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
Overload:
extractMetaboTargetedAssay
(self, spectra, ...)Extract a vector of MetaboTargetedAssays without using fragment annotation
Extract a vector of MetaboTargetedAssays using fragment
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