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

• file_counter – Count if multiple files are used

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, file_counter: int) → 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