/usr/share/openms-common/OpenMS/SCHEMAS/protXML_v6.xsd is in openms-common 1.11.1-5.
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<!-- edited with XMLSPY v2004 rel. 4 U (http://www.xmlspy.com) by Wei Yan (Institute for Systems Biology) -->
<!--W3C Schema generated by XMLSPY v2004 rel. 4 U (http://www.xmlspy.com)-->
<xs:schema targetNamespace="http://regis-web.systemsbiology.net/protXML" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns="http://regis-web.systemsbiology.net/protXML" xmlns:protx="http://regis-web.systemsbiology.net/protXML" elementFormDefault="qualified">
<xs:element name="ASAPRatio_pvalue">
<xs:annotation>
<xs:documentation>Results of ASAPRatio pvalue analysis (adjusting ASAPRatio ratios for offset of dataset, and determining whether ratios are significantly different from chance values originating from 1:1 proteins)</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:attribute name="adj_ratio_mean" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>Ratio adjusted for dataset mean value</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="adj_ratio_standard_dev" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>Error adjusted for dataset mean value</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="heavy2light_adj_ratio_mean" type="xs:double">
<xs:annotation>
<xs:documentation>Heavy2light ratio adjusted for dataset mean value</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="heavy2light_adj_ratio_standard_dev" type="xs:double">
<xs:annotation>
<xs:documentation>Heavy2light error adjusted for dataset mean value</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="pvalue" type="xs:double">
<xs:annotation>
<xs:documentation>pvalue (probability of ratio due by chance to 1:1 protein)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="decimal_pvalue" type="xs:double">
<xs:annotation>
<xs:documentation>decimal representation of pvalue</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="ASAPRatio">
<xs:annotation>
<xs:documentation>Results of ASAPRatio quantitation of protein</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element name="ASAP_Seq" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="ASAP_Peak" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="ASAP_Dta" maxOccurs="unbounded">
<xs:complexType>
<xs:attribute name="peptide_index" type="xs:string" use="required"/>
<xs:attribute name="include" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="status" type="xs:string" use="required"/>
<xs:attribute name="include" type="xs:string" use="required"/>
<xs:attribute name="datanum" type="xs:nonNegativeInteger" use="required"/>
<xs:attribute name="ratio_mean" type="xs:double" use="required"/>
<xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
<xs:attribute name="heavy2light_ratio_mean" type="xs:double" use="required"/>
<xs:attribute name="heavy2light_ratio_standard_dev" type="xs:double" use="required"/>
<xs:attribute name="weight" type="xs:double" use="required"/>
<xs:attribute name="peptide_binary_ind" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="status" type="xs:string" use="required"/>
<xs:attribute name="include" type="xs:string" use="required"/>
<xs:attribute name="datanum" type="xs:nonNegativeInteger" use="required"/>
<xs:attribute name="ratio_mean" type="xs:double" use="required"/>
<xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
<xs:attribute name="heavy2light_ratio_mean" type="xs:double" use="required"/>
<xs:attribute name="heavy2light_ratio_standard_dev" type="xs:double" use="required"/>
<xs:attribute name="weight" type="xs:double" use="required"/>
<xs:attribute name="light_sequence" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="ratio_mean" type="xs:double" use="required"/>
<xs:attribute name="ratio_standard_dev" type="xs:double" use="required"/>
<xs:attribute name="ratio_number_peptides" type="xs:nonNegativeInteger" use="required"/>
<xs:attribute name="heavy2light_ratio_mean" type="xs:double"/>
<xs:attribute name="heavy2light_ratio_standard_dev" type="xs:double"/>
<xs:attribute name="description" type="xs:string"/>
<xs:attribute name="status" type="xs:string"/>
<xs:attribute name="peptide_inds" type="xs:string"/>
</xs:complexType>
</xs:element>
<xs:element name="protein_summary">
<xs:complexType>
<xs:sequence>
<xs:element name="protein_summary_header">
<xs:complexType>
<xs:sequence>
<xs:element name="program_details">
<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 used to infer protein identifications</xs:documentation>
</xs:annotation>
</xs:any>
</xs:sequence>
<xs:attribute name="analysis" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>Name of analysis used for protein identifications</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="time" type="xs:dateTime" use="required">
<xs:annotation>
<xs:documentation>Time of analysis</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="version" type="xs:string"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="reference_database" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>full path database name</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="win-cyg_reference_database" type="xs:string">
<xs:annotation>
<xs:documentation>windows full path database</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="residue_substitution_list" type="xs:string">
<xs:annotation>
<xs:documentation>residues considered equivalent when comparing peptides</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="organism" type="xs:string">
<xs:annotation>
<xs:documentation>sample organism (used for annotation purposes)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="source_files" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>input pepXML files</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="source_files_alt" type="xs:string" use="required"/>
<xs:attribute name="win-cyg_source_files" type="xs:string">
<xs:annotation>
<xs:documentation>windows pepXML file names</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="source_file_xtn" type="xs:string">
<xs:annotation>
<xs:documentation>file type (if not pepXML)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="min_peptide_probability" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>minimum adjusted peptide probability contributing to protein probability</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="min_peptide_weight" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>minimum peptide weight contributing to protein probability</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="num_predicted_correct_prots" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>total number of predicted correct protein ids (sum of probabilities)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="num_input_1_spectra" type="xs:integer" use="required">
<xs:annotation>
<xs:documentation>number of spectra from 1+ precursor ions</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="num_input_2_spectra" type="xs:integer" use="required">
<xs:annotation>
<xs:documentation>number of spectra from 2+ precursor ions</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="num_input_3_spectra" type="xs:integer" use="required">
<xs:annotation>
<xs:documentation>number of spectra from 3+ precursor ions</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="num_input_4_spectra" type="xs:integer" use="required">
<xs:annotation>
<xs:documentation>number of spectra from 4+ precursor ions</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="num_input_5_spectra" type="xs:integer" use="required">
<xs:annotation>
<xs:documentation>number of spectra from 5+ precursor ions</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="initial_min_peptide_prob" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>minimum initial peptide probability to contribute to analysis</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="total_no_spectrum_ids" type="xs:double">
<xs:annotation>
<xs:documentation>total estimated number of correct peptide assignments in dataset</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="sample_enzyme" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>enzyme applied to sample prior to MS/MS</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="analysis_summary" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:any namespace="##any" processContents="lax" minOccurs="0">
<xs:annotation>
<xs:documentation>time of analysis</xs:documentation>
</xs:annotation>
</xs:any>
</xs:sequence>
<xs:attribute name="analysis" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>name of protein-level analysis</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="time" type="xs:dateTime" use="required">
<xs:annotation>
<xs:documentation>time of analysis</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="id" type="xs:nonNegativeInteger" use="required">
<xs:annotation>
<xs:documentation>unique id corresponding with analysis_result elements</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="dataset_derivation">
<xs:annotation>
<xs:documentation>Source and filtering criteria used to generate dataset</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence minOccurs="0" maxOccurs="unbounded">
<xs:element name="data_filter">
<xs:complexType>
<xs:attribute name="number" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>generation number (0 is root)</xs:documentation>
</xs:annotation>
</xs:attribute>
<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:string" use="required">
<xs:annotation>
<xs:documentation>number preceding filter generations</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="protein_group" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="protein" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<!-- note: nameValueType defined below -->
<xs:element name="parameter" 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 to be substituted with element storing analysis-specific result info</xs:documentation>
</xs:annotation>
</xs:any>
</xs:sequence>
<xs:attribute name="analysis" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>name of protein level analysis</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="id" type="xs:nonNegativeInteger" default="1">
<xs:annotation>
<xs:documentation>unique identifier to analysis_summary element</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="annotation" minOccurs="0">
<xs:complexType>
<xs:attribute name="protein_description" type="xs:string" use="required"/>
<xs:attribute name="ipi_name" type="xs:string"/>
<xs:attribute name="refseq_name" type="xs:string"/>
<xs:attribute name="swissprot_name" type="xs:string"/>
<xs:attribute name="ensembl_name" type="xs:string"/>
<xs:attribute name="trembl_name" type="xs:string"/>
<xs:attribute name="locus_link_name" type="xs:string"/>
<xs:attribute name="flybase" type="xs:string"/>
</xs:complexType>
</xs:element>
<xs:element name="indistinguishable_protein" minOccurs="0" maxOccurs="unbounded">
<xs:annotation>
<xs:documentation>other protein sharing corresponding peptides</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<!-- note: nameValueType defined below -->
<xs:element name="parameter" type="nameValueType" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="annotation" minOccurs="0">
<xs:annotation>
<xs:documentation>protein description</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:attribute name="protein_description" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>description</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="ipi_name" type="xs:string"/>
<xs:attribute name="refseq_name" type="xs:string"/>
<xs:attribute name="swissprot_name" type="xs:string"/>
<xs:attribute name="ensembl_name" type="xs:string"/>
<xs:attribute name="trembl_name" type="xs:string"/>
<xs:attribute name="locus_link_name" type="xs:string"/>
<xs:attribute name="flybase" type="xs:string"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="protein_name" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
<xs:element name="peptide" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="parameter" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<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>
</xs:element>
<xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:attribute name="position" type="xs:string" use="required"/>
<xs:attribute name="mass" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="mod_nterm_mass" type="xs:string"/>
<xs:attribute name="mod_cterm_mass" type="xs:string"/>
<xs:attribute name="modified_peptide" type="xs:string"/>
</xs:complexType>
</xs:element>
<xs:element name="peptide_parent_protein" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:attribute name="protein_name" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
<xs:element name="indistinguishable_peptide" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="modification_info" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="mod_aminoacid_mass" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:attribute name="position" type="xs:string" use="required"/>
<xs:attribute name="mass" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="mod_nterm_mass" type="xs:string"/>
<xs:attribute name="mod_cterm_mass" type="xs:string"/>
<xs:attribute name="modified_peptide" type="xs:string"/>
<xs:attribute name="calc_neutral_pep_mass" type="xs:double" use="optional" />
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="peptide_sequence" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="peptide_sequence" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>unmodified aa sequence</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="charge" type="xs:positiveInteger" use="required">
<xs:annotation>
<xs:documentation>precursor ion charge</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="initial_probability" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>prior to nsp adjustment</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="nsp_adjusted_probability" type="xs:double" use="optional">
<xs:annotation>
<xs:documentation>after nsp adjustment</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="ni_adjusted_probability" type="xs:double" use="optional">
<xs:annotation>
<xs:documentation>after ni adjustment</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="exp_sibling_ion_instances" type="xs:double" use="optional">
<xs:annotation>
<xs:documentation>expected sibling ion instances</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="exp_sibling_ion_bin" type="xs:double" use="optional">
<xs:annotation>
<xs:documentation>expected sibling ion bin</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="exp_tot_instances" type="xs:double" use="optional">
<xs:annotation>
<xs:documentation>expected total instances</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="peptide_group_designator" type="xs:string">
<xs:annotation>
<xs:documentation>link to spectra with other precursor ion charges assigned to same peptide</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="weight" type="xs:double" default="1.0"/>
<xs:attribute name="is_nondegenerate_evidence" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>confidence that peptide corresponds with this protein (rather than others in which it occurs)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="n_enzymatic_termini" type="xs:nonNegativeInteger" use="required">
<xs:annotation>
<xs:documentation>number of termini consistent with proteolytic cleavage</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="n_sibling_peptides" type="xs:double">
<xs:annotation>
<xs:documentation>estimated number of sibling peptides (other identified peptides corresponding to same protein)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="n_sibling_peptides_bin" type="xs:integer" default="0">
<xs:annotation>
<xs:documentation>discretized nsp value</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="n_instances" type="xs:integer" use="required">
<xs:annotation>
<xs:documentation>number of times peptide assigned to spectrum of precursor ion charge in dataset</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="calc_neutral_pep_mass" type="xs:double"/>
<xs:attribute name="is_contributing_evidence" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="protein_name" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>database protein name</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="probability" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>confidence of protein id</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="percent_coverage" type="xs:double">
<xs:annotation>
<xs:documentation>percent of protein sequence covered by corresponding peptides</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="n_indistinguishable_proteins" type="xs:integer" use="required">
<xs:annotation>
<xs:documentation>number of proteins with identical corresponding peptides</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="unique_stripped_peptides" type="xs:string"/>
<xs:attribute name="group_sibling_id" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>protein group id</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="total_number_peptides" type="xs:integer">
<xs:annotation>
<xs:documentation>total number of corresponding peptides that contributed to protein probability</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="subsuming_protein_entry" type="xs:string">
<xs:annotation>
<xs:documentation>name of portein containing all corresponding peptides, and more</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="pct_spectrum_ids" type="xs:string">
<xs:annotation>
<xs:documentation>fraction of correct dataset peptide identifications corresponding to protein</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
<xs:unique name="unique_result_analysis_id">
<xs:annotation>
<xs:documentation>can only have one analysis/id combination within each protein element</xs:documentation>
</xs:annotation>
<xs:selector xpath="./protx:analysis_result"/>
<xs:field xpath="@analysis"/>
<xs:field xpath="@id"/>
</xs:unique>
</xs:element>
</xs:sequence>
<xs:attribute name="group_number" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>index</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="pseudo_name" type="xs:string"/>
<xs:attribute name="probability" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>group probability (taking contributions from all group member proteins)</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
<xs:unique name="unique_group_sibling_id">
<xs:annotation>
<xs:documentation>Each group_sibling_id must be unique within a protein group</xs:documentation>
</xs:annotation>
<xs:selector xpath="./protx:protein"/>
<xs:field xpath="@group_sibling_id"/>
</xs:unique>
</xs:element>
</xs:sequence>
<xs:attribute name="summary_xml" type="xs:string"/>
</xs:complexType>
<xs:key name="summary_analysis_id">
<xs:selector xpath="./protx:analysis_summary"/>
<xs:field xpath="@analysis"/>
<xs:field xpath="@id"/>
</xs:key>
<xs:keyref name="result_analysis_id" refer="summary_analysis_id">
<xs:annotation>
<xs:documentation>analysis and id must correspond with those fields in an analysis_summary element</xs:documentation>
</xs:annotation>
<xs:selector xpath="./protx:protein_group/protx:protein/protx:analysis_result"/>
<xs:field xpath="@analysis"/>
<xs:field xpath="@id"/>
</xs:keyref>
<xs:unique name="unique_group_number">
<xs:annotation>
<xs:documentation>Requires group numbers be unique for entire dataset</xs:documentation>
</xs:annotation>
<xs:selector xpath="./protx:protein_group"/>
<xs:field xpath="@group_number"/>
</xs:unique>
</xs:element>
<xs:element name="proteinprophet_details">
<xs:annotation>
<xs:documentation>ProteinProphet analysis details</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element name="nsp_information">
<xs:annotation>
<xs:documentation>learned distributions of estimated number of sibling peptides</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element name="nsp_distribution" maxOccurs="unbounded">
<xs:annotation>
<xs:documentation>histogram slice of estimated number of sibling peptides</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:attribute name="bin_no" type="xs:integer" use="required">
<xs:annotation>
<xs:documentation>discretized bin number</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="nsp_lower_bound_incl" type="xs:double" use="optional">
<xs:annotation>
<xs:documentation>lower bound nsp value (inclusive)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="nsp_upper_bound_excl" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation>upper bound nsp value (exclusive)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="nsp_lower_bound_excl" type="xs:double" use="optional">
<xs:annotation>
<xs:documentation>lower bound nsp value (exclusive)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="nsp_upper_bound_incl" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation>upper bound nsp value (inclusive)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="pos_freq" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>fraction of correct peptides in bin</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="neg_freq" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>fraction of incorrect peptides in bin</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="pos_to_neg_ratio" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>fraction of correct / fraction of incorrect</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="alt_pos_to_neg_ratio" type="xs:double">
<xs:annotation>
<xs:documentation>pos_to_neg_ratio of preceding bin (if greater than that of current bin)</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="neighboring_bin_smoothing" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
<xs:element name="ni_information">
<xs:annotation>
<xs:documentation>learned distributions of estimated number of peptide instances ("number of instances")</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element name="ni_distribution" maxOccurs="unbounded">
<xs:annotation>
<xs:documentation>histogram slice of estimated number of sibling peptides</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:attribute name="bin_no" type="xs:integer" use="required">
<xs:annotation>
<xs:documentation>discretized bin number</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="ni_lower_bound_incl" type="xs:double" use="optional">
<xs:annotation>
<xs:documentation>lower bound nsp value (inclusive)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="ni_upper_bound_excl" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation>upper bound nsp value (exclusive)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="ni_lower_bound_excl" type="xs:double" use="optional">
<xs:annotation>
<xs:documentation>lower bound nsp value (exclusive)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="ni_upper_bound_incl" type="xs:string" use="optional">
<xs:annotation>
<xs:documentation>upper bound nsp value (inclusive)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="pos_freq" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>fraction of correct peptides in bin</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="neg_freq" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>fraction of incorrect peptides in bin</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="pos_to_neg_ratio" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>fraction of correct / fraction of incorrect</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="alt_pos_to_neg_ratio" type="xs:double">
<xs:annotation>
<xs:documentation>pos_to_neg_ratio of preceding bin (if greater than that of current bin)</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
</xs:sequence>
<!--
<xs:attribute name="neighboring_bin_smoothing" type="xs:string" use="required"/>
-->
</xs:complexType>
</xs:element>
<xs:element name="protein_summary_data_filter" maxOccurs="unbounded">
<xs:annotation>
<xs:documentation>predicted error/sensitivity for filtering at minimum probability</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:attribute name="min_probability" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>filter setting</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="sensitivity" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>predicted sensitivity (fraction of correct results passing filter)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="false_positive_error_rate" type="xs:double" use="required">
<xs:annotation>
<xs:documentation>predicted error rate (fraction of results passing filter than are incorrect)</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="predicted_num_correct" type="xs:double">
<xs:annotation>
<xs:documentation>predicted number of correct results passing filter</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="predicted_num_incorrect" type="xs:double">
<xs:annotation>
<xs:documentation>predicted number of incorrect results passing filter</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="occam_flag" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>whether or not occams razor was used to apportion peptides corresponding to multiple proteins</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="groups_flag" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>whether or not related proteins are organized together in common protein groups</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="degen_flag" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>whether or not all proteins corresponding to each identified peptide were used in analysis</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="nsp_flag" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>whether or not peptide probabilities were adjusted for estimated number of sibling peptides</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="initial_peptide_wt_iters" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>proteinprophet number of initial iterations to compute peptide weights</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="nsp_distribution_iters" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>proteinprophet number of interations used to compute nsp distributions</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="final_peptide_wt_iters" type="xs:string" use="required">
<xs:annotation>
<xs:documentation>proteinprophet number of final interations used to compute final peptide weights</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="run_options" type="xs:string">
<xs:annotation>
<xs:documentation>special run options</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="XPress_analysis_summary">
<xs:complexType>
<xs:attribute name="min_peptide_probability" type="xs:double" use="required"/>
<xs:attribute name="min_peptide_weight" type="xs:double" use="required"/>
<xs:attribute name="min_protein_probability" type="xs:double" use="required"/>
<xs:attribute name="reference_isotope" type="xs:string"/>
</xs:complexType>
</xs:element>
<xs:element name="ASAP_prot_analysis_summary">
<xs:complexType>
<xs:attribute name="version" type="xs:string"/>
<xs:attribute name="binary_ref_files" type="xs:string"/>
<xs:attribute name="min_peptide_probability" type="xs:double" use="required"/>
<xs:attribute name="min_peptide_weight" type="xs:double" use="required"/>
<xs:attribute name="min_protein_probability" type="xs:double" use="required"/>
<xs:attribute name="reference_isotope" type="xs:string"/>
</xs:complexType>
</xs:element>
<xs:element name="ASAP_pvalue_analysis_summary">
<xs:complexType>
<xs:attribute name="asapratio_id" type="xs:nonNegativeInteger" default="1"/>
<xs:attribute name="background_ratio_mean" type="xs:double" use="required"/>
<xs:attribute name="background_ratio_stdev" type="xs:double" use="required"/>
<xs:attribute name="background_fitting_error" type="xs:double" use="required"/>
<xs:attribute name="analysis_distribution_file" type="xs:string" use="required"/>
<xs:attribute name="full_analysis_distr_file" type="xs:string"/>
<xs:attribute name="asap_prot_id" type="xs:nonNegativeInteger" default="1"/>
</xs:complexType>
</xs:element>
<xs:simpleType name="positiveInt">
<xs:restriction base="xs:unsignedInt">
<xs:minInclusive value="1"/>
</xs:restriction>
</xs:simpleType>
<xs:element name="libra_result">
<xs:complexType>
<xs:sequence>
<xs:element name="intensity" maxOccurs="unbounded">
<xs:complexType>
<xs:attribute name="mz" type="xs:float" use="required"/>
<xs:attribute name="ratio" type="xs:float" use="required"/>
<xs:attribute name="error" type="xs:float" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="number" type="xs:nonNegativeInteger" use="required"/>
</xs:complexType>
<xs:unique name="libra_result_channel_index">
<xs:selector xpath="."/>
<xs:field xpath="@channel"/>
</xs:unique>
</xs:element>
<xs:element name="libra_summary">
<xs:complexType>
<xs:sequence>
<xs:element name="fragment_masses" maxOccurs="unbounded">
<xs:complexType>
<xs:attribute name="channel" type="positiveInt" use="required"/>
<xs:attribute name="mz" type="xs:float" use="required"/>
</xs:complexType>
</xs:element>
<xs:element name="isotopic_contributions" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:element name="contributing_channel" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="affected_channel" maxOccurs="unbounded">
<xs:complexType>
<xs:attribute name="channel" type="positiveInt" use="required"/>
<xs:attribute name="correction" type="xs:float" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="channel" type="positiveInt" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="mass_tolerance" type="xs:float" use="required"/>
<xs:attribute name="centroiding_preference" type="xs:int" use="required"/>
<xs:attribute name="normalization" type="xs:int" use="required"/>
<xs:attribute name="output_type" type="xs:int" use="required"/>
<xs:attribute name="channel_code" type="xs:string"/>
<xs:attribute name="min_pep_prob" type="xs:float" use="required"/>
<xs:attribute name="min_pep_wt" type="xs:float" use="required"/>
<xs:attribute name="min_prot_prob" type="xs:float" use="required"/>
</xs:complexType>
<xs:key name="libra_channel_index">
<xs:selector xpath="./protx:fragment_masses"/>
<xs:field xpath="@channel"/>
</xs:key>
<xs:keyref name="libra_contr_channel_index_ref" refer="libra_channel_index">
<xs:selector xpath="./protx:isotopic_contributions/protx:contributing_channel"/>
<xs:field xpath="@channel"/>
</xs:keyref>
<xs:keyref name="libra_aff_channel_index_ref" refer="libra_channel_index">
<xs:selector xpath="./protx:isotopic_contributions/protx:contributing_channel/protx:affected_channel"/>
<xs:field xpath="@channel"/>
</xs:keyref>
</xs:element>
<!-- a loosely-defined, general-purpose type used in the "parameter" element, defined above -->
<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>
</xs:schema>
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