="required"/>

<xs:attribute name="area_error" type=" xs:float " use="required"/>

<xs:attribute name="time" type=" xs:float " use="required"/>

<xs:attribute name="time_width" type=" xs:float " use="required"/>

<xs:attribute name="is_heavy" type=" xs:string " use="required"/>

</xs:complexType>

</xs:element>

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Element: asapratio_lc_lightpeak

Name	asapratio_lc_lightpeak
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<asapratio_lc_lightpeak
status=" xs:byte [1]"
left_valley=" xs:int [1]"
right_valley=" xs:int [1]"
background=" xs:float [1]"
area=" xs:float [1]"
area_error=" xs:float [1]"
time=" xs:float [1]"
time_width=" xs:float [1]"
is_heavy=" xs:string [1]"/>

Schema Component Representation

<xs:element name="asapratio_lc_lightpeak">

<xs:complexType>

<xs:attribute name="status" type=" xs:byte " use="required"/>

<xs:attribute name="left_valley" type=" xs:int " use="required"/>

<xs:attribute name="right_valley" type=" xs:int " use="required"/>

<xs:attribute name="background" type=" xs:float " use="required"/>

<xs:attribute name="area" type=" xs:float " use="required"/>

<xs:attribute name="area_error" type=" xs:float " use="required"/>

<xs:attribute name="time" type=" xs:float " use="required"/>

<xs:attribute name="time_width" type=" xs:float " use="required"/>

<xs:attribute name="is_heavy" type=" xs:string " use="required"/>

</xs:complexType>

</xs:element>

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Element: asapratio_peptide_data

Name	asapratio_peptide_data
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<asapratio_peptide_data
status=" xs:byte [1]"
cidIndex=" xs:int [1]"
light_mass=" xs:float [1]"
heavy_mass=" xs:float [1]"
area_flag=" xs:unsignedInt [1]">

<asapratio_contribution> ... </asapratio_contribution> [1..*]

</asapratio_peptide_data>

Schema Component Representation

<xs:element name="asapratio_peptide_data">

<xs:complexType>

<xs:sequence>

<xs:element ref=" asapratio_contribution " maxOccurs="unbounded"/>

</xs:sequence>

<xs:attribute name="status" type=" xs:byte " use="required"/>

<xs:attribute name="cidIndex" type=" xs:int " use="required"/>

<xs:attribute name="light_mass" type=" xs:float " use="required"/>

<xs:attribute name="heavy_mass" type=" xs:float " use="required"/>

<xs:attribute name="area_flag" type=" xs:unsignedInt " use="required"/>

</xs:complexType>

</xs:element>

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Element: asapratio_result

Name	asapratio_result
Type	Locally-defined complex type
Nillable	no
Abstract	no
Documentation	Quantitation

XML Instance Representation

<asapratio_result
mean=" xs:float [1]"
error=" xs:float [1]"
heavy2light_mean=" xs:float [1]"
heavy2light_error=" xs:float [1]">

<asapratio_peptide_data> ... </asapratio_peptide_data> [1]

</asapratio_result>

Schema Component Representation

<xs:element name="asapratio_result">

<xs:complexType>

<xs:sequence>

<xs:element ref=" asapratio_peptide_data "/>

</xs:sequence>

<xs:attribute name="mean" type=" xs:float " use="required"/>

<xs:attribute name="error" type=" xs:float " use="required"/>

<xs:attribute name="heavy2light_mean" type=" xs:float " use="required"/>

<xs:attribute name="heavy2light_error" type=" xs:float " use="required"/>

</xs:complexType>

</xs:element>

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Element: asapratio_summary

Name	asapratio_summary
Type	Locally-defined complex type
Nillable	no
Abstract	no
Documentation	Quantitation

XML Instance Representation

<asapratio_summary
version=" xs:string [1]"
author=" xs:string [1]"
elution=" xs:integer [1] ?"
labeled_residues=" xs:string [1] ?"
area_flag=" xs:nonNegativeInteger [1]"
static_quant=" xs:string [1] ?"/>

Schema Component Representation

<xs:element name="asapratio_summary">

<xs:complexType>

<xs:attribute name="version" type=" xs:string " use="required"/>

<xs:attribute name="author" type=" xs:string " use="required"/>

<xs:attribute name="elution" type=" xs:integer " use="required"/>

<xs:attribute name="labeled_residues" type=" xs:string " use="required"/>

<xs:attribute name="area_flag" type=" xs:nonNegativeInteger " use="required"/>

<xs:attribute name="static_quant" type=" xs:string " use="required"/>

</xs:complexType>

</xs:element>

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Element: asapratio_timestamp

Name	asapratio_timestamp
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<asapratio_timestamp
quant_label_masses=" xs:string [0..1]"
static_quant_label=" xs:string [0..1]"/>

Schema Component Representation

<xs:element name="asapratio_timestamp">

<xs:complexType>

<xs:attribute name="quant_label_masses" type=" xs:string "/>

<xs:attribute name="static_quant_label" type=" xs:string "/>

<-- <xs:attribute name="light_labels" type="xs:string"/> <xs:attribute name="heavy_labels" type="xs:string"/> -->

</xs:complexType>

</xs:element>

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Element: database_refresh_timestamp

Name	database_refresh_timestamp
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<database_refresh_timestamp
database=" xs:string [1]"
min_num_enz_term=" xs:nonNegativeInteger [0..1]"/>

Schema Component Representation

<xs:element name="database_refresh_timestamp">

<xs:complexType>

<xs:attribute name="database" type=" xs:string " use="required"/>

<xs:attribute name="min_num_enz_term" type=" xs:nonNegativeInteger "/>

</xs:complexType>

</xs:element>

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Element: interact_summary

Name	interact_summary
Type	Locally-defined complex type
Nillable	no
Abstract	no
Documentation	Combined datasets

XML Instance Representation

<interact_summary
filename=" xs:string [1]"
directory=" xs:string [1]"
inputfiles=" xs:string [1]"/>

Schema Component Representation

<xs:element name="interact_summary">

<xs:complexType>

<xs:attribute name="filename" type=" xs:string " use="required"/>

<xs:attribute name="directory" type=" xs:string " use="required"/>

<xs:attribute name="inputfiles" type=" xs:string " use="required"/>

</xs:complexType>

</xs:element>

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Element: libra_result

Name	libra_result
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<libra_result>

<intensity
channel=" positiveInt [1]"
target_mass=" xs:float [1]"
absolute=" xs:float [1]"
normalized=" xs:float [1]"/> [1..*]

</libra_result>

Schema Component Representation

<xs:element name="libra_result">

<xs:complexType>

<xs:sequence>

<xs:element name="intensity" maxOccurs="unbounded">

<-- the following are vector<float> -->

<xs:complexType>

<xs:attribute name="channel" type=" positiveInt " use="required"/>

<xs:attribute name="target_mass" type=" xs:float " use="required"/>

<xs:attribute name="absolute" type=" xs:float " use="required"/>

<xs:attribute name="normalized" type=" xs:float " use="required"/>

</xs:complexType>

</xs:element>

</xs:sequence>

</xs:complexType>

<xs:unique name="libra_result_channel_index">

<xs:selector xpath="."/>

<xs:field xpath="@channel"/>

</xs:unique>

</xs:element>

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Element: libra_summary

Name	libra_summary
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<libra_summary
mass_tolerance=" xs:float [1]"
centroiding_preference=" xs:int [1]"
normalization=" xs:int [1]"
output_type=" xs:int [1]"
channel_code=" xs:string [0..1]">

<fragment_masses
channel=" positiveInt [1]"
mz=" xs:float [1]"/> [1..*]

<isotopic_contributions> [0..1]

<contributing_channel
channel=" positiveInt [1]"> [1..*]

<affected_channel
channel=" positiveInt [1]"
correction=" xs:float [1]"/> [1..*]

</contributing_channel>

</isotopic_contributions>

</libra_summary>

Schema Component Representation

<xs:element name="libra_summary">

<xs:complexType>

<xs:sequence>

<xs:element name="fragment_masses" maxOccurs="unbounded">

<xs:complexType>

<xs:attribute name="channel" type=" positiveInt " use="required"/>

<xs:attribute name="mz" type=" xs:float " use="required"/>

</xs:complexType>

</xs:element>

<xs:element name="isotopic_contributions" minOccurs="0">

<xs:complexType>

<xs:sequence>

<xs:element name="contributing_channel" maxOccurs="unbounded">

<xs:complexType>

<xs:sequence>

<xs:element name="affected_channel" maxOccurs="unbounded">

<xs:complexType>

<xs:attribute name="channel" type=" positiveInt " use="required"/>

<xs:attribute name="correction" type=" xs:float " use="required"/>

</xs:complexType>

</xs:element>

</xs:sequence>

<xs:attribute name="channel" type=" positiveInt " use="required"/>

</xs:complexType>

</xs:element>

</xs:sequence>

</xs:complexType>

</xs:element>

</xs:sequence>

<xs:attribute name="mass_tolerance" type=" xs:float " use="required"/>

<xs:attribute name="centroiding_preference" type=" xs:int " use="required"/>

<xs:attribute name="normalization" type=" xs:int " use="required"/>

<xs:attribute name="output_type" type=" xs:int " use="required"/>

<xs:attribute name="channel_code" type=" xs:string "/>

</xs:complexType>

<xs:key name="libra_channel_index">

<xs:selector xpath="./pepx:fragment_masses"/>

<xs:field xpath="@channel"/>

</xs:key>

<xs:keyref name="libra_contr_channel_index_ref" refer=" libra_channel_index ">

<xs:selector xpath="./pepx:isotopic_contributions/pepx:contributing_channel"/>

<xs:field xpath="@channel"/>

</xs:keyref>

<xs:keyref name="libra_aff_channel_index_ref" refer=" libra_channel_index ">

<xs:selector xpath="./pepx:isotopic_contributions/pepx:contributing_channel/pepx:affected_channel"/>

<xs:field xpath="@channel"/>

</xs:keyref>

</xs:element>

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Element: msms_pipeline_analysis

Name	msms_pipeline_analysis
Type	Locally-defined complex type
Nillable	no
Abstract	no

XML Instance Representation

<msms_pipeline_analysis
name=" xs:string [0..1] ?"
date=" xs:dateTime [1] ?"
summary_xml=" xs:string [1] ?">

<analysis_summary
time=" xs:dateTime [1] ?"
analysis=" xs:string [1] ?"
version=" xs:string [0..1] ?"> [0..*] ?

Allow any elements from any namespace (lax validation). [0..1]

</analysis_summary>

<dataset_derivation
generation_no=" xs:nonNegativeInteger [1]"> [0..1] ?

<data_filter
number=" xs:nonNegativeInteger [1]"
parent_file=" xs:string [1]"
windows_parent=" xs:string [0..1]"
description=" xs:string [1] ?"/> [0..*]

</dataset_derivation>

<msms_run_summary
base_name=" xs:string [1] ?"
raw_data_type=" xs:string [1] ?"
raw_data=" xs:string [1] ?"
msManufacturer=" xs:string [0..1] ?"
msModel=" xs:string [0..1] ?"
msIonization=" xs:string [0..1] ?"
msMassAnalyzer=" xs:string [0..1] ?"
msDetector=" xs:string [0..1] ?"> [1..*] ?

<sample_enzyme
name=" xs:string (length >= 1) [1]