MRMAssay#
- class pyopenms.MRMAssay#
Bases:
object
Cython implementation of _MRMAssay
- Original C++ documentation is available here
– Inherits from [‘ProgressLogger’]
Methods
Overload:
detectingTransitions
(self, exp, ...)Select detecting fragment ions
endProgress
(self)Ends the progress display
filterMinMaxTransitionsCompound
(self, exp, ...)Filters target and decoy transitions by intensity, only keeping the top N transitions
filterUnreferencedDecoysCompound
(self, exp)Filters decoy transitions, which do not have respective target transition based on the transitionID.
getLogType
(self)Returns the type of progress log being used
nextProgress
(self)Increment progress by 1 (according to range begin-end)
reannotateTransitions
(self, exp, ...)Annotates and filters transitions in a TargetedExperiment
restrictTransitions
(self, exp, ...)Restrict and filter transitions in a TargetedExperiment
setLogType
(self, in_0)Sets the progress log that should be used.
setProgress
(self, value)Sets the current progress
startProgress
(self, begin, end, label)uisTransitions
(self, exp, fragment_types, ...)Annotate UIS / site-specific transitions
- detectingTransitions(self, exp: TargetedExperiment, min_transitions: int, max_transitions: int) None #
Select detecting fragment ions
- Parameters:
exp – The input, unfiltered transitions
min_transitions – The minimum number of transitions required per assay
max_transitions – The maximum number of transitions required per assay
- endProgress(self) None #
Ends the progress display
- filterMinMaxTransitionsCompound(self, exp: TargetedExperiment, min_transitions: int, max_transitions: int) None #
Filters target and decoy transitions by intensity, only keeping the top N transitions
- Parameters:
exp – The transition list which will be filtered
min_transitions – The minimum number of transitions required per assay (targets only)
max_transitions – The maximum number of transitions allowed per assay
- filterUnreferencedDecoysCompound(self, exp: TargetedExperiment) None #
Filters decoy transitions, which do not have respective target transition based on the transitionID.
References between targets and decoys will be constructed based on the transitionsID and the “_decoy_” string. For example:
target: 84_CompoundName_[M+H]+_88_22 decoy: 84_CompoundName_decoy_[M+H]+_88_22
- Parameters:
exp – The transition list which will be filtered
- getLogType(self) int #
Returns the type of progress log being used
- nextProgress(self) None #
Increment progress by 1 (according to range begin-end)
- reannotateTransitions(self, exp: TargetedExperiment, precursor_mz_threshold: float, product_mz_threshold: float, fragment_types: List[bytes], fragment_charges: List[int], enable_specific_losses: bool, enable_unspecific_losses: bool, round_decPow: int) None #
Annotates and filters transitions in a TargetedExperiment
- Parameters:
exp – The input, unfiltered transitions
precursor_mz_threshold – The precursor m/z threshold in Th for annotation
product_mz_threshold – The product m/z threshold in Th for annotation
fragment_types – The fragment types to consider for annotation
fragment_charges – The fragment charges to consider for annotation
enable_specific_losses – Whether specific neutral losses should be considered
enable_unspecific_losses – Whether unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) should be considered
round_decPow – Round product m/z values to decimal power (default: -4)
- restrictTransitions(self, exp: TargetedExperiment, lower_mz_limit: float, upper_mz_limit: float, swathes: List[List[float, float]]) None #
Restrict and filter transitions in a TargetedExperiment
- Parameters:
exp – The input, unfiltered transitions
lower_mz_limit – The lower product m/z limit in Th
upper_mz_limit – The upper product m/z limit in Th
swathes – The swath window settings (to exclude fragment ions falling into the precursor isolation window)
- setLogType(self, in_0: int) None #
Sets the progress log that should be used. The default type is NONE!
- setProgress(self, value: int) None #
Sets the current progress
- uisTransitions(self, exp: TargetedExperiment, fragment_types: List[bytes], fragment_charges: List[int], enable_specific_losses: bool, enable_unspecific_losses: bool, enable_ms2_precursors: bool, mz_threshold: float, swathes: List[List[float, float]], round_decPow: int, max_num_alternative_localizations: int, shuffle_seed: int) None #
Annotate UIS / site-specific transitions
Performs the following actions:
Step 1: For each peptide, compute all theoretical alternative peptidoforms; see transitions generateTargetInSilicoMap_()
Step 2: Generate target identification transitions; see generateTargetAssays_()
Step 3a: Generate decoy sequences that share peptidoform properties with targets; see generateDecoySequences_()
Step 3b: Generate decoy in silico peptide map containing theoretical transition; see generateDecoyInSilicoMap_()
Step 4: Generate decoy identification transitions; see generateDecoyAssays_()
The IPF algorithm uses the concept of “identification transitions” that are used to discriminate different peptidoforms, these are generated in this function. In brief, the algorithm takes the existing set of peptides and transitions and then appends these “identification transitions” for targets and decoys. The novel transitions are set to be non-detecting and non-quantifying and are annotated with the set of peptidoforms to which they map.
- Parameters:
exp – The input, unfiltered transitions
fragment_types – The fragment types to consider for annotation
fragment_charges – The fragment charges to consider for annotation
enable_specific_losses – Whether specific neutral losses should be considered
enable_unspecific_losses – Whether unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) should be considered
enable_ms2_precursors – Whether MS2 precursors should be considered
mz_threshold – The product m/z threshold in Th for annotation
swathes – The swath window settings (to exclude fragment ions falling
round_decPow – Round product m/z values to decimal power (default: -4)
max_num_alternative_localizations – Maximum number of allowed peptide sequence permutations
shuffle_seed – Set seed for shuffle (-1: select seed based on time)
disable_decoy_transitions – Whether to disable generation of decoy UIS transitions