IDMapper

class pyopenms.IDMapper

Bases: object

Cython implementation of _IDMapper

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1IDMapper.html

– Inherits from [‘DefaultParamHandler’]

__init__()

• Cython signature: void IDMapper() Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications

• Cython signature: void IDMapper(IDMapper &)

Methods

__init__	Cython signature: void IDMapper()
annotate	Cython signature: void annotate(MSExperiment & map_, libcpp_vector[PeptideIdentification] & ids, libcpp_vector[ProteinIdentification] & protein_ids, bool clear_ids, bool mapMS1)
getDefaults	Cython signature: Param getDefaults() Returns the default parameters
getName	Cython signature: String getName() Returns the name
getParameters	Cython signature: Param getParameters() Returns the parameters
getSubsections	Cython signature: libcpp_vector[String] getSubsections()
mapPrecursorsToIdentifications	Cython signature: IDMapper_SpectraIdentificationState mapPrecursorsToIdentifications(MSExperiment spectra, libcpp_vector[PeptideIdentification] & ids, double mz_tol, double rt_tol)
setName	Cython signature: void setName(const String &) Sets the name
setParameters	Cython signature: void setParameters(Param & param) Sets the parameters

annotate()

• Cython signature: void annotate(MSExperiment & map_, libcpp_vector[PeptideIdentification] & ids, libcpp_vector[ProteinIdentification] & protein_ids, bool clear_ids, bool mapMS1)

The identifications stored in a PeptideIdentification instance can be added to the corresponding spectrum Note that a PeptideIdentication is added to ALL spectra which are within the allowed RT and MZ boundaries —– :param map: MSExperiment to receive the identifications :param peptide_ids: PeptideIdentification for the MSExperiment :param protein_ids: ProteinIdentification for the MSExperiment :param clear_ids: Reset peptide and protein identifications of each scan before annotating :param map_ms1: Attach Ids to MS1 spectra using RT mapping only (without precursor, without m/z) :raises:

Exception: MissingInformation is thrown if entries of ‘peptide_ids’ do not contain ‘MZ’ and ‘RT’ information

• Cython signature: void annotate(MSExperiment & map_, FeatureMap & fmap, bool clear_ids, bool mapMS1)

Add peptide identifications stored in a feature map to their corresponding spectrum This function converts the feature map to a vector of peptide identifications (all peptide IDs from each feature are taken) and calls the respective annotate() function RT and m/z are taken from the peptides, or (if missing) from the feature itself —– :param map: MSExperiment to receive the identifications :param fmap: FeatureMap with PeptideIdentifications for the MSExperiment :param clear_ids: Reset peptide and protein identifications of each scan before annotating :param map_ms1: Attach Ids to MS1 spectra using RT mapping only (without precursor, without m/z)

• Cython signature: void annotate(FeatureMap & map_, libcpp_vector[PeptideIdentification] & ids, libcpp_vector[ProteinIdentification] & protein_ids, bool use_centroid_rt, bool use_centroid_mz, MSExperiment & spectra)

Parameters

• map – MSExperiment to receive the identifications

• ids – PeptideIdentification for the MSExperiment

• protein_ids – ProteinIdentification for the MSExperiment

• use_centroid_rt – Whether to use the RT value of feature centroids even if convex hulls are present

• use_centroid_mz – Whether to use the m/z value of feature centroids even if convex hulls are present

• spectra – Whether precursors not contained in the identifications are annotated with an empty PeptideIdentification object containing the scan index

Raises

Exception: MissingInformation is thrown if entries of ‘ids’ do not contain ‘MZ’ and ‘RT’ information

• Cython signature: void annotate(ConsensusMap & map_, libcpp_vector[PeptideIdentification] & ids, libcpp_vector[ProteinIdentification] & protein_ids, bool measure_from_subelements, bool annotate_ids_with_subelements, MSExperiment & spectra)

Parameters

• map – MSExperiment to receive the identifications

• ids – PeptideIdentification for the MSExperiment

• protein_ids – ProteinIdentification for the MSExperiment

• measure_from_subelements – Boolean operator set to true if distance estimate from FeatureHandles instead of Centroid

• annotate_ids_with_subelements – Boolean operator set to true if store map index of FeatureHandle in peptide identification

• spectra – Whether precursors not contained in the identifications are annotated with an empty PeptideIdentification object containing the scan index

Raises

Exception: MissingInformation is thrown if entries of ‘ids’ do not contain ‘MZ’ and ‘RT’ information

getDefaults()

Cython signature: Param getDefaults() Returns the default parameters

getName()

Cython signature: String getName() Returns the name

getParameters()

Cython signature: Param getParameters() Returns the parameters

getSubsections()

Cython signature: libcpp_vector[String] getSubsections()

mapPrecursorsToIdentifications()

Cython signature: IDMapper_SpectraIdentificationState mapPrecursorsToIdentifications(MSExperiment spectra, libcpp_vector[PeptideIdentification] & ids, double mz_tol, double rt_tol)

Mapping of peptide identifications to spectra This helper function partitions all spectra into those that had: - no precursor (e.g. MS1 spectra), - at least one identified precursor, - or only unidentified precursor —– :param spectra: The mass spectra :param ids: The peptide identifications :param mz_tol: Tolerance used to map to precursor m/z :param rt_tol: Tolerance used to map to spectrum retention time :returns: A struct of vectors holding spectra indices of the partitioning

setName()

Cython signature: void setName(const String &) Sets the name

setParameters()

Cython signature: void setParameters(Param & param) Sets the parameters