MRMDecoy#
- class pyopenms.MRMDecoy#
Bases:
object
Cython implementation of _MRMDecoy
- Original C++ documentation is available here
– Inherits from [‘ProgressLogger’]
Methods
Overload:
endProgress
(self)Ends the progress display
findFixedResidues
(self, sequence, keepN, ...)Find all residues in a sequence that should not be reversed / shuffled
generateDecoys
(self, exp, dec, method, ...)Generate decoys from a TargetedExperiment
getLogType
(self)Returns the type of progress log being used
nextProgress
(self)Increment progress by 1 (according to range begin-end)
setLogType
(self, in_0)Sets the progress log that should be used.
setProgress
(self, value)Sets the current progress
startProgress
(self, begin, end, label)- endProgress(self) None #
Ends the progress display
- findFixedResidues(self, sequence: bytes | str | String, keepN: bool, keepC: bool, keep_const_pattern: bytes | str | String) List[int] #
Find all residues in a sequence that should not be reversed / shuffled
- Parameters:
sequence – The amino acid sequence
keepN – Whether to keep N terminus constant
keepC – Whether to keep C terminus constant
keep_const_pattern – A string containing the AA to not change (e.g. ‘KRP’)
- generateDecoys(self, exp: TargetedExperiment, dec: TargetedExperiment, method: bytes | str | String, aim_decoy_fraction: float, switchKR: bool, decoy_tag: bytes | str | String, max_attempts: int, identity_threshold: float, precursor_mz_shift: float, product_mz_shift: 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 #
Generate decoys from a TargetedExperiment
Will generate decoy peptides for each target peptide provided in exp and write them into the decoy experiment
Valid methods: shuffle, reverse, pseudo-reverse
If theoretical is true, the target transitions will be returned but their masses will be adjusted to match the theoretical value of the fragment ion that is the most likely explanation for the product
mz_threshold is used for the matching of theoretical ion series to the observed one
To generate decoys with different precursor mass, use the “switchKR” flag which switches terminal K/R (switches K to R and R to K). This generates different precursor m/z and ensures that the y ion series has a different mass. For a description of the procedure, see (supplemental material)
Bruderer et al. Mol Cell Proteomics. 2017. 10.1074/mcp.RA117.000314.
- getLogType(self) int #
Returns the type of progress log being used
- nextProgress(self) None #
Increment progress by 1 (according to range begin-end)
- 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