MetaboTargetedAssay

class pyopenms.MetaboTargetedAssay

Bases: object

Cython implementation of _MetaboTargetedAssay

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1MetaboTargetedAssay.html

__init__()

  • Cython signature: void MetaboTargetedAssay() This class provides methods for the extraction of targeted assays for metabolomics

  • Cython signature: void MetaboTargetedAssay(MetaboTargetedAssay &)

Methods

__init__

  • Cython signature: void MetaboTargetedAssay()

extractMetaboTargetedAssay

Cython signature: libcpp_vector[MetaboTargetedAssay] extractMetaboTargetedAssay(MSExperiment & spectra, FeatureMapping_FeatureToMs2Indices & feature_ms2_index, double & precursor_rt_tol, double & precursor_mz_distance, double & cosine_sim_threshold, double & transition_threshold, double & min_fragment_mz, double & max_fragment_mz, bool & method_consensus_spectrum, bool & exclude_ms2_precursor, unsigned int & file_counter)

extractMetaboTargetedAssayFragmentAnnotation

Cython signature: libcpp_vector[MetaboTargetedAssay] extractMetaboTargetedAssayFragmentAnnotation(libcpp_vector[MetaboTargetedAssay_CompoundTargetDecoyPair] & v_cmp_spec, double & transition_threshold, double & min_fragment_mz, double & max_fragment_mz, bool & use_exact_mass, bool & exclude_ms2_precursor, unsigned int & file_counter)

pairCompoundWithAnnotatedTDSpectraPairs

Cython signature: libcpp_vector[MetaboTargetedAssay_CompoundTargetDecoyPair] pairCompoundWithAnnotatedTDSpectraPairs(libcpp_vector[SiriusMSFile_CompoundInfo] & v_cmpinfo, libcpp_vector[SiriusFragmentAnnotation_SiriusTargetDecoySpectra] & annotated_spectra)
extractMetaboTargetedAssay()

Cython signature: libcpp_vector[MetaboTargetedAssay] extractMetaboTargetedAssay(MSExperiment & spectra, FeatureMapping_FeatureToMs2Indices & feature_ms2_index, double & precursor_rt_tol, double & precursor_mz_distance, double & cosine_sim_threshold, double & transition_threshold, double & min_fragment_mz, double & max_fragment_mz, bool & method_consensus_spectrum, bool & exclude_ms2_precursor, unsigned int & file_counter)

Parameters

  • spectra – Input of MSExperiment with spectra information

  • feature_ms2_spectra_map – FeatureMapping class with associated MS2 spectra

  • precursor_rt_tol – Retention time tolerance of the precursor

  • precursor_mz_distance – Max m/z distance of the precursor entries of two spectra to be merged

  • cosine_sim_threshold – Cosine similarty threshold for the usage of SpectraMerger

  • transition_threshold – Intensity threshold for MS2 peak used in MetaboTargetedAssay

  • min_fragment_mz – Minimum m/z a fragment ion has to have to be considered as a transition

  • max_fragment_mz – Maximum m/z a fragment ion has to have to be considered as a transition

  • method_consensus_spectrum – Boolean to use consensus spectrum method

  • exclude_ms2_precursor – Boolean to exclude MS2 precursor from MetaboTargetedAssay

  • file_counter – Count if multiple files are used

Returns

Vector of MetaboTargetedAssay

extractMetaboTargetedAssayFragmentAnnotation()

Cython signature: libcpp_vector[MetaboTargetedAssay] extractMetaboTargetedAssayFragmentAnnotation(libcpp_vector[MetaboTargetedAssay_CompoundTargetDecoyPair] & v_cmp_spec, double & transition_threshold, double & min_fragment_mz, double & max_fragment_mz, bool & use_exact_mass, bool & exclude_ms2_precursor, unsigned int & file_counter)

Parameters

  • v_cmp_spec – Vector of CompoundInfo with associated fragment annotated MSspectrum

  • transition_threshold – Intensity threshold for MS2 peak used in MetaboTargetedAssay

  • min_fragment_mz – Minimum m/z a fragment ion has to have to be considered as a transition

  • max_fragment_mz – Maximum m/z a fragment ion has to have to be considered as a transition

  • use_exact_mass – Boolean if exact mass should be used as peak mass for annotated fragments

  • exclude_ms2_precursor – Boolean to exclude MS2 precursor from MetaboTargetedAssay

  • file_counter – Count if multiple files are used.

Returns

Vector of MetaboTargetedAssay

pairCompoundWithAnnotatedTDSpectraPairs()

Cython signature: libcpp_vector[MetaboTargetedAssay_CompoundTargetDecoyPair] pairCompoundWithAnnotatedTDSpectraPairs(libcpp_vector[SiriusMSFile_CompoundInfo] & v_cmpinfo, libcpp_vector[SiriusFragmentAnnotation_SiriusTargetDecoySpectra] & annotated_spectra)

Parameters

  • v_cmpinfo – Vector of SiriusMSFile::CompoundInfo

  • annotated_spectra – Vector of SiriusTargetDecoySpectra

Returns

Vector of MetaboTargetedAssay::CompoundTargetDecoyPair