MetaboTargetedTargetDecoy

class pyopenms.MetaboTargetedTargetDecoy

Bases: object

Cython implementation of _MetaboTargetedTargetDecoy

Original C++ documentation is available here

__init__()

Overload:

__init__(self) → None

Resolve overlapping fragments and missing decoys for experimental specific decoy generation in targeted/pseudo targeted metabolomics

Overload:

__init__(self, in_0: MetaboTargetedTargetDecoy) → None

Methods

__init__

Overload:

constructTargetDecoyMassMapping(self, t_exp)

Constructs a mass mapping of targets and decoys using the unique m_id identifier

generateMissingDecoysByMassShift(self, ...)

Generate a decoy for targets where fragmentation tree re-rooting was not possible, by adding a specifiable mass to the target fragments

resolveOverlappingTargetDecoyMassesByIndividualMassShift(...)

Resolves overlapping target and decoy transition masses by adding a specifiable mass (e.g.
constructTargetDecoyMassMapping(self, t_exp: TargetedExperiment) → List[MetaboTargetedTargetDecoy_MetaboTargetDecoyMassMapping]

Constructs a mass mapping of targets and decoys using the unique m_id identifier

Parameters

t_exp – TransitionExperiment holds compound and transition information used for the mapping

generateMissingDecoysByMassShift(self, t_exp: TargetedExperiment, mappings: List[MetaboTargetedTargetDecoy_MetaboTargetDecoyMassMapping], mass_to_add: float) → None

Generate a decoy for targets where fragmentation tree re-rooting was not possible, by adding a specifiable mass to the target fragments

Parameters

  • t_exp – TransitionExperiment holds compound and transition information

  • mappings – Map of identifier to target and decoy masses

  • mass_to_add – The maximum number of transitions required per assay

resolveOverlappingTargetDecoyMassesByIndividualMassShift(self, t_exp: TargetedExperiment, mappings: List[MetaboTargetedTargetDecoy_MetaboTargetDecoyMassMapping], mass_to_add: float) → None

Resolves overlapping target and decoy transition masses by adding a specifiable mass (e.g. CH2) to the overlapping decoy fragment

Parameters

  • t_exp – TransitionExperiment holds compound and transition information

  • mappings – Map of identifier to target and decoy masses

  • mass_to_add – (e.g. CH2)