Components of mzIdentML

class psims.mzid.components.AmbiguousResidue(code, params=None, context={}, **kwargs)

XSD Description

Ambiguous residues e.g. X can be specified by the Code attribute and a set of parameters for example giving the different masses that will be used in the search.

class psims.mzid.components.AnalysisData(identification_lists=(), protein_detection_lists=(), context={})

XSD Description

Data sets generated by the analyses, including peptide and protein lists.

class psims.mzid.components.AnalysisProtocolCollection(spectrum_identification_protocols=(), protein_detection_protocols=(), context={})

XSD Description

The collection of protocols which include the parameters and settings of the performed analyses.

class psims.mzid.components.AnalysisSampleCollection(samples=None, context={})

XSD Description

The samples analysed can optionally be recorded using CV terms for descriptions. If a composite sample has been analysed, the subsample association can be used to build a hierarchical description.

class psims.mzid.components.AnalysisSoftware(name, id=1, version=None, uri=None, contact='PERSON_DOC_OWNER', role='software vendor', customization=None, context={}, **kwargs)

XSD Description

The software used for performing the analyses.

class psims.mzid.components.AnalysisSoftwareList(analysis_software_list, context={})

XSD Description

The software packages used to perform the analyses.

class psims.mzid.components.AuditCollection(persons=None, organizations=None, context={})

XSD Description

The complete set of Contacts (people and organisations) for this file.

class psims.mzid.components.BibliographicReference(id, authors=None, doi=None, editor=None, issue=None, names=None, pages=None, publication=None, publisher=None, title=None, volume=None, year=None, context={})

XSD Description

Represents bibliographic references.

class psims.mzid.components.CVList(cv_list=None, context={})

XSD Description

Container for one or more controlled vocabulary definitions.

class psims.mzid.components.ComponentBase(*args, **kwargs)

class psims.mzid.components.ComponentDispatcher(*args, **kwargs)

class psims.mzid.components.DBSequence(accession: str, sequence: Optional[str] = None, id: Optional[Union[str, int]] = None, search_database_id: Optional[Union[str, int]] = 1, params: Optional[List[Union[str, collections.abc.Mapping, psims.xml.CVParam, psims.xml.UserParam]]] = None, name: Optional[str] = None, context={}, **kwargs)

XSD Description

A database sequence from the specified SearchDatabase (nucleic acid or amino acid). If the sequence is nucleic acid, the source nucleic acid sequence should be given in the seq attribute rather than a translated sequence.

class psims.mzid.components.DataCollection(inputs, analysis_data, context={})

XSD Description

The collection of input and output data sets of the analyses.

class psims.mzid.components.DatabaseTranslation(translation_tables, frames=None, context={})

XSD Description

A specification of how a nucleic acid sequence database was translated for searching.

class psims.mzid.components.Enzyme(name, missed_cleavages=1, id=None, semi_specific=False, site_regexp=None, min_distance=None, n_term_gain=None, c_term_gain=None, params=None, context={}, **kwargs)

XSD Description

The details of an individual cleavage enzyme should be provided by giving a regular expression or a CV term if a "standard" enzyme cleavage has been performed.

class psims.mzid.components.Enzymes(enzymes=None, independent=None, context={})

XSD Description

The list of enzymes used in experiment

class psims.mzid.components.Filter(filter_type, include=None, exclude=None, context={})

XSD Description

Filters applied to the search database. The filter must include at least one of Include and Exclude. If both are used, it is assumed that inclusion is performed first.

class psims.mzid.components.FragmentTolerance(low, high=None, unit='parts per million', context={})

class psims.mzid.components.FragmentationTable(measures=None, context={})

XSD Description

Contains the types of measures that will be reported in generic arrays for each SpectrumIdentificationItem e.g. product ion m/z, product ion intensity, product ion m/z error

class psims.mzid.components.GenericCollection(tag_name, members, context={})

class psims.mzid.components.IDGenericCollection(tag_name, members, id, context={})

class psims.mzid.components.Inputs(source_files=(), search_databases=(), spectra_data=(), context={})

XSD Description

The inputs to the analyses including the databases searched, the spectral data and the source file converted to mzIdentML.

class psims.mzid.components.IonType(series, indices, charge_state, measures=None, params=None, context={}, **kwargs)

XSD Description

IonType defines the index of fragmentation ions being reported, importing a CV term for the type of ion e.g. b ion. Example: if b3 b7 b8 and b10 have been identified, the index attribute will contain 3 7 8 10, and the corresponding values will be reported in parallel arrays below

class psims.mzid.components.MassTable(id, ms_level, residues=None, ambiguous_residues=None, name=None, params=None, context={}, **kwargs)

XSD Description

The masses of residues used in the search.

class psims.mzid.components.Measure(name=None, id=None, param=None, getter=None, context={})

XSD Description

References to CV terms defining the measures about product ions to be reported in SpectrumIdentificationItem

class psims.mzid.components.Modification(monoisotopic_mass_delta=None, location=None, name=None, accession=None, params=None, residues=None, value=None, avg_mass_delta=None, context={}, **kwargs)

XSD Description

A molecule modification specification. If n modifications have been found on a peptide, there should be n instances of Modification. If multiple modifications are provided as cvParams, it is assumed that the modification is ambiguous i.e. one modification or another. A cvParam must be provided with the identification of the modification sourced from a suitable CV e.g. UNIMOD. If the modification is not present in the CV (and this will be checked by the semantic validator within a given tolerance window), there is a “unknown modification” CV term that must be used instead. A neutral loss should be defined as an additional CVParam within Modification. If more complex information should be given about neutral losses (such as presence/absence on particular product ions), this can additionally be encoded within the FragmentationArray.

class psims.mzid.components.MzIdentML(**attrs)

XSD Description

The upper-most hierarchy level of mzIdentML with sub-containers for example describing software, protocols and search results (spectrum identifications or protein detection results).

class psims.mzid.components.Organization(name=None, id='ORG_DOC_OWNER', params=None, parent=None, context={}, **kwargs)

XSD Description

Organizations are entities like companies, universities, government agencies. Any additional information such as the address, email etc. should be supplied either as CV parameters or as user parameters.

class psims.mzid.components.ParentTolerance(low, high=None, unit='parts per million', context={})

class psims.mzid.components.Peptide(peptide_sequence, id, modifications=None, substitutions=None, params=None, name=None, context={}, **kwargs)

XSD Description

One (poly)peptide (a sequence with modifications). The combination of Peptide sequence and modifications must be unique in the file.

class psims.mzid.components.PeptideEvidence(peptide_id, db_sequence_id, id, start_position, end_position, is_decoy=False, pre=None, post=None, params=None, frame=None, translation_table_id=None, context={}, **kwargs)

XSD Description

PeptideEvidence links a specific Peptide element to a specific position in a DBSequence. There must only be one PeptideEvidence item per Peptide-to-DBSequence-position.

class psims.mzid.components.PeptideHypothesis(peptide_evidence_id, spectrum_identification_ids, params=None, context={}, **kwargs)

XSD Description

Peptide evidence on which this ProteinHypothesis is based by reference to a PeptideEvidence element.

class psims.mzid.components.Person(first_name=None, last_name=None, middle_initial=None, id='PERSON_DOC_OWNER', affiliations='ORG_DOC_OWNER', params=None, context={}, **kwargs)

XSD Description

A person's name and contact details. Any additional information such as the address, contact email etc. should be supplied using CV parameters or user parameters.

class psims.mzid.components.ProteinAmbiguityGroup(id, protein_detection_hypotheses, pass_threshold=True, params=None, context={}, **kwargs)

XSD Description

A set of logically related results from a protein detection, for example to represent conflicting assignments of peptides to proteins.

class psims.mzid.components.ProteinDetection(spectrum_identification_ids_used, protein_detection_list_id=1, protein_detection_protocol_id=1, id=1, activity_date=None, name=None, context={})

XSD Description

An Analysis which assembles a set of peptides (e.g. from a spectra search analysis) to proteins.

class psims.mzid.components.ProteinDetectionHypothesis(id, db_sequence_id, peptide_hypotheses, pass_threshold=True, leading=None, params=None, name=None, context={}, **kwargs)

XSD Description

A single result of the ProteinDetection analysis (i.e. a protein).

class psims.mzid.components.ProteinDetectionList(ambiguity_groups=None, count=<object object>, id=1, params=None, context={}, **kwargs)

XSD Description

The protein list resulting from a protein detection process.

class psims.mzid.components.ProteinDetectionProtocol(id=1, params=None, analysis_software_id=1, threshold=None, name=None, context={}, **kwargs)

XSD Description

The parameters and settings of a ProteinDetection process.

class psims.mzid.components.Provider(id='PROVIDER', role='researcher', analysis_software_id=None, contact='PERSON_DOC_OWNER', context={}, **kwargs)

XSD Description

The provider of the document in terms of the Contact and the software the produced the document instance.

class psims.mzid.components.Residue(mass, code, context={})

XSD Description

The single letter code for the residue.

class psims.mzid.components.Sample(id, name=None, contact=None, role=None, sub_samples=None, params=None, context={}, **kwargs)

XSD Description

Expansible description of the sample used to generate the dataset, named in sampleName.

class psims.mzid.components.SearchDatabase(name, file_format=None, location=None, id=None, external_format=None, num_database_sequences=None, num_residues=None, release_date=None, version=None, params=None, context={}, **kwargs)

XSD Description

A database for searching mass spectra. Examples include a set of amino acid sequence entries, nucleotide databases (e.g. 6 frame translated) or annotated spectra libraries.

class psims.mzid.components.SearchModification(mass_delta, fixed, residues, name=None, accession=None, value=None, specificity=None, params=None, context={}, **kwargs)

XSD Description

Specification of a search modification as parameter for a spectra search. Contains the name of the modification, the mass, the specificity and whether it is a static modification.

class psims.mzid.components.SequenceCollection(db_sequences, peptides, peptide_evidence, context={})

XSD Description

The collection of sequences (DBSequence or Peptide) identified and their relationship between each other (PeptideEvidence) to be referenced elsewhere in the results.

class psims.mzid.components.SourceFile(location, file_format=None, id=None, external_format=None, params=None, name=None, context={}, **kwargs)

XSD Description

Description of the source file, including location and type.

class psims.mzid.components.SpecificityRules(params=None, context={}, **kwargs)

XSD Description

The specificity rules of the searched modification including for example the probability of a modification's presence or peptide or protein termini. Standard fixed or variable status should be provided by the attribute fixedMod.

class psims.mzid.components.SpectraData(location, file_format=None, spectrum_id_format=None, id=None, external_format=None, params=None, name=None, context={}, **kwargs)

XSD Description

A data set containing spectra data (consisting of one or more spectra).

class psims.mzid.components.SpectrumIdentification(spectra_data_ids_used=None, search_database_ids_used=None, spectrum_identification_list_id=1, spectrum_identification_protocol_id=1, id=1, activity_date=None, name=None, context={})

XSD Description

An Analysis which tries to identify peptides in input spectra, referencing the database searched, the input spectra, the output results and the protocol that is run.

class psims.mzid.components.SpectrumIdentificationItem(experimental_mass_to_charge, charge_state, peptide_id, peptide_evidence_ids, id, score=None, ion_types=None, params=None, pass_threshold=True, rank=1, calculated_mass_to_charge=None, calculated_pi=None, name=None, mass_table_id=None, sample_id=None, context={}, **kwargs)

XSD Description

An identification of a single (poly)peptide, resulting from querying an input spectra, along with the set of confidence values for that identification. PeptideEvidence elements should be given for all mappings of the corresponding Peptide sequence within protein sequences.

class psims.mzid.components.SpectrumIdentificationList(identification_results, id, fragmentation_table=None, params=None, context={}, name=None, **kwargs)

XSD Description

Represents the set of all search results from SpectrumIdentification.

class psims.mzid.components.SpectrumIdentificationProtocol(search_type, analysis_software_id=1, id=1, additional_search_params=None, modification_params=None, enzymes=None, fragment_tolerance=None, parent_tolerance=None, threshold=None, filters=None, mass_tables=None, database_translation=None, name=None, context={})

XSD Description

The parameters and settings of a SpectrumIdentification analysis.

class psims.mzid.components.SpectrumIdentificationResult(spectra_data_id, spectrum_id, id=None, identifications=None, params=None, name=None, context={}, **kwargs)

XSD Description

All identifications made from searching one spectrum. For PMF data, all peptide identifications will be listed underneath as SpectrumIdentificationItems. For MS/MS data, there will be ranked SpectrumIdentificationItems corresponding to possible different peptide IDs.

class psims.mzid.components.SubstitutionModification(original_residue, replacement_residue, monoisotopic_mass_delta=None, location=None, context={})

XSD Description

A modification where one residue is substituted by another (amino acid change).

class psims.mzid.components.Threshold(params=None, context={}, **kwargs)

class psims.mzid.components.TranslationTable(id, name=None, params=None, context={}, **kwargs)

XSD Description

The table used to translate codons into nucleic acids e.g. by reference to the NCBI translation table.