XML Schema Documentation

Schema Document Properties
Global Declarations
- Element: quantitation
Global Definitions

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Glossary

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Schema Document Properties

Target Namespace	http://www.matrixscience.com/xmlns/schema/quantitation_1
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.

Declared Namespaces

Prefix	Namespace
xml	http://www.w3.org/XML/1998/namespace
xs	http://www.w3.org/2001/XMLSchema
mqm	http://www.matrixscience.com/xmlns/schema/quantitation_1

Schema Component Representation

<xs:schema targetNamespace="http://www.matrixscience.com/xmlns/schema/quantitation_1" elementFormDefault="qualified" attributeFormDefault="unqualified">

...

</xs:schema>

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Global Declarations

Element: quantitation

Name	quantitation
Type	mqm:quantitationType
Nillable	no
Abstract	no
Documentation	Configuration file for Mascot quantitation methods

XML Instance Representation

<mqm:quantitation
majorVersion="1 [1] ?"
minorVersion=" mqm:minorVersion_t [1] ?">

<mqm:method> mqm:methodType

</mqm:method> [1..*] ?

</mqm:quantitation>

Schema Component Representation

<xs:element name="quantitation" type=" mqm:quantitationType ">

<xs:unique name="method_name_unique">

<xs:selector xpath="mqm:method"/>

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

</xs:unique>

</xs:element>

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Super-types:	compositionType < NeutralLossType (by extension)
Sub-types:	None

Name	NeutralLossType
Abstract	no
Documentation	Type created to simplify xml validation

Super-types:	compositionType < PepNeutralLossType (by extension)
Sub-types:	None

Name	PepNeutralLossType
Abstract	no
Documentation	Type created to simplify xml validation

Super-types:	parametersType < averageType (by extension)
Sub-types:	None

Name	averageType
Abstract	no
Documentation	Type created to simplify xml validation

Name	componentType
Abstract	no
Documentation	Data for individual peak

Name	compositionType
Abstract	no
Documentation	Unimod composition

Super-types:	xs:double < correctionType (by extension)
Sub-types:	None

Name	correctionType
Abstract	no
Documentation	Type created to simplify xml validation

Name	elementRefType
Abstract	no
Documentation	Type created to simplify xml validation

Super-types:	parametersType < integrationType (by extension)
Sub-types:	None

Name	integrationType
Abstract	no
Documentation	Type created to simplify xml validation

<...
method=" mqm:integrationMethodType [1] ?"
source=" mqm:scanType [0..1] ?"
mass_delta=" xs:double [0..1] ?"
mass_delta_unit=" mqm:massUnitType [0..1] ?"
elution_time_delta=" xs:double [0..1] ?"
elution_time_delta_unit=" mqm:timeUnitType [0..1] ?"
elution_profile_correlation_threshold=" xs:double [0..1] ?"
processing_options=" mqm:processing_optionsType [0..1] ?"
precursor_range=" mqm:precursorRangeType [0..1] ?">

<mqm:parameter> mqm:parameterType </mqm:parameter> [0..*] ?

</...>

Schema Component Representation

<xs:complexType name="integrationType">

<xs:complexContent>

<xs:extension base=" mqm:parametersType ">

<xs:attribute name="method" type=" mqm:integrationMethodType " use="required"/>

<xs:attribute name="source" type=" mqm:scanType " use="optional" default="survey"/>

<xs:attribute name="mass_delta" type=" xs:double " use="optional"/>

<xs:attribute name="mass_delta_unit" type=" mqm:massUnitType " use="optional" default="Da"/>

<xs:attribute name="elution_time_delta" type=" xs:double " use="optional"/>

<xs:attribute name="elution_time_delta_unit" type=" mqm:timeUnitType " use="optional" default="seconds"/>

<xs:attribute name="elution_profile_correlation_threshold" type=" xs:double " use="optional"/>

<xs:attribute name="processing_options" type=" mqm:processing_optionsType " use="optional"/>

<xs:attribute name="precursor_range" type=" mqm:precursorRangeType " use="optional" default="envelope"/>

</xs:extension>

</xs:complexContent>

</xs:complexType>

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Complex Type: isotopeType

Super-types:	None
Sub-types:	None

Name	isotopeType
Abstract	no
Documentation	Specifies which element should be substituted by which isotope. Empty element means "no substitutions".

XML Instance Representation

<...>

<mqm:old> mqm:elementType </mqm:old> [0..1] ?

<mqm:new> mqm:elementType </mqm:new> [0..1] ?

</...>

Schema Component Representation

<xs:complexType name="isotopeType">

<xs:sequence>

<xs:element name="old" type=" mqm:elementType " minOccurs="0"/>

<xs:element name="new" type=" mqm:elementType " minOccurs="0"/>

</xs:sequence>

</xs:complexType>

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Complex Type: local_definitionType

Super-types:	None
Sub-types:	None

Name	local_definitionType
Abstract	no
Documentation	Composition based modification definition

XML Instance Representation

<...
title=" xs:string [1] ?">

<mqm:specificity> mqm:specificityType </mqm:specificity> [1..*] ?

<mqm:delta> mqm:compositionType </mqm:delta> [1] ?

<mqm:Ignore> mqm:compositionType </mqm:Ignore> [0..*] ?

</...>

Schema Component Representation

<xs:complexType name="local_definitionType">

<xs:sequence>

<xs:element name="specificity" type=" mqm:specificityType " maxOccurs="unbounded"/>

<xs:element name="delta" type=" mqm:compositionType "/>

<xs:element name="Ignore" type=" mqm:compositionType " minOccurs="0" maxOccurs="unbounded"/>

</xs:sequence>

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

</xs:complexType>

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Complex Type: methodType

Super-types:	None
Sub-types:	None

Name	methodType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...
name=" mqm:methodNameType [1] ?"
constrain_search=" xs:boolean [0..1] ?"
protein_ratio_type=" mqm:calcType [0..1] ?"
report_detail=" xs:boolean [0..1] ?"
min_num_peptides=" xs:integer [0..1] ?"
prot_score_type=" mqm:proteinScoreType [0..1] ?"
sig_threshold_value=" mqm:sig_threshold_valueType [0..1] ?"
show_sub_sets=" xs:double [0..1] ?"
require_bold_red=" xs:boolean [0..1] ?"
description=" xs:string [0..1] ?">

<mqm:modifications> mqm:modification_groupType </mqm:modifications> [0..*] ?

<mqm:component> mqm:componentType </mqm:component> [0..*] ?

<mqm:report_ratio> mqm:ratioType </mqm:report_ratio> [0..*] ?

<mqm:exclusion> xs:string </mqm:exclusion> [0..*] ?

<mqm:seq> mqm:seqType </mqm:seq> [0..*] ?

<mqm:comp> mqm:compType </mqm:comp> [0..1] ?

<mqm:quality> mqm:qualityType </mqm:quality> [0..1] ?

<mqm:integration> mqm:integrationType </mqm:integration> [0..1] ?

<mqm:outliers> mqm:outliersType </mqm:outliers> [0..1] ?

<mqm:normalisation> mqm:normalisationType </mqm:normalisation> [0..1] ?

<mqm:protocol> mqm:protocolType </mqm:protocol> [1] ?

</...>

Schema Component Representation

<xs:complexType name="methodType">

<xs:sequence>

<xs:element name="modifications" type=" mqm:modification_groupType " minOccurs="0" maxOccurs="unbounded"/>

<xs:element name="component" type=" mqm:componentType " minOccurs="0" maxOccurs="unbounded"/>

<xs:element name="report_ratio" type=" mqm:ratioType " minOccurs="0" maxOccurs="unbounded"/>

<xs:element name="exclusion" type=" xs:string " minOccurs="0" maxOccurs="unbounded"/>

<xs:element name="seq" type=" mqm:seqType " minOccurs="0" maxOccurs="unbounded"/>

<xs:element name="comp" type=" mqm:compType " minOccurs="0"/>

<xs:element name="quality" type=" mqm:qualityType " minOccurs="0"/>

<xs:element name="integration" type=" mqm:integrationType " minOccurs="0"/>

<xs:element name="outliers" type=" mqm:outliersType " minOccurs="0"/>

<xs:element name="normalisation" type=" mqm:normalisationType " minOccurs="0"/>

<xs:element name="protocol" type=" mqm:protocolType "/>

</xs:sequence>

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

<xs:attribute name="constrain_search" type=" xs:boolean " use="optional" default="true"/>

<xs:attribute name="protein_ratio_type" type=" mqm:calcType " use="optional" default="average"/>

<xs:attribute name="report_detail" type=" xs:boolean " use="optional" default="true"/>

<xs:attribute name="min_num_peptides" type=" xs:integer " use="optional" default="2"/>

<xs:attribute name="prot_score_type" type=" mqm:proteinScoreType " use="optional"/>

<xs:attribute name="sig_threshold_value" type=" mqm:sig_threshold_valueType " use="optional"/>

<xs:attribute name="show_sub_sets" type=" xs:double " use="optional"/>

<xs:attribute name="require_bold_red" type=" xs:boolean " use="optional"/>

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

</xs:complexType>

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Complex Type: modification_groupType

Super-types:	None
Sub-types:	None

Name	modification_groupType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...
name=" xs:string [0..1] ?"
mode=" mqm:modeType [1] ?">

<mqm:mod_file> mqm:mod_fileType </mqm:mod_file> [0..*] ?

<mqm:unmodified> mqm:unmodifiedType </mqm:unmodified> [0..*] ?

<mqm:local_definition> mqm:local_definitionType </mqm:local_definition> [0..*] ?

</...>

Schema Component Representation

<xs:complexType name="modification_groupType">

<xs:sequence>

<xs:element name="mod_file" type=" mqm:mod_fileType " minOccurs="0" maxOccurs="unbounded"/>

<xs:element name="unmodified" type=" mqm:unmodifiedType " minOccurs="0" maxOccurs="unbounded"/>

<xs:element name="local_definition" type=" mqm:local_definitionType " minOccurs="0" maxOccurs="unbounded"/>

</xs:sequence>

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

<xs:attribute name="mode" type=" mqm:modeType " use="required"/>

</xs:complexType>

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Complex Type: moverzType

Super-types:	None
Sub-types:	None

Name	moverzType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...
monoisotopic=" mqm:massType [1] ?"
average=" mqm:massType [1] ?"/>

Schema Component Representation

<xs:complexType name="moverzType">

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

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

</xs:complexType>

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Complex Type: multiplexType

Super-types:	parametersType < multiplexType (by extension)
Sub-types:	None

Name	multiplexType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...
exclude_internal_label=" xs:boolean [0..1] ?"
ion_intensity_threshold=" xs:double [0..1] ?"
exclude_isobaric_fragments=" xs:boolean [0..1] ?"
min_ion_pairs=" xs:integer [0..1] ?">

<mqm:parameter> mqm:parameterType </mqm:parameter> [0..*] ?

<mqm:ion_series> mqm:ionSeriesType </mqm:ion_series> [0..1] ?

</...>

Schema Component Representation

<xs:complexType name="multiplexType">

<xs:complexContent>

<xs:extension base=" mqm:parametersType ">

<xs:sequence>

<xs:element name="ion_series" type=" mqm:ionSeriesType " minOccurs="0"/>

</xs:sequence>

<xs:attribute name="exclude_internal_label" type=" xs:boolean " use="optional" default="true"/>

<xs:attribute name="ion_intensity_threshold" type=" xs:double " use="optional" default="0.1"/>

<xs:attribute name="exclude_isobaric_fragments" type=" xs:boolean " use="optional" default="true"/>

<xs:attribute name="min_ion_pairs" type=" xs:integer " use="optional" default="4"/>

</xs:extension>

</xs:complexContent>

</xs:complexType>

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Complex Type: normalisationType

Super-types:	parametersType < normalisationType (by extension)
Sub-types:	None

Name	normalisationType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...
method=" mqm:normaliseType [1] ?">

<mqm:parameter> mqm:parameterType </mqm:parameter> [0..*] ?

</...>

Schema Component Representation

<xs:complexType name="normalisationType">

<xs:complexContent>

<xs:extension base=" mqm:parametersType ">

<xs:attribute name="method" type=" mqm:normaliseType " use="required"/>

</xs:extension>

</xs:complexContent>

</xs:complexType>

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Complex Type: numerator_denominatorType

Super-types:	xs:string < numerator_denominatorType (by extension)
Sub-types:	None

Name	numerator_denominatorType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...
name=" xs:string [1] ?"
coefficient=" xs:double [0..1] ?">
xs:string
</...>

Schema Component Representation

<xs:complexType name="numerator_denominatorType">

<xs:simpleContent>

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

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

<xs:attribute name="coefficient" type=" xs:double " use="optional" default="1.0"/>

</xs:extension>

</xs:simpleContent>

</xs:complexType>

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Complex Type: outliersType

Super-types:	parametersType < outliersType (by extension)
Sub-types:	None

Name	outliersType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...
method=" mqm:outlierType [1] ?">

<mqm:parameter> mqm:parameterType </mqm:parameter> [0..*] ?

</...>

Schema Component Representation

<xs:complexType name="outliersType">

<xs:complexContent>

<xs:extension base=" mqm:parametersType ">

<xs:attribute name="method" type=" mqm:outlierType " use="required"/>

</xs:extension>

</xs:complexContent>

</xs:complexType>

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Complex Type: parameterType

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

Name	parameterType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...
name=" mqm:parameterNameType [1] ?"
description=" xs:string [0..1] ?">
xs:anySimpleType
</...>

Schema Component Representation

<xs:complexType name="parameterType">

<xs:simpleContent>

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

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

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

</xs:extension>

</xs:simpleContent>

</xs:complexType>

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Complex Type: parametersType

Super-types:	None
Sub-types:	averageType (by extension) integrationType (by extension) multiplexType (by extension) normalisationType (by extension) outliersType (by extension) precursorType (by extension) qualityType (by extension) replicateType (by extension) reporterType (by extension)

Name	parametersType
Abstract	no
Documentation	Parameter name and value pair

XML Instance Representation

<...>

<mqm:parameter> mqm:parameterType </mqm:parameter> [0..*] ?

</...>

Schema Component Representation

<xs:complexType name="parametersType">

<xs:sequence>

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

</xs:sequence>

</xs:complexType>

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Complex Type: precursorType

Super-types:	parametersType < precursorType (by extension)
Sub-types:	None

Name	precursorType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...
allow_mass_time_match=" xs:boolean [1] ?"
allow_elution_shift=" xs:boolean [0..1] ?"
all_charge_states=" xs:boolean [0..1] ?">

<mqm:parameter> mqm:parameterType </mqm:parameter> [0..*] ?

</...>

Schema Component Representation

<xs:complexType name="precursorType">

<xs:complexContent>

<xs:extension base=" mqm:parametersType ">

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

<xs:attribute name="allow_elution_shift" type=" xs:boolean " use="optional" default="false"/>

<xs:attribute name="all_charge_states" type=" xs:boolean " use="optional" default="false"/>

</xs:extension>

</xs:complexContent>

</xs:complexType>

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Complex Type: protocolType

Super-types:	None
Sub-types:	None

Name	protocolType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...>
Start Choice [1]

<mqm:null> mqm:emptyType </mqm:null> [1] ?

<mqm:reporter> mqm:reporterType </mqm:reporter> [1] ?

<mqm:precursor> mqm:precursorType </mqm:precursor> [1] ?

<mqm:multiplex> mqm:multiplexType </mqm:multiplex> [1] ?

<mqm:replicate> mqm:replicateType </mqm:replicate> [1] ?

<mqm:average> mqm:averageType </mqm:average> [1] ?

End Choice
</...>

Schema Component Representation

<xs:complexType name="protocolType">

<xs:choice>

<xs:element name="null" type=" mqm:emptyType "/>

<xs:element name="reporter" type=" mqm:reporterType "/>

<xs:element name="precursor" type=" mqm:precursorType "/>

<xs:element name="multiplex" type=" mqm:multiplexType "/>

<xs:element name="replicate" type=" mqm:replicateType "/>

<xs:element name="average" type=" mqm:averageType "/>

</xs:choice>

</xs:complexType>

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Complex Type: qualityType

Super-types:	parametersType < qualityType (by extension)
Sub-types:	None

Name	qualityType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...
min_precursor_charge=" xs:integer [0..1] ?"
isolated_precursor=" xs:boolean [0..1] ?"
minimum_a1=" xs:double [0..1] ?"
pep_threshold_type=" mqm:thresholdType [0..1] ?"
pep_threshold_value=" xs:double [0..1] ?">

<mqm:parameter> mqm:parameterType </mqm:parameter> [0..*] ?

</...>

Schema Component Representation

<xs:complexType name="qualityType">

<xs:complexContent>

<xs:extension base=" mqm:parametersType ">

<xs:attribute name="min_precursor_charge" type=" xs:integer " use="optional" default="1"/>

<xs:attribute name="isolated_precursor" type=" xs:boolean " use="optional" default="false"/>

<xs:attribute name="minimum_a1" type=" xs:double " use="optional" default="0.0"/>

<xs:attribute name="pep_threshold_type" type=" mqm:thresholdType " use="optional" default="maximum expect"/>

<xs:attribute name="pep_threshold_value" type=" xs:double " use="optional" default="0.05"/>

</xs:extension>

</xs:complexContent>

</xs:complexType>

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Complex Type: quantitationType

Super-types:	None
Sub-types:	None

Name	quantitationType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...
majorVersion="1 [1] ?"
minorVersion=" mqm:minorVersion_t [1] ?">

<mqm:method> mqm:methodType

</mqm:method> [1..*] ?

</...>

Schema Component Representation

<xs:complexType name="quantitationType">

<xs:sequence>

<xs:element name="method" type=" mqm:methodType " maxOccurs="unbounded">

<xs:unique name="component_name_unique">

<xs:selector xpath="mqm:component"/>

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

</xs:unique>

<xs:key name="component_name_key">

<xs:selector xpath="mqm:component"/>

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

</xs:key>

<xs:unique name="report_ratio_name_unique">

<xs:selector xpath="mqm:report_ratio"/>

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

</xs:unique>

<xs:keyref name="report_ratio_numerator_constraint" refer=" mqm:component_name_key ">

<xs:selector xpath="mqm:report_ratio/mqm:numerator_component"/>

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

</xs:keyref>

<xs:keyref name="report_ratio_denominator_constraint" refer=" mqm:component_name_key ">

<xs:selector xpath="mqm:report_ratio/mqm:denominator_component"/>

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

</xs:keyref>

</xs:element>

</xs:sequence>

<xs:attribute name="majorVersion" type=" xs:unsignedShort " use="required" fixed="1"/>

<xs:attribute name="minorVersion" type=" mqm:minorVersion_t " use="required"/>

</xs:complexType>

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Complex Type: ratioType

Super-types:	None
Sub-types:	None

Name	ratioType
Abstract	no
Documentation	A ratio to be reported

XML Instance Representation

<...
name=" mqm:ratioNameType [1] ?">

<mqm:numerator_component> mqm:numerator_denominatorType </mqm:numerator_component> [1..*] ?

<mqm:denominator_component> mqm:numerator_denominatorType </mqm:denominator_component> [1..*] ?

</...>

Schema Component Representation

<xs:complexType name="ratioType">

<xs:sequence>

<xs:element name="numerator_component" type=" mqm:numerator_denominatorType " maxOccurs="unbounded"/>

<xs:element name="denominator_component" type=" mqm:numerator_denominatorType " maxOccurs="unbounded"/>

</xs:sequence>

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

</xs:complexType>

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Complex Type: replicateType

Super-types:	parametersType < replicateType (by extension)
Sub-types:	None

Name	replicateType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...>

<mqm:parameter> mqm:parameterType </mqm:parameter> [0..*] ?

</...>

Schema Component Representation

<xs:complexType name="replicateType">

<xs:complexContent>

<xs:extension base=" mqm:parametersType "/>

</xs:complexContent>

</xs:complexType>

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Complex Type: reporterType

Super-types:	parametersType < reporterType (by extension)
Sub-types:	None

Name	reporterType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...>

<mqm:parameter> mqm:parameterType </mqm:parameter> [0..*] ?

</...>

Schema Component Representation

<xs:complexType name="reporterType">

<xs:complexContent>

<xs:extension base=" mqm:parametersType "/>

</xs:complexContent>

</xs:complexType>

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Complex Type: specificityType

Super-types:	None
Sub-types:	None

Name	specificityType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...
site=" mqm:siteType [1] ?"
position=" mqm:positionType [1] ?">

<mqm:NeutralLoss> mqm:NeutralLossType </mqm:NeutralLoss> [0..*] ?

<mqm:PepNeutralLoss> mqm:PepNeutralLossType </mqm:PepNeutralLoss> [0..*] ?

</...>

Schema Component Representation

<xs:complexType name="specificityType">

<xs:sequence>

<xs:element name="NeutralLoss" type=" mqm:NeutralLossType " minOccurs="0" maxOccurs="unbounded"/>

<xs:element name="PepNeutralLoss" type=" mqm:PepNeutralLossType " minOccurs="0" maxOccurs="unbounded"/>

</xs:sequence>

<xs:attribute name="site" type=" mqm:siteType " use="required"/>

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

</xs:complexType>

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Complex Type: unmodifiedType

Super-types:	xs:string < unmodifiedType (by extension)
Sub-types:	None

Name	unmodifiedType
Abstract	no
Documentation	Type created to simplify xml validation

XML Instance Representation

<...
site=" mqm:siteType [1] ?"
position=" mqm:positionType [1] ?">
xs:string
</...>

Schema Component Representation

<xs:complexType name="unmodifiedType">

<xs:simpleContent>

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

<xs:attribute name="site" type=" mqm:siteType " use="required"/>

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

</xs:extension>

</xs:simpleContent>

</xs:complexType>

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Simple Type: calcType

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

Name

calcType

Content

Base XSD Type: string

value comes from list: {'median'|'average'|'weighted'}

Documentation

How to calculate ratio for protein

Schema Component Representation

<xs:simpleType name="calcType">

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

<xs:enumeration value="median"/>

<xs:enumeration value="average"/>

<xs:enumeration value="weighted"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: compType

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

Name

compType

Content

Base XSD Type: string

length >= 4

Documentation

Type created to simplify xml validation

Schema Component Representation

<xs:simpleType name="compType">

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

<xs:minLength value="4"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: componentNameType

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

Name

componentNameType

Content

Base XSD Type: string

length >= 1

Documentation

Type created to simplify xml validation

Schema Component Representation

<xs:simpleType name="componentNameType">

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

<xs:minLength value="1"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: correctionTypeType

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

Name

correctionTypeType

Content

Base XSD Type: string

value comes from list: {'AB certificate'|'averagine'|'impurity'}

Documentation

Isotope corrrection factor

Schema Component Representation

<xs:simpleType name="correctionTypeType">

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

<xs:enumeration value="AB certificate"/>

<xs:enumeration value="averagine"/>

<xs:enumeration value="impurity"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: elementType

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

Name

elementType

Content

Base XSD Type: string

length >= 0

Documentation

symbols for elements

Schema Component Representation

<xs:simpleType name="elementType">

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

<xs:minLength value="0"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: emptyType

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

Name

emptyType

Content

Base XSD Type: string

length <= 0

Documentation

Type created to simplify xml validation

Schema Component Representation

<xs:simpleType name="emptyType">

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

<xs:maxLength value="0"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: file_indexType

Super-types:	xs:integer < file_indexType (by restriction)
Sub-types:	None

Name

file_indexType

Content

Base XSD Type: integer

value >= 1

Documentation

Type created to simplify xml validation

Schema Component Representation

<xs:simpleType name="file_indexType">

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

<xs:minInclusive value="1"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: integrationMethodType

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

Name

integrationMethodType

Content

Base XSD Type: string

value comes from list: {'none'|'simpsons'|'gaussian'|'trapezium'|'emg'|'quadratic'|'quartic'}

Documentation

Integration method

Schema Component Representation

<xs:simpleType name="integrationMethodType">

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

<xs:enumeration value="none"/>

<xs:enumeration value="simpsons"/>

<xs:enumeration value="gaussian"/>

<xs:enumeration value="trapezium"/>

<xs:enumeration value="emg"/>

<xs:enumeration value="quadratic"/>

<xs:enumeration value="quartic"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: ionSeriesType

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

Name

ionSeriesType

Content

Base XSD Type: string

value comes from list: {'a'|'b'|'c'|'x'|'y'|'z'|'z+1'|'z+2'}

Documentation

symbols for sequence ion series

Schema Component Representation

<xs:simpleType name="ionSeriesType">

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

<xs:enumeration value="a"/>

<xs:enumeration value="b"/>

<xs:enumeration value="c"/>

<xs:enumeration value="x"/>

<xs:enumeration value="y"/>

<xs:enumeration value="z"/>

<xs:enumeration value="z+1"/>

<xs:enumeration value="z+2"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: massType

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

Name

massType

Content

Base XSD Type: double

value >= 0.0

Documentation

Type created to simplify xml validation

Schema Component Representation

<xs:simpleType name="massType">

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

<xs:minInclusive value="0.0"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: massUnitType

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

Name

massUnitType

Content

Base XSD Type: string

value comes from list: {'Da'|'mmu'|'%'|'ppm'}

Documentation

mass tolerance units

Schema Component Representation

<xs:simpleType name="massUnitType">

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

<xs:enumeration value="Da"/>

<xs:enumeration value="mmu"/>

<xs:enumeration value="%"/>

<xs:enumeration value="ppm"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: methodNameType

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

Name

methodNameType

Content

Base XSD Type: string

length >= 1

Documentation

Type created to simplify xml validation

Schema Component Representation

<xs:simpleType name="methodNameType">

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

<xs:minLength value="1"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: minorVersion_t

Super-types:	xs:unsignedShort < minorVersion_t (by restriction)
Sub-types:	None

Name

minorVersion_t

Content

Base XSD Type: unsignedShort

value <= 0

Documentation

Schema minor version number

Schema Component Representation

<xs:simpleType name="minorVersion_t">

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

<xs:maxInclusive value="0"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: mod_fileType

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

Name

mod_fileType

Content

Base XSD Type: string

length >= 1

Documentation

Type created to simplify xml validation

Schema Component Representation

<xs:simpleType name="mod_fileType">

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

<xs:minLength value="1"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: modeType

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

Name

modeType

Content

Base XSD Type: string

value comes from list: {'fixed'|'variable'|'exclusive'}

Documentation

Specificity for a group of modifications

Schema Component Representation

<xs:simpleType name="modeType">

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

<xs:enumeration value="fixed"/>

<xs:enumeration value="variable"/>

<xs:enumeration value="exclusive"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: modification_groupNameType

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

Name

modification_groupNameType

Content

Base XSD Type: string

length >= 1

Documentation

Type created to simplify xml validation

Schema Component Representation

<xs:simpleType name="modification_groupNameType">

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

<xs:minLength value="1"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: normaliseType

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

Name

normaliseType

Content

Base XSD Type: string

value comes from list: {'none'|'sum'|'average'|'median'}

Documentation

normalisation method

Schema Component Representation

<xs:simpleType name="normaliseType">

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

<xs:enumeration value="none"/>

<xs:enumeration value="sum"/>

<xs:enumeration value="average"/>

<xs:enumeration value="median"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: outlierType

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

Name

outlierType

Content

Base XSD Type: string

value comes from list: {'none'|'dixons'|'auto'|'grubbs'|'rosners'}

Documentation

method of detecting outliers

Schema Component Representation

<xs:simpleType name="outlierType">

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

<xs:enumeration value="none"/>

<xs:enumeration value="dixons"/>

<xs:enumeration value="auto"/>

<xs:enumeration value="grubbs"/>

<xs:enumeration value="rosners"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: parameterNameType

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

Name

parameterNameType

Content

Base XSD Type: string

length >= 1

Documentation

Type created to simplify xml validation

Schema Component Representation

<xs:simpleType name="parameterNameType">

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

<xs:minLength value="1"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: positionType

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

Name

positionType

Content

Base XSD Type: string

value comes from list: {'Anywhere'|'Any N-term'|'Any C-term'|'Protein N-term'|'Protein C-term'}

Documentation

Unimod position

Schema Component Representation

<xs:simpleType name="positionType">

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

<xs:enumeration value="Anywhere"/>

<xs:enumeration value="Any N-term"/>

<xs:enumeration value="Any C-term"/>

<xs:enumeration value="Protein N-term"/>

<xs:enumeration value="Protein C-term"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: precursorRangeType

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

Name

precursorRangeType

Content

Base XSD Type: string

value comes from list: {'envelope'|'monoisotopic 5%'|'monoisotopic 50%'}

Documentation

Integration mass range

Schema Component Representation

<xs:simpleType name="precursorRangeType">

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

<xs:enumeration value="envelope"/>

<xs:enumeration value="monoisotopic 5%"/>

<xs:enumeration value="monoisotopic 50%"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: processing_optionsType

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

Name

processing_optionsType

Content

Base XSD Type: string

length >= 5

Documentation

Type created to simplify xml validation

Schema Component Representation

<xs:simpleType name="processing_optionsType">

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

<xs:minLength value="5"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: proteinScoreType

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

Name

proteinScoreType

Content

Base XSD Type: string

value comes from list: {'standard'|'mudpit'}

Documentation

Mascot protein score method

Schema Component Representation

<xs:simpleType name="proteinScoreType">

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

<xs:enumeration value="standard"/>

<xs:enumeration value="mudpit"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: ratioNameType

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

Name

ratioNameType

Content

Base XSD Type: string

length >= 1

Documentation

Type created to simplify xml validation

Schema Component Representation

<xs:simpleType name="ratioNameType">

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

<xs:minLength value="1"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: scanType

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

Name

scanType

Content

Base XSD Type: string

value comes from list: {'survey'|'zoom'|'header'|'fragments'|'mrm'}

Documentation

Data source for integration

Schema Component Representation

<xs:simpleType name="scanType">

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

<xs:enumeration value="survey"/>

<xs:enumeration value="zoom"/>

<xs:enumeration value="header"/>

<xs:enumeration value="fragments"/>

<xs:enumeration value="mrm"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: seqType

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

Name

seqType

Content

Base XSD Type: string

length >= 2

Documentation

Type created to simplify xml validation

Schema Component Representation

<xs:simpleType name="seqType">

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

<xs:minLength value="2"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: sig_threshold_valueType

Super-types:	xs:double < sig_threshold_valueType (by restriction)
Sub-types:	None

Name

sig_threshold_valueType

Content

Base XSD Type: double

1E-18 <= value <= 1E-1

Documentation

Type created to simplify xml validation

Schema Component Representation

<xs:simpleType name="sig_threshold_valueType">

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

<xs:minInclusive value="1E-18"/>

<xs:maxInclusive value="1E-1"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: siteType

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

Name

siteType

Content

Base XSD Type: string

value comes from list: {'A'|'C'|'D'|'E'|'F'|'G'|'H'|'I'|'J'|'K'|'L'|'M'|'N'|'O'|'P'|'Q'|'R'|'S'|'T'|'U'|'V'|'W'|'Y'|'N-term'|'C-term'}

Documentation

Unimod site

Schema Component Representation

<xs:simpleType name="siteType">

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

<xs:enumeration value="A"/>

<xs:enumeration value="C"/>

<xs:enumeration value="D"/>

<xs:enumeration value="E"/>

<xs:enumeration value="F"/>

<xs:enumeration value="G"/>

<xs:enumeration value="H"/>

<xs:enumeration value="I"/>

<xs:enumeration value="J"/>

<xs:enumeration value="K"/>

<xs:enumeration value="L"/>

<xs:enumeration value="M"/>

<xs:enumeration value="N"/>

<xs:enumeration value="O"/>

<xs:enumeration value="P"/>

<xs:enumeration value="Q"/>

<xs:enumeration value="R"/>

<xs:enumeration value="S"/>

<xs:enumeration value="T"/>

<xs:enumeration value="U"/>

<xs:enumeration value="V"/>

<xs:enumeration value="W"/>

<xs:enumeration value="Y"/>

<xs:enumeration value="N-term"/>

<xs:enumeration value="C-term"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: thresholdType

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

Name

thresholdType

Content

Base XSD Type: string

value comes from list: {'minimum score'|'maximum expect'|'at least identity'|'at least homology'}

Documentation

Significance threshold for peptide matches

Schema Component Representation

<xs:simpleType name="thresholdType">

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

<xs:enumeration value="minimum score"/>

<xs:enumeration value="maximum expect"/>

<xs:enumeration value="at least identity"/>

<xs:enumeration value="at least homology"/>

</xs:restriction>

</xs:simpleType>

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Simple Type: timeUnitType

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

Name

timeUnitType

Content

Base XSD Type: string

value comes from list: {'seconds'|'minutes'|'%'|'ppm'}

Documentation

time unit units

Schema Component Representation

<xs:simpleType name="timeUnitType">

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

<xs:enumeration value="seconds"/>

<xs:enumeration value="minutes"/>

<xs:enumeration value="%"/>

<xs:enumeration value="ppm"/>

</xs:restriction>

</xs:simpleType>

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Legend

Complex Type:

Schema Component Type

AusAddress

Schema Component Name

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

If this schema component is a type definition, its type hierarchy is shown in a gray-bordered box.

Name	AusAddress
Abstract	no

The table above displays the properties of this schema component.

XML Instance Representation

<... country="Australia" >
<unitNo> string </unitNo> [0..1]
<houseNo> string </houseNo> [1]
<street> string </street> [1]
Start Choice [1]
<city> string </city> [1]
<town> string </town> [1]
End Choice
<state> AusStates </state> [1]
<postcode> string <<pattern = [1-9][0-9]{3}>> </postcode> [1] ?
</...>

The XML Instance Representation table above shows the schema component's content as an XML instance.

The minimum and maximum occurrence of elements and attributes are provided in square brackets, e.g. [0..1].
Model group information are shown in gray, e.g. Start Choice ... End Choice.
For type derivations, the elements and attributes that have been added to or changed from the base type's content are shown in bold.
If an element/attribute has a fixed value, the fixed value is shown in green, e.g. country="Australia".
Otherwise, the type of the element/attribute is displayed.
- If the element/attribute's type is in the schema, a link is provided to it.
- For local simple type definitions, the constraints are displayed in angle brackets, e.g. <<pattern = [1-9][0-9]{3}>>.
If a local element/attribute has documentation, it will be displayed in a window that pops up when the question mark inside the attribute or next to the element is clicked, e.g. <postcode>.

Schema Component Representation

The Schema Component Representation table above displays the underlying XML representation of the schema component. (Annotations are not shown.)

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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: quantitation

Global Definitions

Complex Type: NeutralLossType

Complex Type: PepNeutralLossType

Complex Type: averageType

Complex Type: componentType

Complex Type: compositionType

Complex Type: correctionType

Complex Type: elementRefType

Complex Type: integrationType

Complex Type: isotopeType

Complex Type: local_definitionType

Complex Type: methodType

Complex Type: modification_groupType

Complex Type: moverzType

Complex Type: multiplexType

Complex Type: normalisationType

Complex Type: numerator_denominatorType

Complex Type: outliersType

Complex Type: parameterType

Complex Type: parametersType

Complex Type: precursorType

Complex Type: protocolType

Complex Type: qualityType

Complex Type: quantitationType

Complex Type: ratioType

Complex Type: replicateType

Complex Type: reporterType

Complex Type: specificityType

Complex Type: unmodifiedType

Simple Type: calcType

Simple Type: compType

Simple Type: componentNameType

Simple Type: correctionTypeType

Simple Type: elementType

Simple Type: emptyType

Simple Type: file_indexType

Simple Type: integrationMethodType

Simple Type: ionSeriesType

Simple Type: massType

Simple Type: massUnitType

Simple Type: methodNameType

Simple Type: minorVersion_t

Simple Type: mod_fileType

Simple Type: modeType

Simple Type: modification_groupNameType

Simple Type: normaliseType

Simple Type: outlierType

Simple Type: parameterNameType

Simple Type: positionType

Simple Type: precursorRangeType

Simple Type: processing_optionsType

Simple Type: proteinScoreType

Simple Type: ratioNameType

Simple Type: scanType

Simple Type: seqType

Simple Type: sig_threshold_valueType

Simple Type: siteType

Simple Type: thresholdType

Simple Type: timeUnitType

Legend

Complex Type:

AusAddress

Glossary