XML Schema Documentation

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.

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

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

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

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

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

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

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

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

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

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

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

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

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] ?"
description=" xs:string [0..1] ?"
fidelity=" xs:string (value comes from list: {'specific'|'semispecific'|'nonspecific'}) [0..1] ?"
independent=" xs:boolean [0..1] ?"> [1] ?

<specificity
sense=" xs:string (value comes from list: {'C'|'N'}) [1] ?"
min_spacing=" xs:nonNegativeInteger [0..1] ?"
cut=" xs:string (pattern = [A,C-I,K-N,P-T,VWY]+) (length >= 1) [1] ?"
no_cut=" xs:string (length >= 0) [0..1] ?"/> [0..*] ?

</sample_enzyme>

<search_summary
base_name=" xs:string [1] ?"
search_engine=" engineType [1] ?"
precursor_mass_type=" massType [1] ?"
fragment_mass_type=" massType [1] ?"
out_data_type=" xs:string [1] ?"
out_data=" xs:string [1] ?"
search_id=" positiveInt [1] ?"> [1..*] ?

<search_database
local_path=" xs:string [1] ?"
URL=" xs:string [0..1]"
database_name=" xs:string [0..1]"
orig_database_url=" xs:string [0..1]"
database_release_date=" xs:dateTime [0..1]"
database_release_identifier=" xs:string [0..1]"
size_in_db_entries=" xs:nonNegativeInteger [0..1]"
size_of_residues=" xs:nonNegativeInteger [0..1]"
type=" xs:string (value comes from list: {'AA'|'NA'}) [1] ?"/> [0..1]

<enzymatic_search_constraint
enzyme=" xs:string [1]"
max_num_internal_cleavages=" xs:nonNegativeInteger [1] ?"
min_number_termini=" xs:nonNegativeInteger [1] ?"/> [0..1] ?

<sequence_search_constraint
sequence=" xs:string [1] ?"/> [0..*] ?

<aminoacid_modification
aminoacid=" xs:string [1]"
massdiff=" xs:string [1] ?"
mass=" xs:float [1] ?"
variable=" xs:string [1] ?"
peptide_terminus=" xs:string [0..1] ?"
symbol=" aa_symbolType [0..1] ?"
binary=" xs:string [0..1] ?"
description=" xs:string [0..1]"/> [0..*] ?

<terminal_modification
terminus=" xs:string [1] ?"
massdiff=" xs:string [1] ?"
mass=" xs:float [1] ?"
variable=" xs:string [1] ?"
symbol=" term_symbolType [0..1] ?"
protein_terminus=" xs:string [1] ?"
description=" xs:string [0..1]"/> [0..*] ?

<parameter> nameValueType </parameter> [0..*]

</search_summary>

<analysis_timestamp
time=" xs:dateTime [1] ?"
analysis=" xs:string [1] ?"
id=" positiveInt [1] ?"> [0..*] ?

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

</analysis_timestamp>

<spectrum_query
spectrum=" xs:string [1]"
start_scan=" xs:unsignedInt [1] ?"
end_scan=" xs:unsignedInt [1] ?"
precursor_neutral_mass=" xs:float [1]"
assumed_charge=" xs:nonNegativeInteger [1] ?"
search_specification=" xs:string [0..1] ?"
index=" positiveInt [1] ?"> [0..*] ?

<search_result
search_id=" positiveInt [0..1] ?"> [0..*]

<search_hit
hit_rank=" positiveInt [1]"
peptide=" xs:string [1] ?"
peptide_prev_aa=" xs:string [0..1] ?"
peptide_next_aa=" xs:string [0..1] ?"
protein=" xs:string [1]"
num_tot_proteins=" xs:unsignedInt [1] ?"
num_matched_ions=" xs:nonNegativeInteger [0..1] ?"
tot_num_ions=" xs:nonNegativeInteger [0..1] ?"
calc_neutral_pep_mass=" xs:float [1]"
massdiff=" xs:string [1] ?"
num_tol_term=" xs:nonNegativeInteger [0..1] ?"
num_missed_cleavages=" xs:integer [0..1] ?"
is_rejected=" xs:nonNegativeInteger (value comes from list: {'0'|'1'}) [0..1] ?"
protein_descr=" xs:string [0..1] ?"
calc_pI=" xs:string [0..1]"
protein_mw=" xs:double [0..1]"> [0..*] ?

<alternative_protein
protein=" xs:string [1]"
protein_descr=" xs:string [0..1]"
num_tol_term=" xs:nonNegativeInteger [0..1]"
protein_mw=" xs:double [0..1]"/> [0..*] ?

<modification_info
mod_nterm_mass=" xs:double [0..1] ?"
mod_cterm_mass=" xs:double [0..1] ?"
modified_peptide=" xs:string [0..1] ?"> [0..1] ?

<mod_aminoacid_mass
position=" xs:nonNegativeInteger [1] ?"
mass=" xs:double [1] ?"/> [0..*]

</modification_info>

<search_score> nameValueType </search_score> [0..*]

<analysis_result
analysis=" xs:string [1]"
id=" positiveInt [0..1]"> [0..*]

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

</analysis_result>

<parameter> nameValueType </parameter> [0..*]

</search_hit>

</search_result>

</spectrum_query>

</msms_run_summary>

</msms_pipeline_analysis>

Schema Component Representation

<xs:element name="msms_pipeline_analysis">

<xs:complexType>

<xs:sequence>

<xs:element name="analysis_summary" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

<xs:sequence>

<xs:any namespace="##any" processContents="lax" minOccurs="0"/>

</xs:sequence>

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

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

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

</xs:complexType>

</xs:element>

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

<xs:complexType>

<xs:sequence>

<xs:element name="data_filter" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

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

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

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

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

</xs:complexType>

</xs:element>

</xs:sequence>

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

</xs:complexType>

</xs:element>

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

<xs:complexType>

<xs:sequence>

<xs:element name="sample_enzyme">

<xs:complexType>

<xs:sequence>

<xs:element name="specificity" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

<xs:attribute name="sense" use="required">

<xs:simpleType>

<xs:restriction base=" xs:string ">

<xs:enumeration value="C"/>

<xs:enumeration value="N"/>

</xs:restriction>

</xs:simpleType>

</xs:attribute>

<xs:attribute name="min_spacing" type=" xs:nonNegativeInteger " default="1"/>

<xs:attribute name="cut" use="required">

<xs:simpleType>

<xs:restriction base=" xs:string ">

<xs:minLength value="1"/>

<xs:maxLength value="20"/>

<xs:pattern value="[A,C-I,K-N,P-T,VWY]+"/>

</xs:restriction>

</xs:simpleType>

</xs:attribute>

<xs:attribute name="no_cut" use="optional">

<xs:simpleType>

<xs:restriction base=" xs:string ">

<xs:minLength value="0"/>

<xs:maxLength value="20"/>

</xs:restriction>

</xs:simpleType>

</xs:attribute>

</xs:complexType>

</xs:element>

</xs:sequence>

<xs:attribute name="name" use="required">

<xs:simpleType>

<xs:restriction base=" xs:string ">

<xs:minLength value="1"/>

</xs:restriction>

</xs:simpleType>

</xs:attribute>

<xs:attribute name="description" type=" xs:string " use="optional"/>

<xs:attribute name="fidelity" use="optional" default="specific">

<xs:simpleType>

<xs:restriction base=" xs:string ">

<xs:enumeration value="specific"/>

<xs:enumeration value="semispecific"/>

<xs:enumeration value="nonspecific"/>

</xs:restriction>

</xs:simpleType>

</xs:attribute>

<xs:attribute name="independent" type=" xs:boolean " use="optional" default="1"/>

</xs:complexType>

</xs:element>

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

<xs:complexType>

<xs:sequence>

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

<xs:complexType>

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

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

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

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

<xs:attribute name="database_release_date" type=" xs:dateTime "/>

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

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

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

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

<xs:simpleType>

<xs:restriction base=" xs:string ">

<xs:enumeration value="AA"/>

<xs:enumeration value="NA"/>

</xs:restriction>

</xs:simpleType>

</xs:attribute>

</xs:complexType>

</xs:element>

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

<xs:complexType>

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

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

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

</xs:complexType>

</xs:element>

<xs:element name="sequence_search_constraint" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

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

</xs:complexType>

</xs:element>

<xs:element name="aminoacid_modification" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

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

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

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

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

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

<xs:attribute name="symbol" type=" aa_symbolType "/>

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

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

</xs:complexType>

</xs:element>

<xs:element name="terminal_modification" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

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

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

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

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

<xs:attribute name="symbol" type=" term_symbolType "/>

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

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

</xs:complexType>

</xs:element>

<xs:element name="parameter" type=" nameValueType " minOccurs="0" maxOccurs="unbounded"/>

</xs:sequence>

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

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

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

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

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

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

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

</xs:complexType>

</xs:element>

<xs:element name="analysis_timestamp" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

<xs:sequence>

<xs:any namespace="##any" processContents="lax" minOccurs="0"/>

</xs:sequence>

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

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

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

</xs:complexType>

</xs:element>

<xs:element name="spectrum_query" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

<xs:sequence>

<xs:element name="search_result" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

<xs:sequence>

<xs:element name="search_hit" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

<xs:sequence>

<xs:element name="alternative_protein" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

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

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

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

<xs:attribute name="protein_mw" type=" xs:double "/>

</xs:complexType>

</xs:element>

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

<xs:complexType>

<xs:sequence>

<xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

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

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

</xs:complexType>

</xs:element>

</xs:sequence>

<xs:attribute name="mod_nterm_mass" type=" xs:double "/>

<xs:attribute name="mod_cterm_mass" type=" xs:double "/>

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

</xs:complexType>

</xs:element>

<xs:element name="search_score" type=" nameValueType " minOccurs="0" maxOccurs="unbounded"/>

<xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

<xs:sequence>

<xs:any namespace="##any" processContents="lax"/>

</xs:sequence>

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

<xs:attribute name="id" type=" positiveInt " default="1"/>

</xs:complexType>

</xs:element>

<xs:element name="parameter" type=" nameValueType " minOccurs="0" maxOccurs="unbounded"/>

</xs:sequence>

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

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

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

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

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

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

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

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

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

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

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

<xs:attribute name="num_missed_cleavages" type=" xs:integer "/>

<xs:attribute name="is_rejected" default="0">

<xs:simpleType>

<xs:restriction base=" xs:nonNegativeInteger ">

<xs:enumeration value="0"/>

<xs:enumeration value="1"/>

</xs:restriction>

</xs:simpleType>

</xs:attribute>

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

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

<xs:attribute name="protein_mw" type=" xs:double "/>

</xs:complexType>

<xs:unique name="unique_result_analysis_id">

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

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

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

</xs:unique>

</xs:element>

</xs:sequence>

<xs:attribute name="search_id" type=" positiveInt " default="1"/>

</xs:complexType>

</xs:element>

<-- search result -->

</xs:sequence>

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

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

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

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

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

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

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

</xs:complexType>

<xs:unique name="unique_search_id">

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

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

</xs:unique>

</xs:element>

<-- <xs:element name="msInstrument" minOccurs="0"> <xs:annotation> <xs:documentation>General information about the MS instrument. (cf. mzXML msInstrument)</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="msManufacturer"> <xs:complexType> <xs:complexContent> <xs:extension base="ontologyEntryType"/> </xs:complexContent> </xs:complexType> </xs:element> <xs:element name="msModel" type="ontologyEntryType"/> <xs:element name="msIonisation" type="ontologyEntryType"/> <xs:element name="msMassAnalyzer"> <xs:complexType> <xs:complexContent> <xs:extension base="ontologyEntryType"/> </xs:complexContent> </xs:complexType> </xs:element> </xs:sequence> </xs:complexType> </xs:element> -->

</xs:sequence>

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

<-- <xs:attribute name="search_engine" type="engineType" use="required"> <xs:annotation> <xs:documentation>SEQUEST, Mascot, COMET, etc</xs:documentation> </xs:annotation> </xs:attribute> -->

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

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

<-- <xs:attribute name="out_data_type" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Format of file storing the runner up peptides (if not present in pepXML)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="out_data" type="xs:string" use="required"> <xs:annotation> <xs:documentation>runner up search hit data type extension (e.g. .tgz)</xs:documentation> </xs:annotation> </xs:attribute> -->

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

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

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

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

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

</xs:complexType>

<xs:unique name="unique_timestamp_analysis_time">

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

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

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

</xs:unique>

<xs:key name="search_summary_id">

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

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

</xs:key>

<xs:keyref name="search_result_id" refer=" search_summary_id ">

<xs:selector xpath="./pepx:spectrum_query/pepx:search_result"/>

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

</xs:keyref>

<xs:key name="timestamp_analysis_id">

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

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

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

</xs:key>

<xs:keyref name="result_analysis_id" refer=" timestamp_analysis_id ">

<xs:selector xpath="./pepx:spectrum_query/pepx:search_result/pepx:search_hit/pepx:analysis_result"/>

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

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

</xs:keyref>

</xs:element>

</xs:sequence>

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

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

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

</xs:complexType>

<xs:key name="summary_analysis_time">

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

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

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

</xs:key>

<xs:keyref name="timestamp_analysis_time" refer=" summary_analysis_time ">

<xs:selector xpath="./pepx:msms_run_summary/pepx:analysis_timestamp"/>

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

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

</xs:keyref>

<xs:unique name="unique_search_summary_basename">

<xs:selector xpath="./pepx:msms_run_summary/pepx:search_summary"/>

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

</xs:unique>

</xs:element>

Element: peptideprophet_result

Name	peptideprophet_result
Type	Locally-defined complex type
Nillable	no
Abstract	no
Documentation	Validation

XML Instance Representation

<peptideprophet_result
probability=" xs:float [1]"
all_ntt_prob=" xs:string [0..1]"
analysis=" xs:string [0..1]">

<search_score_summary> [0..1]

<parameter> nameValueType </parameter> [2..*]

</search_score_summary>

</peptideprophet_result>

Schema Component Representation

<xs:element name="peptideprophet_result">

<xs:complexType>

<xs:sequence>

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

<xs:complexType>

<xs:sequence>

<xs:element name="parameter" type=" nameValueType " minOccurs="2" maxOccurs="unbounded"/>

</xs:sequence>

</xs:complexType>

</xs:element>

</xs:sequence>

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

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

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

</xs:complexType>

</xs:element>

Element: peptideprophet_summary

Name	peptideprophet_summary
Type	Locally-defined complex type
Nillable	no
Abstract	no
Documentation	Validation of search results

XML Instance Representation

<peptideprophet_summary
version=" xs:string [1]"
author=" xs:string [1]"
inputfiles=" xs:string [1]"
min_prob=" xs:float [1] ?"
options=" xs:string [0..1] ?"
est_tot_num_correct=" xs:float [0..1] ?">

<roc_data_point
min_prob=" xs:float [1] ?"
sensitivity=" xs:float [1] ?"
error=" xs:float [1] ?"
num_corr=" xs:unsignedInt [1] ?"
num_incorr=" xs:unsignedInt [1] ?"/> [0..*]

<error_point
error=" xs:float [1] ?"
min_prob=" xs:float [1] ?"
num_corr=" xs:unsignedInt [1] ?"
num_incorr=" xs:unsignedInt [1] ?"/> [0..*]

<distribution_point
fvalue=" xs:float [1] ?"
obs_1_distr=" xs:nonNegativeInteger [1] ?"
model_1_pos_distr=" xs:float [1] ?"
model_1_neg_distr=" xs:float [1] ?"
obs_2_distr=" xs:nonNegativeInteger [1] ?"
model_2_pos_distr=" xs:float [1] ?"
model_2_neg_distr=" xs:float [1] ?"
obs_3_distr=" xs:nonNegativeInteger [1] ?"
model_3_pos_distr=" xs:float [1] ?"
model_3_neg_distr=" xs:float [1] ?"/> [0..*]

<mixture_model
precursor_ion_charge=" xs:nonNegativeInteger [1]"
comments=" xs:string [1]"
prior_probability=" xs:float [1] ?"
est_tot_correct=" xs:float [1]"
tot_num_spectra=" xs:nonNegativeInteger [1] ?"
num_iterations=" xs:nonNegativeInteger [1] ?"> [0..*]

<mixturemodel_distribution
name=" xs:string [1]"> [1..*]

<posmodel_distribution
type=" model_dis_type [0..1]"> [1]

<parameter> nameValueType </parameter> [1..*]

</posmodel_distribution>

<negmodel_distribution
type=" model_dis_type [0..1]"> [1]

<parameter> nameValueType </parameter> [1..*]

</negmodel_distribution>

</mixturemodel_distribution>

</mixture_model>

</peptideprophet_summary>

Schema Component Representation

<xs:element name="peptideprophet_summary">

<xs:complexType>

<xs:sequence>

<xs:element name="roc_data_point" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

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

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

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

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

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

</xs:complexType>

</xs:element>

<xs:element name="error_point" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

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

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

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

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

</xs:complexType>

</xs:element>

<xs:element name="distribution_point" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

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

<xs:attribute name="obs_1_distr" type=" xs:nonNegativeInteger " use="required"/>

<xs:attribute name="model_1_pos_distr" type=" xs:float " use="required"/>

<xs:attribute name="model_1_neg_distr" type=" xs:float " use="required"/>

<xs:attribute name="obs_2_distr" type=" xs:nonNegativeInteger " use="required"/>

<xs:attribute name="model_2_pos_distr" type=" xs:float " use="required"/>

<xs:attribute name="model_2_neg_distr" type=" xs:float " use="required"/>

<xs:attribute name="obs_3_distr" type=" xs:nonNegativeInteger " use="required"/>

<xs:attribute name="model_3_pos_distr" type=" xs:float " use="required"/>

<xs:attribute name="model_3_neg_distr" type=" xs:float " use="required"/>

</xs:complexType>

</xs:element>

<xs:element name="mixture_model" minOccurs="0" maxOccurs="unbounded">

<xs:complexType>

<xs:sequence>

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

<xs:complexType>

<xs:sequence>

<xs:element name="posmodel_distribution">

<xs:complexType>

<xs:sequence>

<xs:element name="parameter" type=" nameValueType " maxOccurs="unbounded"/>

</xs:sequence>

<xs:attribute name="type" type=" model_dis_type "/>

</xs:complexType>

</xs:element>

<xs:element name="negmodel_distribution">

<xs:complexType>

<xs:sequence>

<xs:element name="parameter" type=" nameValueType " maxOccurs="unbounded"/>

</xs:sequence>

<xs:attribute name="type" type=" model_dis_type "/>

</xs:complexType>

</xs:element>

</xs:sequence>

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

</xs:complexType>

</xs:element>

</xs:sequence>

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

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

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

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

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

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

</xs:complexType>

</xs:element>

</xs:sequence>

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

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

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

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

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

<xs:attribute name="est_tot_num_correct" type=" xs:float "/>

</xs:complexType>

</xs:element>

Element: xpressratio_result

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

XML Instance Representation

<xpressratio_result
light_firstscan=" xs:unsignedInt [1]"
light_lastscan=" xs:unsignedInt [1]"
light_mass=" xs:float [1]"
heavy_firstscan=" xs:unsignedInt [1]"
heavy_lastscan=" xs:unsignedInt [1]"
heavy_mass=" xs:float [1]"
mass_tol=" xs:float [1]"
ratio=" xs:string [1]"
heavy2light_ratio=" xs:string [1]"
light_area=" xs:float [1]"
heavy_area=" xs:float [1]"
decimal_ratio=" xs:decimal [1]"/>

Schema Component Representation

<xs:element name="xpressratio_result">

<xs:complexType>

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

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

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

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

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

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

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

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

<xs:attribute name="heavy2light_ratio" type=" xs:string " use="required"/>

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

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

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

</xs:complexType>

</xs:element>

Element: xpressratio_summary

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

XML Instance Representation

<xpressratio_summary
version=" xs:string [1]"
author=" xs:string [1]"
same_scan_range=" xs:string [1]"
labeled_residues=" xs:string [1]"
xpress_light=" xs:unsignedInt [1]"
massdiff=" xs:string [1]"
masstol=" xs:float [1]"/>

Schema Component Representation

<xs:element name="xpressratio_summary">

<xs:complexType>

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

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

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

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

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

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

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

</xs:complexType>

</xs:element>

Element: xpressratio_timestamp

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

XML Instance Representation

<xpressratio_timestamp
xpress_light=" xs:integer [1]"/>

Schema Component Representation

<xs:element name="xpressratio_timestamp">

<xs:complexType>

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

</xs:complexType>

</xs:element>

Global Definitions

Complex Type: nameValueType

Super-types:	xs:anySimpleType < nameValueType (by extension)
Sub-types:	None

Name	nameValueType
Abstract	no

XML Instance Representation

<...
name=" xs:string [1]"
value=" xs:anySimpleType [1]"
type=" xs:anySimpleType [0..1]">
xs:anySimpleType
</...>

Schema Component Representation

<xs:complexType name="nameValueType">

<xs:simpleContent>

<xs:extension base=" xs:anySimpleType ">

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

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

<xs:attribute name="type" type=" xs:anySimpleType "/>

</xs:extension>

</xs:simpleContent>

</xs:complexType>

Simple Type: aa_symbolType

Super-types:	xs:string < aa_symbolType (by restriction)
Sub-types:	None

Name	aa_symbolType
Content	Base XSD Type: string value comes from list: {'1'\|'2'\|'3'\|'4'\|'5'\|'6'\|'7'\|'8'\|'9'\|'#'\|'@'\|'*'\|'~'\|'''\|''''\|'$'\|'!'\|'^'\|'?'}

Schema Component Representation

<xs:simpleType name="aa_symbolType">

<xs:restriction base=" xs:string ">

<xs:enumeration value="1"/>

<xs:enumeration value="2"/>

<xs:enumeration value="3"/>

<xs:enumeration value="4"/>

<xs:enumeration value="5"/>

<xs:enumeration value="6"/>

<xs:enumeration value="7"/>

<xs:enumeration value="8"/>

<xs:enumeration value="9"/>

<xs:enumeration value="#"/>

<xs:enumeration value="@"/>

<xs:enumeration value="*"/>

<xs:enumeration value="~"/>

<xs:enumeration value="'"/>

<xs:enumeration value="''"/>

<xs:enumeration value="$"/>

<xs:enumeration value="!"/>

<xs:enumeration value="^"/>

<xs:enumeration value="?"/>

</xs:restriction>

</xs:simpleType>

Simple Type: engineType

Super-types:	xs:string < engineType (by restriction)
Sub-types:	None

Name	engineType
Content	Base XSD Type: string value comes from list: {'SEQUEST'\|'MASCOT'\|'COMET'\|'PROBID'}

Schema Component Representation

<xs:simpleType name="engineType">

<xs:restriction base=" xs:string ">

<xs:enumeration value="SEQUEST"/>

<xs:enumeration value="MASCOT"/>

<xs:enumeration value="COMET"/>

<xs:enumeration value="PROBID"/>

</xs:restriction>

</xs:simpleType>

Simple Type: massType

Super-types:	xs:string < massType (by restriction)
Sub-types:	None

Name	massType
Content	Base XSD Type: string value comes from list: {'monoisotopic'\|'average'}

Schema Component Representation

<xs:simpleType name="massType">

<xs:restriction base=" xs:string ">

<xs:enumeration value="monoisotopic"/>

<xs:enumeration value="average"/>

</xs:restriction>

</xs:simpleType>

Simple Type: model_dis_type

Super-types:	xs:string < model_dis_type (by restriction)
Sub-types:	None

Name	model_dis_type
Content	Base XSD Type: string value comes from list: {'discrete'\|'gaussian'\|'extremevalue'\|'gamma'\|'evd'}

Schema Component Representation

<xs:simpleType name="model_dis_type">

<xs:restriction base=" xs:string ">

<xs:enumeration value="discrete"/>

<xs:enumeration value="gaussian"/>

<xs:enumeration value="extremevalue"/>

<xs:enumeration value="gamma"/>

<xs:enumeration value="evd"/>

</xs:restriction>

</xs:simpleType>

Simple Type: positiveInt

Super-types:	xs:unsignedInt < positiveInt (by restriction)
Sub-types:	None

Name	positiveInt
Content	Base XSD Type: unsignedInt value >= 1

Schema Component Representation

<xs:simpleType name="positiveInt">

<xs:restriction base=" xs:unsignedInt ">

<xs:minInclusive value="1"/>

</xs:restriction>

</xs:simpleType>

Simple Type: term_symbolType

Super-types:	xs:string < term_symbolType (by restriction)
Sub-types:	None

Name	term_symbolType
Content	Base XSD Type: string value comes from list: {','\|';'\|':'}

Schema Component Representation

<xs:simpleType name="term_symbolType">

<xs:restriction base=" xs:string ">

<xs:enumeration value=","/>

<xs:enumeration value=";"/>

<xs:enumeration value=":"/>

</xs:restriction>

</xs:simpleType>

Super-types:	Address < AusAddress (by extension)
Sub-types:	QLDAddress (by restriction)

Name	AusAddress
Abstract	no

Glossary

Abstract (Applies to complex type definitions and element declarations). An abstract element or complex type cannot used to validate an element instance. If there is a reference to an abstract element, only element declarations that can substitute the abstract element can be used to validate the instance. For references to abstract type definitions, only derived types can be used.

All Model Group Child elements can be provided in any order in instances. See: http://www.w3.org/TR/xmlschema-1/#element-all.

Choice Model Group Only one from the list of child elements and model groups can be provided in instances. See: http://www.w3.org/TR/xmlschema-1/#element-choice.

Collapse Whitespace Policy Replace tab, line feed, and carriage return characters with space character (Unicode character 32). Then, collapse contiguous sequences of space characters into single space character, and remove leading and trailing space characters.

Disallowed Substitutions (Applies to element declarations). If substitution is specified, then substitution group members cannot be used in place of the given element declaration to validate element instances. If derivation methods, e.g. extension, restriction, are specified, then the given element declaration will not validate element instances that have types derived from the element declaration's type using the specified derivation methods. Normally, element instances can override their declaration's type by specifying an xsi:type attribute.

Key Constraint Like Uniqueness Constraint, but additionally requires that the specified value(s) must be provided. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

Key Reference Constraint Ensures that the specified value(s) must match value(s) from a Key Constraint or Uniqueness Constraint. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

Model Group Groups together element content, specifying the order in which the element content can occur and the number of times the group of element content may be repeated. See: http://www.w3.org/TR/xmlschema-1/#Model_Groups.

Nillable (Applies to element declarations). If an element declaration is nillable, instances can use the xsi:nil attribute. The xsi:nil attribute is the boolean attribute, nil, from the http://www.w3.org/2001/XMLSchema-instance namespace. If an element instance has an xsi:nil attribute set to true, it can be left empty, even though its element declaration may have required content.

Notation A notation is used to identify the format of a piece of data. Values of elements and attributes that are of type, NOTATION, must come from the names of declared notations. See: http://www.w3.org/TR/xmlschema-1/#cNotation_Declarations.

Preserve Whitespace Policy Preserve whitespaces exactly as they appear in instances.

Prohibited Derivations (Applies to type definitions). Derivation methods that cannot be used to create sub-types from a given type definition.

Prohibited Substitutions (Applies to complex type definitions). Prevents sub-types that have been derived using the specified derivation methods from validating element instances in place of the given type definition.

Replace Whitespace Policy Replace tab, line feed, and carriage return characters with space character (Unicode character 32).

Sequence Model Group Child elements and model groups must be provided in the specified order in instances. See: http://www.w3.org/TR/xmlschema-1/#element-sequence.

Substitution Group Elements that are members of a substitution group can be used wherever the head element of the substitution group is referenced.

Substitution Group Exclusions (Applies to element declarations). Prohibits element declarations from nominating themselves as being able to substitute a given element declaration, if they have types that are derived from the original element's type using the specified derivation methods.

Target Namespace The target namespace identifies the namespace that components in this schema belongs to. If no target namespace is provided, then the schema components do not belong to any namespace.

Uniqueness Constraint Ensures uniqueness of an element/attribute value, or a combination of values, within a specified scope. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

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XML Schema Documentation

Table of Contents

Schema Document Properties

Declared Namespaces

Global Declarations

Element: asapratio_contribution

Element: asapratio_lc_heavypeak

Element: asapratio_lc_lightpeak

Element: asapratio_peptide_data

Element: asapratio_result

Element: asapratio_summary

Element: asapratio_timestamp

Element: database_refresh_timestamp

Element: interact_summary

Element: libra_result

Element: libra_summary

Element: msms_pipeline_analysis

Element: peptideprophet_result

Element: peptideprophet_summary

Element: xpressratio_result

Element: xpressratio_summary

Element: xpressratio_timestamp

Global Definitions

Complex Type: nameValueType

Simple Type: aa_symbolType

Simple Type: engineType

Simple Type: massType

Simple Type: model_dis_type

Simple Type: positiveInt

Simple Type: term_symbolType

Legend

Complex Type:

AusAddress

Glossary