MetaboTargetedAssay#

class pyopenms.MetaboTargetedAssay#

Bases: object

Cython implementation of _MetaboTargetedAssay

Original C++ documentation is available here

__init__()#

Overload:

__init__(self) None

This class provides methods for the extraction of targeted assays for metabolomics

Overload:

__init__(self, in_0: MetaboTargetedAssay) None

Methods

__init__

Overload:

extractMetaboTargetedAssay(self, spectra, ...)

Extract a vector of MetaboTargetedAssays without using fragment annotation

extractMetaboTargetedAssayFragmentAnnotation(...)

Extract a vector of MetaboTargetedAssays using fragment

pairCompoundWithAnnotatedTDSpectraPairs(...)

Pair compound information (SiriusMSFile) with the annotated target and decoy spectrum from SIRIUS/Passatutto based on the m_id (unique identifier composed of description_filepath_native_id_k introduced in the SiriusMSConverter)

extractMetaboTargetedAssay(self, spectra: MSExperiment, feature_ms2_index: FeatureMapping_FeatureToMs2Indices, precursor_rt_tol: float, precursor_mz_distance: float, cosine_sim_threshold: float, transition_threshold: float, min_fragment_mz: float, max_fragment_mz: float, method_consensus_spectrum: bool, exclude_ms2_precursor: bool, file_counter: int) List[MetaboTargetedAssay]#

Extract a vector of MetaboTargetedAssays without using fragment annotation

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

Returns:

Vector of MetaboTargetedAssay

extractMetaboTargetedAssayFragmentAnnotation(self, v_cmp_spec: List[MetaboTargetedAssay_CompoundTargetDecoyPair], transition_threshold: float, min_fragment_mz: float, max_fragment_mz: float, use_exact_mass: bool, exclude_ms2_precursor: bool) List[MetaboTargetedAssay]#

Extract a vector of MetaboTargetedAssays using fragment

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(self, v_cmpinfo: List[SiriusMSFile_CompoundInfo], annotated_spectra: List[SiriusFragmentAnnotation_SiriusTargetDecoySpectra]) List[MetaboTargetedAssay_CompoundTargetDecoyPair]#

Pair compound information (SiriusMSFile) with the annotated target and decoy spectrum from SIRIUS/Passatutto based on the m_id (unique identifier composed of description_filepath_native_id_k introduced in the SiriusMSConverter)

Parameters:
  • v_cmpinfo – Vector of SiriusMSFile::CompoundInfo

  • annotated_spectra – Vector of SiriusTargetDecoySpectra

Returns:

Vector of MetaboTargetedAssay::CompoundTargetDecoyPair