schema location: | http://localhost/pepXML_v18.xsd |
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element form default: | qualified |
targetNamespace: | http://regis-web.systemsbiology.net/pepXML |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||
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children | asapratio_lc_lightpeak asapratio_lc_heavypeak | ||||||||||||||||||||||||||||||
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source | <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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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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source | <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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source | <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||
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children | asapratio_contribution | ||||||||||||||||||||||||||||||||||||
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source | <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||
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children | asapratio_peptide_data | ||||||||||||||||||||||||||||||
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annotation |
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source | <xs:element name="asapratio_result"> <xs:annotation> <xs:documentation>ASAPRatio quantitation results for search hit</xs:documentation> </xs:annotation> <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||||
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annotation |
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source | <xs:element name="asapratio_summary"> <xs:annotation> <xs:documentation>Quantitation</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Elution order of light vs heavy labeled peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="labeled_residues" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Aminoacids and termini that are differentially labeled for quantitaiton</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="area_flag" type="xs:nonNegativeInteger" use="required"/> <xs:attribute name="static_quant" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Y if dataset is all light or heavy labeled, N if dataset is mixed heavy and light labeled</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||
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source | <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:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||
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source | <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:annotation> <xs:documentation>minimum number of termini compaitble with enzyme used (should correspond with search enzyme constraint)</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||
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children | inputfile | ||||||||||||||||||||||
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annotation |
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source | <xs:element name="interact_summary"> <xs:annotation> <xs:documentation>Combined datasets</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="inputfile" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Input file</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="name" type="xs:string" use="required"/> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="filename" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Self reference</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="directory" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Directory of self</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||
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annotation |
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source | <xs:element name="inputfile" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Input file</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="name" type="xs:string" use="required"/> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||
properties |
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children | intensity | ||||||||||||||
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identity constraints |
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annotation |
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source | <xs:element name="libra_result"> <xs:annotation> <xs:documentation>libra quantitation for search hit</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="intensity" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>integrated mass intensity</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="channel" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>mass channel number</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="target_mass" type="xs:float" use="required"> <xs:annotation> <xs:documentation>mass of channel</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="absolute" type="xs:float" use="required"> <xs:annotation> <xs:documentation>absolute integrated intensity</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="normalized" type="xs:float" use="required"> <xs:annotation> <xs:documentation>normalized integrated intensity (normalization channel stored in libra_summary)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="reject" type="xs:boolean" use="optional" default="0"> <xs:annotation> <xs:documentation>whether or not to reject this ratio as valid</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="is_rejected" type="xs:boolean" use="optional" default="0"> <xs:annotation> <xs:documentation>whether or not to reject this ratio as valid</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> <xs:unique name="libra_result_channel_index"> <xs:annotation> <xs:documentation>channel number must be unique</xs:documentation> </xs:annotation> <xs:selector xpath="."/> <xs:field xpath="@channel"/> </xs:unique> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||
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source | <xs:element name="intensity" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>integrated mass intensity</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="channel" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>mass channel number</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="target_mass" type="xs:float" use="required"> <xs:annotation> <xs:documentation>mass of channel</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="absolute" type="xs:float" use="required"> <xs:annotation> <xs:documentation>absolute integrated intensity</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="normalized" type="xs:float" use="required"> <xs:annotation> <xs:documentation>normalized integrated intensity (normalization channel stored in libra_summary)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="reject" type="xs:boolean" use="optional" default="0"> <xs:annotation> <xs:documentation>whether or not to reject this ratio as valid</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||
properties |
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children | fragment_masses isotopic_contributions | ||||||||||||||||||||||||||||||||||||||||||
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identity constraints |
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annotation |
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source | <xs:element name="libra_summary"> <xs:annotation> <xs:documentation>summary info for libra quantitation analysis</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="fragment_masses" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>quantitation channel</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="channel" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>channel number</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mz" type="xs:float" use="required"> <xs:annotation> <xs:documentation>channel mass</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="offset" type="xs:float"> <xs:annotation> <xs:documentation>mass offset from mz value</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="isotopic_contributions" minOccurs="0"> <xs:annotation> <xs:documentation>isotopic contributions from one channel to others</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="contributing_channel" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>channel donor</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="affected_channel" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>channel recipient</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="channel" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>channel number</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="correction" type="xs:float" use="required"> <xs:annotation> <xs:documentation>fraction of affected channel due to contributing</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="channel" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>channel number</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> </xs:sequence> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="mass_tolerance" type="xs:float" use="required"> <xs:annotation> <xs:documentation>channel mass width</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="centroiding_preference" type="xs:int" use="required"/> <xs:attribute name="normalization" type="xs:int" use="required"> <xs:annotation> <xs:documentation>channel used as denominator for normalized integrated intensities (0 means use channel with strongest absolute integrated intensity)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="output_type" type="xs:int" use="required"/> <xs:attribute name="channel_code" type="xs:string"> <xs:annotation> <xs:documentation>concatenated channel masses (used as signature for defined channel masses)</xs:documentation> </xs:annotation> </xs:attribute> </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:annotation> <xs:documentation>contributing channel numbers must correspond with defined channels</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>contributing channel numbers must correspond with defined channels</xs:documentation> </xs:annotation> <xs:selector xpath="./pepx:isotopic_contributions/pepx:contributing_channel/pepx:affected_channel"/> <xs:field xpath="@channel"/> </xs:keyref> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||
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source | <xs:element name="fragment_masses" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>quantitation channel</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="channel" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>channel number</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mz" type="xs:float" use="required"> <xs:annotation> <xs:documentation>channel mass</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="offset" type="xs:float"> <xs:annotation> <xs:documentation>mass offset from mz value</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||
properties |
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children | contributing_channel | ||||
annotation |
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source | <xs:element name="isotopic_contributions" minOccurs="0"> <xs:annotation> <xs:documentation>isotopic contributions from one channel to others</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="contributing_channel" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>channel donor</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="affected_channel" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>channel recipient</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="channel" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>channel number</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="correction" type="xs:float" use="required"> <xs:annotation> <xs:documentation>fraction of affected channel due to contributing</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="channel" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>channel number</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> </xs:sequence> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||
properties |
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children | affected_channel | ||||||||||||||
attributes |
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annotation |
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source | <xs:element name="contributing_channel" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>channel donor</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="affected_channel" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>channel recipient</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="channel" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>channel number</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="correction" type="xs:float" use="required"> <xs:annotation> <xs:documentation>fraction of affected channel due to contributing</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="channel" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>channel number</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||
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annotation |
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source | <xs:element name="affected_channel" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>channel recipient</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="channel" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>channel number</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="correction" type="xs:float" use="required"> <xs:annotation> <xs:documentation>fraction of affected channel due to contributing</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||
properties |
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children | analysis_summary dataset_derivation msms_run_summary | ||||||||||||||||||||||||||||||
attributes |
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identity constraints |
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source | <xs:element name="msms_pipeline_analysis"> <xs:complexType> <xs:sequence> <xs:element name="analysis_summary" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Summary of analysis subjected to run(s)</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:any namespace="##any" processContents="lax" minOccurs="0"> <xs:annotation> <xs:documentation>Wildcard for summary info customized for a particular analysis</xs:documentation> </xs:annotation> </xs:any> </xs:sequence> <xs:attribute name="time" type="xs:dateTime" use="required"> <xs:annotation> <xs:documentation>Time analysis complete (unique id)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="analysis" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Name of analysis program</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="version" type="xs:string"> <xs:annotation> <xs:documentation>Release</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="dataset_derivation" minOccurs="0"> <xs:annotation> <xs:documentation>Source and filtering criteria used to generate dataset</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>File from which derived</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="windows_parent" type="xs:string"/> <xs:attribute name="description" type="xs:string" use="required"> <xs:annotation> <xs:documentation>filtering criteria applied to data</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="generation_no" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>number preceding filter generations</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="msms_run_summary" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Search results for LC/MS/MS run</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="sample_enzyme"> <xs:annotation> <xs:documentation>Defines the net cleavage specificity of an enzyme, chemical reagent, or a mixture of these, for mass spectrometry purposes</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="specificity" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Component cleavage specificity. Must be at least one specificity unless enzymeType:fidelity is nonspecific </xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="sense" use="required"> <xs:annotation> <xs:documentation>Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>minimum separation between adjacent cleavages</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="cut" use="required"> <xs:annotation> <xs:documentation>One or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Zero or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Controlled code name for the enzyme that can be referred to by applications</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Free text to describe alternative names, special conditions, etc.</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="fidelity" use="optional" default="specific"> <xs:annotation> <xs:documentation>Semispecific means that at least one end of a pepide must conform to the cleavage specificity, (unless the peptide was at the terminus of the parent sequence). Nonspecific means that neither end of a peptide must conform to the cleavage specificity.</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>If there are multiple specificities and independent is true, then a single peptide cannot exhibit one specificity at one terminus and a different specificity at the other. If independent is false, then a single peptide can exhibit mixed specificities.</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="search_summary" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Database search settings</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="search_database" minOccurs="0"> <xs:complexType> <xs:attribute name="local_path" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Full path address of database on local computer</xs:documentation> </xs:annotation> </xs:attribute> <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:annotation> <xs:documentation>Database type (AA=amino acid, NA=nucleic acid)</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Required peptide termini</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="enzyme" type="xs:string" use="required"/> <xs:attribute name="max_num_internal_cleavages" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Maximum number of enzyme cleavage sites allowable within peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="min_number_termini" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Minimum number of termini compatible with enzymatic cleavage</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="sequence_search_constraint" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Required amino acid string</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="sequence" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Required amino acid string</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="aminoacid_modification" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Modified aminoacid, static or variable</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="aminoacid" type="xs:string" use="required"/> <xs:attribute name="massdiff" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Mass difference with respect to unmodified aminoacid, must begin with either + (nonnegative) or - [e.g. +1.05446 or -2.3342]</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Mass of modified aminoacid</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="variable" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Y if both modified and unmodified aminoacid could be present in the dataset, N if only modified aminoacid can be present</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="peptide_terminus" type="xs:string"> <xs:annotation> <xs:documentation>whether modification can reside only at protein terminus (specified 'n', 'c', or 'nc')</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="symbol" type="aa_symbolType"> <xs:annotation> <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="binary" type="xs:string"> <xs:annotation> <xs:documentation>Y if each peptide must have only modified or unmodified aminoacid, N if a peptide may contain both modified and unmodified aminoacid</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="description" type="xs:string"/> </xs:complexType> </xs:element> <xs:element name="terminal_modification" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Modification to the N or C terminus, static or variable</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="terminus" type="xs:string" use="required"> <xs:annotation> <xs:documentation>n for N-terminus, c for C-terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="massdiff" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Mass difference with respect to unmodified terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Mass of modified terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="variable" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Y if both modified and unmodified terminus could be present in the dataset, N if only modified terminus can be present</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="symbol" type="term_symbolType"> <xs:annotation> <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="protein_terminus" type="xs:string" use="required"> <xs:annotation> <xs:documentation>whether modification can reside only at protein terminus (specified n or c)</xs:documentation> </xs:annotation> </xs:attribute> <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:annotation> <xs:documentation>Full path location of mzXML file for this search run (without the .mzXML extension)</xs:documentation> </xs:annotation> </xs:attribute> <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="precursor_mass_type" type="massType" use="required"> <xs:annotation> <xs:documentation>average or monoisotopic</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="fragment_mass_type" type="massType" use="required"> <xs:annotation> <xs:documentation>average or monoisotopic</xs:documentation> </xs:annotation> </xs:attribute> <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="search_id" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>matches id in search hit</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="analysis_timestamp" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Reference for analysis applied to current run (time corresponds with analysis_summary/@time, id corresponds with analysis_result/@id)</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:any namespace="##any" processContents="lax" minOccurs="0"> <xs:annotation> <xs:documentation>Wildcard for timestamp info customized for a particular analysis</xs:documentation> </xs:annotation> </xs:any> </xs:sequence> <xs:attribute name="time" type="xs:dateTime" use="required"> <xs:annotation> <xs:documentation>Date of analysis</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="analysis" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Analysis name</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="id" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>Unique identifier for each type of analysis</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="spectrum_query" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>MS/MS spectrum, precursor ion charge and mass</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Peptide assignment</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="alternative_protein" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Other protein in search database that contains peptide</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Positions and masses of modifications</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>modified aminoacid position in peptide [ranging from 1 to peptide length]</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:double" use="required"> <xs:annotation> <xs:documentation>modified mass of aminoacid</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="mod_nterm_mass" type="xs:double"> <xs:annotation> <xs:documentation>Mass of modified N terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mod_cterm_mass" type="xs:double"> <xs:annotation> <xs:documentation>Mass of modified C terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="modified_peptide" type="xs:string"> <xs:annotation> <xs:documentation>Peptide sequence (with indicated modifications)</xs:documentation> </xs:annotation> </xs:attribute> </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:annotation> <xs:documentation>Wildcard for result info customized for a particular analysis</xs:documentation> </xs:annotation> </xs:any> </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:annotation> <xs:documentation>Peptide aminoacid sequence (with no indicated modifications)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="peptide_prev_aa" type="xs:string"> <xs:annotation> <xs:documentation>Aminoacid preceding peptide (- if none)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="peptide_next_aa" type="xs:string"> <xs:annotation> <xs:documentation>Aminoacid following peptide (- if none)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="protein" type="xs:string" use="required"/> <xs:attribute name="num_tot_proteins" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>Number of unique proteins in search database containing peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_matched_ions" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide fragment ions found in spectrum</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="tot_num_ions" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide fragment ions predicted for peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="calc_neutral_pep_mass" type="xs:float" use="required"/> <xs:attribute name="massdiff" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Mass(precursor ion) - Mass(peptide)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide termini consistent with cleavage by sample enzyme</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_missed_cleavages" type="xs:integer"> <xs:annotation> <xs:documentation>Number of sample enzyme cleavage sites internal to peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="is_rejected" default="0"> <xs:annotation> <xs:documentation>Potential use in future for user manual validation (0 or 1)</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Extracted from search database</xs:documentation> </xs:annotation> </xs:attribute> <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:annotation> <xs:documentation>analysis and id must be unique within a search_hit</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Unique identifier to search summary</xs:documentation> </xs:annotation> </xs:attribute> </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:annotation> <xs:documentation>first scan number integrated into MS/MS spectrum</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="end_scan" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>last scan number integrated into MS/MS spectrum</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="precursor_neutral_mass" type="xs:float" use="required"/> <xs:attribute name="assumed_charge" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Precursor ion charge used for search</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="search_specification" type="xs:string"> <xs:annotation> <xs:documentation>Search constraint applied specifically to this query</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="index" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>Unique identifier</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> <xs:unique name="unique_search_id"> <xs:annotation> <xs:documentation>search_id must be unique within each msms_run_summary</xs:documentation> </xs:annotation> <xs:selector xpath="./pepx:search_result"/> <xs:field xpath="@search_id"/> </xs:unique> </xs:element> </xs:sequence> <xs:attribute name="base_name" type="xs:string" use="required"> <xs:annotation> <xs:documentation>full path file name of mzXML (minus the .mzXML)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="raw_data_type" type="xs:string" use="required"> <xs:annotation> <xs:documentation>raw data type extension (e.g. .mzXML)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="raw_data" type="xs:string" use="required"> <xs:annotation> <xs:documentation>raw data type extension (e.g. .mzXML)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="msManufacturer" type="xs:string"> <xs:annotation> <xs:documentation>Manufacturer of MS/MS instrument</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="msModel" type="xs:string"> <xs:annotation> <xs:documentation>Instrument model (cf mzXML)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="msIonization" type="xs:string"> <xs:annotation> <xs:documentation>Instrument model (cf mzXML)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="msMassAnalyzer" type="xs:string"> <xs:annotation> <xs:documentation>Ion trap, etc (cf mzXML)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="msDetector" type="xs:string"> <xs:annotation> <xs:documentation>EMT, etc(cf mzXML)</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> <xs:unique name="unique_timestamp_analysis_time"> <xs:annotation> <xs:documentation>analysis_timestamp analysis and time must be unique within each msms_run_summary</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>search_id within each search_hit must correspond with that of a search_summary</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>analysis and id in analysis_result must correspond with those in an analysis_timestamp element</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Summary name (currently not used)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="date" type="xs:dateTime" use="required"> <xs:annotation> <xs:documentation>Date pepXML file was written</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="summary_xml" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Full path self reference</xs:documentation> </xs:annotation> </xs:attribute> </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:annotation> <xs:documentation>time and analysis within timestamp must correspond with those within analysis_summary element</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>search_summary base_name (mzXML file) must be unique within document</xs:documentation> </xs:annotation> <xs:selector xpath="./pepx:msms_run_summary/pepx:search_summary"/> <xs:field xpath="@base_name"/> </xs:unique> <xs:unique name="unique_query_index"> <xs:annotation> <xs:documentation>spectrum_query index must be unique in document</xs:documentation> </xs:annotation> <xs:selector xpath="./pepx:msms_run_summary/pepx:spectrum_query"/> <xs:field xpath="@index"/> </xs:unique> </xs:element> |
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source | <xs:element name="analysis_summary" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Summary of analysis subjected to run(s)</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:any namespace="##any" processContents="lax" minOccurs="0"> <xs:annotation> <xs:documentation>Wildcard for summary info customized for a particular analysis</xs:documentation> </xs:annotation> </xs:any> </xs:sequence> <xs:attribute name="time" type="xs:dateTime" use="required"> <xs:annotation> <xs:documentation>Time analysis complete (unique id)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="analysis" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Name of analysis program</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="version" type="xs:string"> <xs:annotation> <xs:documentation>Release</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||
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source | <xs:element name="dataset_derivation" minOccurs="0"> <xs:annotation> <xs:documentation>Source and filtering criteria used to generate dataset</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>File from which derived</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="windows_parent" type="xs:string"/> <xs:attribute name="description" type="xs:string" use="required"> <xs:annotation> <xs:documentation>filtering criteria applied to data</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="generation_no" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>number preceding filter generations</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||
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source | <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:annotation> <xs:documentation>File from which derived</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="windows_parent" type="xs:string"/> <xs:attribute name="description" type="xs:string" use="required"> <xs:annotation> <xs:documentation>filtering criteria applied to data</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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children | sample_enzyme search_summary analysis_timestamp spectrum_query | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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source | <xs:element name="msms_run_summary" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Search results for LC/MS/MS run</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="sample_enzyme"> <xs:annotation> <xs:documentation>Defines the net cleavage specificity of an enzyme, chemical reagent, or a mixture of these, for mass spectrometry purposes</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="specificity" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Component cleavage specificity. Must be at least one specificity unless enzymeType:fidelity is nonspecific </xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="sense" use="required"> <xs:annotation> <xs:documentation>Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>minimum separation between adjacent cleavages</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="cut" use="required"> <xs:annotation> <xs:documentation>One or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Zero or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Controlled code name for the enzyme that can be referred to by applications</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Free text to describe alternative names, special conditions, etc.</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="fidelity" use="optional" default="specific"> <xs:annotation> <xs:documentation>Semispecific means that at least one end of a pepide must conform to the cleavage specificity, (unless the peptide was at the terminus of the parent sequence). Nonspecific means that neither end of a peptide must conform to the cleavage specificity.</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>If there are multiple specificities and independent is true, then a single peptide cannot exhibit one specificity at one terminus and a different specificity at the other. If independent is false, then a single peptide can exhibit mixed specificities.</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="search_summary" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Database search settings</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="search_database" minOccurs="0"> <xs:complexType> <xs:attribute name="local_path" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Full path address of database on local computer</xs:documentation> </xs:annotation> </xs:attribute> <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:annotation> <xs:documentation>Database type (AA=amino acid, NA=nucleic acid)</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Required peptide termini</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="enzyme" type="xs:string" use="required"/> <xs:attribute name="max_num_internal_cleavages" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Maximum number of enzyme cleavage sites allowable within peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="min_number_termini" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Minimum number of termini compatible with enzymatic cleavage</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="sequence_search_constraint" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Required amino acid string</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="sequence" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Required amino acid string</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="aminoacid_modification" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Modified aminoacid, static or variable</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="aminoacid" type="xs:string" use="required"/> <xs:attribute name="massdiff" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Mass difference with respect to unmodified aminoacid, must begin with either + (nonnegative) or - [e.g. +1.05446 or -2.3342]</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Mass of modified aminoacid</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="variable" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Y if both modified and unmodified aminoacid could be present in the dataset, N if only modified aminoacid can be present</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="peptide_terminus" type="xs:string"> <xs:annotation> <xs:documentation>whether modification can reside only at protein terminus (specified 'n', 'c', or 'nc')</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="symbol" type="aa_symbolType"> <xs:annotation> <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="binary" type="xs:string"> <xs:annotation> <xs:documentation>Y if each peptide must have only modified or unmodified aminoacid, N if a peptide may contain both modified and unmodified aminoacid</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="description" type="xs:string"/> </xs:complexType> </xs:element> <xs:element name="terminal_modification" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Modification to the N or C terminus, static or variable</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="terminus" type="xs:string" use="required"> <xs:annotation> <xs:documentation>n for N-terminus, c for C-terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="massdiff" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Mass difference with respect to unmodified terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Mass of modified terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="variable" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Y if both modified and unmodified terminus could be present in the dataset, N if only modified terminus can be present</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="symbol" type="term_symbolType"> <xs:annotation> <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="protein_terminus" type="xs:string" use="required"> <xs:annotation> <xs:documentation>whether modification can reside only at protein terminus (specified n or c)</xs:documentation> </xs:annotation> </xs:attribute> <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:annotation> <xs:documentation>Full path location of mzXML file for this search run (without the .mzXML extension)</xs:documentation> </xs:annotation> </xs:attribute> <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="precursor_mass_type" type="massType" use="required"> <xs:annotation> <xs:documentation>average or monoisotopic</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="fragment_mass_type" type="massType" use="required"> <xs:annotation> <xs:documentation>average or monoisotopic</xs:documentation> </xs:annotation> </xs:attribute> <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="search_id" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>matches id in search hit</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="analysis_timestamp" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Reference for analysis applied to current run (time corresponds with analysis_summary/@time, id corresponds with analysis_result/@id)</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:any namespace="##any" processContents="lax" minOccurs="0"> <xs:annotation> <xs:documentation>Wildcard for timestamp info customized for a particular analysis</xs:documentation> </xs:annotation> </xs:any> </xs:sequence> <xs:attribute name="time" type="xs:dateTime" use="required"> <xs:annotation> <xs:documentation>Date of analysis</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="analysis" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Analysis name</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="id" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>Unique identifier for each type of analysis</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="spectrum_query" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>MS/MS spectrum, precursor ion charge and mass</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Peptide assignment</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="alternative_protein" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Other protein in search database that contains peptide</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Positions and masses of modifications</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>modified aminoacid position in peptide [ranging from 1 to peptide length]</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:double" use="required"> <xs:annotation> <xs:documentation>modified mass of aminoacid</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="mod_nterm_mass" type="xs:double"> <xs:annotation> <xs:documentation>Mass of modified N terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mod_cterm_mass" type="xs:double"> <xs:annotation> <xs:documentation>Mass of modified C terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="modified_peptide" type="xs:string"> <xs:annotation> <xs:documentation>Peptide sequence (with indicated modifications)</xs:documentation> </xs:annotation> </xs:attribute> </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:annotation> <xs:documentation>Wildcard for result info customized for a particular analysis</xs:documentation> </xs:annotation> </xs:any> </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:annotation> <xs:documentation>Peptide aminoacid sequence (with no indicated modifications)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="peptide_prev_aa" type="xs:string"> <xs:annotation> <xs:documentation>Aminoacid preceding peptide (- if none)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="peptide_next_aa" type="xs:string"> <xs:annotation> <xs:documentation>Aminoacid following peptide (- if none)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="protein" type="xs:string" use="required"/> <xs:attribute name="num_tot_proteins" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>Number of unique proteins in search database containing peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_matched_ions" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide fragment ions found in spectrum</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="tot_num_ions" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide fragment ions predicted for peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="calc_neutral_pep_mass" type="xs:float" use="required"/> <xs:attribute name="massdiff" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Mass(precursor ion) - Mass(peptide)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide termini consistent with cleavage by sample enzyme</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_missed_cleavages" type="xs:integer"> <xs:annotation> <xs:documentation>Number of sample enzyme cleavage sites internal to peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="is_rejected" default="0"> <xs:annotation> <xs:documentation>Potential use in future for user manual validation (0 or 1)</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Extracted from search database</xs:documentation> </xs:annotation> </xs:attribute> <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:annotation> <xs:documentation>analysis and id must be unique within a search_hit</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Unique identifier to search summary</xs:documentation> </xs:annotation> </xs:attribute> </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:annotation> <xs:documentation>first scan number integrated into MS/MS spectrum</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="end_scan" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>last scan number integrated into MS/MS spectrum</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="precursor_neutral_mass" type="xs:float" use="required"/> <xs:attribute name="assumed_charge" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Precursor ion charge used for search</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="search_specification" type="xs:string"> <xs:annotation> <xs:documentation>Search constraint applied specifically to this query</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="index" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>Unique identifier</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> <xs:unique name="unique_search_id"> <xs:annotation> <xs:documentation>search_id must be unique within each msms_run_summary</xs:documentation> </xs:annotation> <xs:selector xpath="./pepx:search_result"/> <xs:field xpath="@search_id"/> </xs:unique> </xs:element> </xs:sequence> <xs:attribute name="base_name" type="xs:string" use="required"> <xs:annotation> <xs:documentation>full path file name of mzXML (minus the .mzXML)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="raw_data_type" type="xs:string" use="required"> <xs:annotation> <xs:documentation>raw data type extension (e.g. .mzXML)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="raw_data" type="xs:string" use="required"> <xs:annotation> <xs:documentation>raw data type extension (e.g. .mzXML)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="msManufacturer" type="xs:string"> <xs:annotation> <xs:documentation>Manufacturer of MS/MS instrument</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="msModel" type="xs:string"> <xs:annotation> <xs:documentation>Instrument model (cf mzXML)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="msIonization" type="xs:string"> <xs:annotation> <xs:documentation>Instrument model (cf mzXML)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="msMassAnalyzer" type="xs:string"> <xs:annotation> <xs:documentation>Ion trap, etc (cf mzXML)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="msDetector" type="xs:string"> <xs:annotation> <xs:documentation>EMT, etc(cf mzXML)</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> <xs:unique name="unique_timestamp_analysis_time"> <xs:annotation> <xs:documentation>analysis_timestamp analysis and time must be unique within each msms_run_summary</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>search_id within each search_hit must correspond with that of a search_summary</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>analysis and id in analysis_result must correspond with those in an analysis_timestamp element</xs:documentation> </xs:annotation> <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||
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children | specificity | ||||||||||||||||||||||||||||||||||||||
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source | <xs:element name="sample_enzyme"> <xs:annotation> <xs:documentation>Defines the net cleavage specificity of an enzyme, chemical reagent, or a mixture of these, for mass spectrometry purposes</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="specificity" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Component cleavage specificity. Must be at least one specificity unless enzymeType:fidelity is nonspecific </xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="sense" use="required"> <xs:annotation> <xs:documentation>Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>minimum separation between adjacent cleavages</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="cut" use="required"> <xs:annotation> <xs:documentation>One or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Zero or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Controlled code name for the enzyme that can be referred to by applications</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Free text to describe alternative names, special conditions, etc.</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="fidelity" use="optional" default="specific"> <xs:annotation> <xs:documentation>Semispecific means that at least one end of a pepide must conform to the cleavage specificity, (unless the peptide was at the terminus of the parent sequence). Nonspecific means that neither end of a peptide must conform to the cleavage specificity.</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>If there are multiple specificities and independent is true, then a single peptide cannot exhibit one specificity at one terminus and a different specificity at the other. If independent is false, then a single peptide can exhibit mixed specificities.</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||
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source | <xs:element name="specificity" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Component cleavage specificity. Must be at least one specificity unless enzymeType:fidelity is nonspecific </xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="sense" use="required"> <xs:annotation> <xs:documentation>Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>minimum separation between adjacent cleavages</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="cut" use="required"> <xs:annotation> <xs:documentation>One or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Zero or more 1-letter residue codes. Enzyme cleaves on the sense side of the residue(s) listed in cut unless one of the residues listed in no_cut is adjacent to the potential cleavage site</xs:documentation> </xs:annotation> <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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children | search_database enzymatic_search_constraint sequence_search_constraint aminoacid_modification terminal_modification parameter | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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source | <xs:element name="search_summary" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Database search settings</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="search_database" minOccurs="0"> <xs:complexType> <xs:attribute name="local_path" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Full path address of database on local computer</xs:documentation> </xs:annotation> </xs:attribute> <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:annotation> <xs:documentation>Database type (AA=amino acid, NA=nucleic acid)</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Required peptide termini</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="enzyme" type="xs:string" use="required"/> <xs:attribute name="max_num_internal_cleavages" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Maximum number of enzyme cleavage sites allowable within peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="min_number_termini" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Minimum number of termini compatible with enzymatic cleavage</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="sequence_search_constraint" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Required amino acid string</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="sequence" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Required amino acid string</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="aminoacid_modification" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Modified aminoacid, static or variable</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="aminoacid" type="xs:string" use="required"/> <xs:attribute name="massdiff" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Mass difference with respect to unmodified aminoacid, must begin with either + (nonnegative) or - [e.g. +1.05446 or -2.3342]</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Mass of modified aminoacid</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="variable" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Y if both modified and unmodified aminoacid could be present in the dataset, N if only modified aminoacid can be present</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="peptide_terminus" type="xs:string"> <xs:annotation> <xs:documentation>whether modification can reside only at protein terminus (specified 'n', 'c', or 'nc')</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="symbol" type="aa_symbolType"> <xs:annotation> <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="binary" type="xs:string"> <xs:annotation> <xs:documentation>Y if each peptide must have only modified or unmodified aminoacid, N if a peptide may contain both modified and unmodified aminoacid</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="description" type="xs:string"/> </xs:complexType> </xs:element> <xs:element name="terminal_modification" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Modification to the N or C terminus, static or variable</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="terminus" type="xs:string" use="required"> <xs:annotation> <xs:documentation>n for N-terminus, c for C-terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="massdiff" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Mass difference with respect to unmodified terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Mass of modified terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="variable" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Y if both modified and unmodified terminus could be present in the dataset, N if only modified terminus can be present</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="symbol" type="term_symbolType"> <xs:annotation> <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="protein_terminus" type="xs:string" use="required"> <xs:annotation> <xs:documentation>whether modification can reside only at protein terminus (specified n or c)</xs:documentation> </xs:annotation> </xs:attribute> <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:annotation> <xs:documentation>Full path location of mzXML file for this search run (without the .mzXML extension)</xs:documentation> </xs:annotation> </xs:attribute> <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="precursor_mass_type" type="massType" use="required"> <xs:annotation> <xs:documentation>average or monoisotopic</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="fragment_mass_type" type="massType" use="required"> <xs:annotation> <xs:documentation>average or monoisotopic</xs:documentation> </xs:annotation> </xs:attribute> <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="search_id" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>matches id in search hit</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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source | <xs:element name="search_database" minOccurs="0"> <xs:complexType> <xs:attribute name="local_path" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Full path address of database on local computer</xs:documentation> </xs:annotation> </xs:attribute> <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:annotation> <xs:documentation>Database type (AA=amino acid, NA=nucleic acid)</xs:documentation> </xs:annotation> <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||
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source | <xs:element name="enzymatic_search_constraint" minOccurs="0"> <xs:annotation> <xs:documentation>Required peptide termini</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="enzyme" type="xs:string" use="required"/> <xs:attribute name="max_num_internal_cleavages" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Maximum number of enzyme cleavage sites allowable within peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="min_number_termini" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Minimum number of termini compatible with enzymatic cleavage</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||
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source | <xs:element name="sequence_search_constraint" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Required amino acid string</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="sequence" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Required amino acid string</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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source | <xs:element name="aminoacid_modification" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Modified aminoacid, static or variable</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="aminoacid" type="xs:string" use="required"/> <xs:attribute name="massdiff" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Mass difference with respect to unmodified aminoacid, must begin with either + (nonnegative) or - [e.g. +1.05446 or -2.3342]</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Mass of modified aminoacid</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="variable" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Y if both modified and unmodified aminoacid could be present in the dataset, N if only modified aminoacid can be present</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="peptide_terminus" type="xs:string"> <xs:annotation> <xs:documentation>whether modification can reside only at protein terminus (specified 'n', 'c', or 'nc')</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="symbol" type="aa_symbolType"> <xs:annotation> <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="binary" type="xs:string"> <xs:annotation> <xs:documentation>Y if each peptide must have only modified or unmodified aminoacid, N if a peptide may contain both modified and unmodified aminoacid</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="description" type="xs:string"/> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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source | <xs:element name="terminal_modification" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Modification to the N or C terminus, static or variable</xs:documentation> </xs:annotation> <xs:complexType> <xs:attribute name="terminus" type="xs:string" use="required"> <xs:annotation> <xs:documentation>n for N-terminus, c for C-terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="massdiff" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Mass difference with respect to unmodified terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Mass of modified terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="variable" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Y if both modified and unmodified terminus could be present in the dataset, N if only modified terminus can be present</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="symbol" type="term_symbolType"> <xs:annotation> <xs:documentation>Special symbol used by search engine to designate this modification</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="protein_terminus" type="xs:string" use="required"> <xs:annotation> <xs:documentation>whether modification can reside only at protein terminus (specified n or c)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="description" type="xs:string"/> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||
type | nameValueType | ||||||||||||||||||||||||
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source | <xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||
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source | <xs:element name="analysis_timestamp" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Reference for analysis applied to current run (time corresponds with analysis_summary/@time, id corresponds with analysis_result/@id)</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:any namespace="##any" processContents="lax" minOccurs="0"> <xs:annotation> <xs:documentation>Wildcard for timestamp info customized for a particular analysis</xs:documentation> </xs:annotation> </xs:any> </xs:sequence> <xs:attribute name="time" type="xs:dateTime" use="required"> <xs:annotation> <xs:documentation>Date of analysis</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="analysis" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Analysis name</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="id" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>Unique identifier for each type of analysis</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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children | search_result | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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source | <xs:element name="spectrum_query" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>MS/MS spectrum, precursor ion charge and mass</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Peptide assignment</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="alternative_protein" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Other protein in search database that contains peptide</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Positions and masses of modifications</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>modified aminoacid position in peptide [ranging from 1 to peptide length]</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:double" use="required"> <xs:annotation> <xs:documentation>modified mass of aminoacid</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="mod_nterm_mass" type="xs:double"> <xs:annotation> <xs:documentation>Mass of modified N terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mod_cterm_mass" type="xs:double"> <xs:annotation> <xs:documentation>Mass of modified C terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="modified_peptide" type="xs:string"> <xs:annotation> <xs:documentation>Peptide sequence (with indicated modifications)</xs:documentation> </xs:annotation> </xs:attribute> </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:annotation> <xs:documentation>Wildcard for result info customized for a particular analysis</xs:documentation> </xs:annotation> </xs:any> </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:annotation> <xs:documentation>Peptide aminoacid sequence (with no indicated modifications)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="peptide_prev_aa" type="xs:string"> <xs:annotation> <xs:documentation>Aminoacid preceding peptide (- if none)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="peptide_next_aa" type="xs:string"> <xs:annotation> <xs:documentation>Aminoacid following peptide (- if none)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="protein" type="xs:string" use="required"/> <xs:attribute name="num_tot_proteins" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>Number of unique proteins in search database containing peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_matched_ions" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide fragment ions found in spectrum</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="tot_num_ions" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide fragment ions predicted for peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="calc_neutral_pep_mass" type="xs:float" use="required"/> <xs:attribute name="massdiff" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Mass(precursor ion) - Mass(peptide)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide termini consistent with cleavage by sample enzyme</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_missed_cleavages" type="xs:integer"> <xs:annotation> <xs:documentation>Number of sample enzyme cleavage sites internal to peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="is_rejected" default="0"> <xs:annotation> <xs:documentation>Potential use in future for user manual validation (0 or 1)</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Extracted from search database</xs:documentation> </xs:annotation> </xs:attribute> <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:annotation> <xs:documentation>analysis and id must be unique within a search_hit</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Unique identifier to search summary</xs:documentation> </xs:annotation> </xs:attribute> </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:annotation> <xs:documentation>first scan number integrated into MS/MS spectrum</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="end_scan" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>last scan number integrated into MS/MS spectrum</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="precursor_neutral_mass" type="xs:float" use="required"/> <xs:attribute name="assumed_charge" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Precursor ion charge used for search</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="search_specification" type="xs:string"> <xs:annotation> <xs:documentation>Search constraint applied specifically to this query</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="index" type="positiveInt" use="required"> <xs:annotation> <xs:documentation>Unique identifier</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> <xs:unique name="unique_search_id"> <xs:annotation> <xs:documentation>search_id must be unique within each msms_run_summary</xs:documentation> </xs:annotation> <xs:selector xpath="./pepx:search_result"/> <xs:field xpath="@search_id"/> </xs:unique> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||
properties |
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children | search_hit | ||||||||||||||
attributes |
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source | <xs:element name="search_result" minOccurs="0" maxOccurs="unbounded"> <xs:complexType> <xs:sequence> <xs:element name="search_hit" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Peptide assignment</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="alternative_protein" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Other protein in search database that contains peptide</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Positions and masses of modifications</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>modified aminoacid position in peptide [ranging from 1 to peptide length]</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:double" use="required"> <xs:annotation> <xs:documentation>modified mass of aminoacid</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="mod_nterm_mass" type="xs:double"> <xs:annotation> <xs:documentation>Mass of modified N terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mod_cterm_mass" type="xs:double"> <xs:annotation> <xs:documentation>Mass of modified C terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="modified_peptide" type="xs:string"> <xs:annotation> <xs:documentation>Peptide sequence (with indicated modifications)</xs:documentation> </xs:annotation> </xs:attribute> </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:annotation> <xs:documentation>Wildcard for result info customized for a particular analysis</xs:documentation> </xs:annotation> </xs:any> </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:annotation> <xs:documentation>Peptide aminoacid sequence (with no indicated modifications)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="peptide_prev_aa" type="xs:string"> <xs:annotation> <xs:documentation>Aminoacid preceding peptide (- if none)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="peptide_next_aa" type="xs:string"> <xs:annotation> <xs:documentation>Aminoacid following peptide (- if none)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="protein" type="xs:string" use="required"/> <xs:attribute name="num_tot_proteins" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>Number of unique proteins in search database containing peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_matched_ions" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide fragment ions found in spectrum</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="tot_num_ions" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide fragment ions predicted for peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="calc_neutral_pep_mass" type="xs:float" use="required"/> <xs:attribute name="massdiff" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Mass(precursor ion) - Mass(peptide)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide termini consistent with cleavage by sample enzyme</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_missed_cleavages" type="xs:integer"> <xs:annotation> <xs:documentation>Number of sample enzyme cleavage sites internal to peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="is_rejected" default="0"> <xs:annotation> <xs:documentation>Potential use in future for user manual validation (0 or 1)</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Extracted from search database</xs:documentation> </xs:annotation> </xs:attribute> <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:annotation> <xs:documentation>analysis and id must be unique within a search_hit</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Unique identifier to search summary</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
properties |
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children | alternative_protein modification_info search_score analysis_result parameter | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
attributes |
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identity constraints |
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annotation |
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source | <xs:element name="search_hit" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Peptide assignment</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="alternative_protein" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Other protein in search database that contains peptide</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Positions and masses of modifications</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>modified aminoacid position in peptide [ranging from 1 to peptide length]</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:double" use="required"> <xs:annotation> <xs:documentation>modified mass of aminoacid</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="mod_nterm_mass" type="xs:double"> <xs:annotation> <xs:documentation>Mass of modified N terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mod_cterm_mass" type="xs:double"> <xs:annotation> <xs:documentation>Mass of modified C terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="modified_peptide" type="xs:string"> <xs:annotation> <xs:documentation>Peptide sequence (with indicated modifications)</xs:documentation> </xs:annotation> </xs:attribute> </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:annotation> <xs:documentation>Wildcard for result info customized for a particular analysis</xs:documentation> </xs:annotation> </xs:any> </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:annotation> <xs:documentation>Peptide aminoacid sequence (with no indicated modifications)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="peptide_prev_aa" type="xs:string"> <xs:annotation> <xs:documentation>Aminoacid preceding peptide (- if none)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="peptide_next_aa" type="xs:string"> <xs:annotation> <xs:documentation>Aminoacid following peptide (- if none)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="protein" type="xs:string" use="required"/> <xs:attribute name="num_tot_proteins" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>Number of unique proteins in search database containing peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_matched_ions" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide fragment ions found in spectrum</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="tot_num_ions" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide fragment ions predicted for peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="calc_neutral_pep_mass" type="xs:float" use="required"/> <xs:attribute name="massdiff" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Mass(precursor ion) - Mass(peptide)</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_tol_term" type="xs:nonNegativeInteger"> <xs:annotation> <xs:documentation>Number of peptide termini consistent with cleavage by sample enzyme</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_missed_cleavages" type="xs:integer"> <xs:annotation> <xs:documentation>Number of sample enzyme cleavage sites internal to peptide</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="is_rejected" default="0"> <xs:annotation> <xs:documentation>Potential use in future for user manual validation (0 or 1)</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>Extracted from search database</xs:documentation> </xs:annotation> </xs:attribute> <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:annotation> <xs:documentation>analysis and id must be unique within a search_hit</xs:documentation> </xs:annotation> <xs:selector xpath="./pepx:analysis_result"/> <xs:field xpath="@analysis"/> <xs:field xpath="@id"/> </xs:unique> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||
properties |
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attributes |
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annotation |
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source | <xs:element name="alternative_protein" minOccurs="0" maxOccurs="unbounded"> <xs:annotation> <xs:documentation>Other protein in search database that contains peptide</xs:documentation> </xs:annotation> <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||
properties |
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children | mod_aminoacid_mass | ||||||||||||||||||||||||||||||
attributes |
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annotation |
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source | <xs:element name="modification_info" minOccurs="0"> <xs:annotation> <xs:documentation>Positions and masses of modifications</xs:documentation> </xs:annotation> <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:annotation> <xs:documentation>modified aminoacid position in peptide [ranging from 1 to peptide length]</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:double" use="required"> <xs:annotation> <xs:documentation>modified mass of aminoacid</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="mod_nterm_mass" type="xs:double"> <xs:annotation> <xs:documentation>Mass of modified N terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mod_cterm_mass" type="xs:double"> <xs:annotation> <xs:documentation>Mass of modified C terminus</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="modified_peptide" type="xs:string"> <xs:annotation> <xs:documentation>Peptide sequence (with indicated modifications)</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||
properties |
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attributes |
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source | <xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded"> <xs:complexType> <xs:attribute name="position" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>modified aminoacid position in peptide [ranging from 1 to peptide length]</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="mass" type="xs:double" use="required"> <xs:annotation> <xs:documentation>modified mass of aminoacid</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||
type | nameValueType | ||||||||||||||||||||||||
properties |
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attributes |
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source | <xs:element name="search_score" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||
properties |
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attributes |
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source | <xs:element name="analysis_result" minOccurs="0" maxOccurs="unbounded"> <xs:complexType> <xs:sequence> <xs:any namespace="##any" processContents="lax"> <xs:annotation> <xs:documentation>Wildcard for result info customized for a particular analysis</xs:documentation> </xs:annotation> </xs:any> </xs:sequence> <xs:attribute name="analysis" type="xs:string" use="required"/> <xs:attribute name="id" type="positiveInt" default="1"/> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||
type | nameValueType | ||||||||||||||||||||||||
properties |
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attributes |
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source | <xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||
properties |
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children | search_score_summary | ||||||||||||||||||||||||
attributes |
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annotation |
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source | <xs:element name="peptideprophet_result"> <xs:annotation> <xs:documentation>PeptideProphet validation results for search hit</xs:documentation> </xs:annotation> <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||
properties |
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children | parameter | ||||
source | <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||
type | nameValueType | ||||||||||||||||||||||||
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source | <xs:element name="parameter" type="nameValueType" minOccurs="2" maxOccurs="unbounded"/> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||
properties |
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children | inputfile roc_data_point error_point distribution_point mixture_model | ||||||||||||||||||||||||||||||||||||||||||
attributes |
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annotation |
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source | <xs:element name="peptideprophet_summary"> <xs:annotation> <xs:documentation>Summary information for PeptideProphet analysis</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element name="inputfile" maxOccurs="unbounded"> <xs:complexType> <xs:attribute name="name" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Input file</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> <xs:element name="roc_data_point" minOccurs="0" maxOccurs="unbounded"> <xs:complexType> <xs:attribute name="min_prob" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Filter threshold</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="sensitivity" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Predicted sensitivity</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="error" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Predicted false positive error rate</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_corr" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>Predicted number of correct results passing filter</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_incorr" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>Predicted number of incorrect results passing filter</xs:documentation> </xs:annotation> </xs:attribute> </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:annotation> <xs:documentation>Predicted false positive error rate</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="min_prob" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Filter threshold</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_corr" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>Predicted number of correct results passing filter</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_incorr" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>Predicted number of incorrect results passing filter</xs:documentation> </xs:annotation> </xs:attribute> </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:annotation> <xs:documentation>Discriminant Score (fval) bin</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="obs_1_distr" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Number of 1+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="model_1_pos_distr" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Inferred number of correct 1+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="model_1_neg_distr" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Inferred number of incorrect 1+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="obs_2_distr" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Number of 2+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="model_2_pos_distr" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Inferred number of correct 2+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="model_2_neg_distr" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Inferred number of incorrect 2+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="obs_3_distr" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Number of 3+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="model_3_pos_distr" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Inferred number of correct 3+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="model_3_neg_distr" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Inferred number of incorrect 3+ spectra</xs:documentation> </xs:annotation> </xs:attribute> </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:annotation> <xs:documentation>Fraction of results inferred to be correct</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="est_tot_correct" type="xs:float" use="required"/> <xs:attribute name="tot_num_spectra" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Number of input spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_iterations" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Number of EM interations prior to convergence</xs:documentation> </xs:annotation> </xs:attribute> </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="min_prob" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Min probability to be included in output</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="options" type="xs:string"> <xs:annotation> <xs:documentation>User specified run options</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="est_tot_num_correct" type="xs:float"> <xs:annotation> <xs:documentation>Total inferred number of correct results</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||
properties |
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attributes |
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source | <xs:element name="inputfile" maxOccurs="unbounded"> <xs:complexType> <xs:attribute name="name" type="xs:string" use="required"> <xs:annotation> <xs:documentation>Input file</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||
properties |
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attributes |
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source | <xs:element name="roc_data_point" minOccurs="0" maxOccurs="unbounded"> <xs:complexType> <xs:attribute name="min_prob" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Filter threshold</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="sensitivity" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Predicted sensitivity</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="error" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Predicted false positive error rate</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_corr" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>Predicted number of correct results passing filter</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_incorr" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>Predicted number of incorrect results passing filter</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||
properties |
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attributes |
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source | <xs:element name="error_point" minOccurs="0" maxOccurs="unbounded"> <xs:complexType> <xs:attribute name="error" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Predicted false positive error rate</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="min_prob" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Filter threshold</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_corr" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>Predicted number of correct results passing filter</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_incorr" type="xs:unsignedInt" use="required"> <xs:annotation> <xs:documentation>Predicted number of incorrect results passing filter</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
properties |
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attributes |
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source | <xs:element name="distribution_point" minOccurs="0" maxOccurs="unbounded"> <xs:complexType> <xs:attribute name="fvalue" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Discriminant Score (fval) bin</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="obs_1_distr" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Number of 1+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="model_1_pos_distr" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Inferred number of correct 1+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="model_1_neg_distr" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Inferred number of incorrect 1+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="obs_2_distr" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Number of 2+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="model_2_pos_distr" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Inferred number of correct 2+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="model_2_neg_distr" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Inferred number of incorrect 2+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="obs_3_distr" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Number of 3+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="model_3_pos_distr" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Inferred number of correct 3+ spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="model_3_neg_distr" type="xs:float" use="required"> <xs:annotation> <xs:documentation>Inferred number of incorrect 3+ spectra</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||||
properties |
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children | mixturemodel_distribution | ||||||||||||||||||||||||||||||||||||||||||||||||
attributes |
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source | <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:annotation> <xs:documentation>Fraction of results inferred to be correct</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="est_tot_correct" type="xs:float" use="required"/> <xs:attribute name="tot_num_spectra" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Number of input spectra</xs:documentation> </xs:annotation> </xs:attribute> <xs:attribute name="num_iterations" type="xs:nonNegativeInteger" use="required"> <xs:annotation> <xs:documentation>Number of EM interations prior to convergence</xs:documentation> </xs:annotation> </xs:attribute> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||
properties |
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children | posmodel_distribution negmodel_distribution | ||||||||||||
attributes |
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source | <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||
properties |
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children | parameter | ||||||||||||
attributes |
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source | <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||
type | nameValueType | ||||||||||||||||||||||||
properties |
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attributes |
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source | <xs:element name="parameter" type="nameValueType" maxOccurs="unbounded"/> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||
properties |
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children | parameter | ||||||||||||
attributes |
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source | <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||
type | nameValueType | ||||||||||||||||||||||||
properties |
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attributes |
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source | <xs:element name="parameter" type="nameValueType" maxOccurs="unbounded"/> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
properties |
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attributes |
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annotation |
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source | <xs:element name="xpressratio_result"> <xs:annotation> <xs:documentation>Quantitation</xs:documentation> </xs:annotation> <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||||||||||||
properties |
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attributes |
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annotation |
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source | <xs:element name="xpressratio_summary"> <xs:annotation> <xs:documentation>Quantitation</xs:documentation> </xs:annotation> <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> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||
properties |
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attributes |
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source | <xs:element name="xpressratio_timestamp"> <xs:complexType> <xs:attribute name="xpress_light" type="xs:integer" use="required"/> </xs:complexType> </xs:element> |
diagram | ![]() |
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namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||
type | extension of xs:anySimpleType | ||||||||||||||||||||||||
properties |
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used by | |||||||||||||||||||||||||
attributes |
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source | <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> |
namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||||||||||||||||||||||||||||||
type | restriction of xs:string | ||||||||||||||||||||||||||||||||||||||
used by |
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facets |
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source | <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> |
namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||
type | restriction of xs:string | ||||||||
used by |
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facets |
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source | <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> |
namespace | http://regis-web.systemsbiology.net/pepXML | ||||
type | restriction of xs:string | ||||
used by |
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||||
facets |
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||||
source | <xs:simpleType name="massType"> <xs:restriction base="xs:string"> <xs:enumeration value="monoisotopic"/> <xs:enumeration value="average"/> </xs:restriction> </xs:simpleType> |
namespace | http://regis-web.systemsbiology.net/pepXML | ||||||||||
type | restriction of xs:string | ||||||||||
used by |
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facets |
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source | <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> |
namespace | http://regis-web.systemsbiology.net/pepXML | ||
type | restriction of xs:unsignedInt | ||
used by | |||
facets |
|
||
source | <xs:simpleType name="positiveInt"> <xs:restriction base="xs:unsignedInt"> <xs:minInclusive value="1"/> </xs:restriction> </xs:simpleType> |
namespace | http://regis-web.systemsbiology.net/pepXML | ||||||
type | restriction of xs:string | ||||||
used by |
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||||||
facets |
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||||||
source | <xs:simpleType name="term_symbolType"> <xs:restriction base="xs:string"> <xs:enumeration value=","/> <xs:enumeration value=";"/> <xs:enumeration value=":"/> </xs:restriction> </xs:simpleType> |