MRMDecoy#

class pyopenms.MRMDecoy#

Bases: object

Cython implementation of _MRMDecoy

Original C++ documentation is available here: – Inherits from [‘ProgressLogger’]

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: MRMDecoy) → None

Methods

`__init__`	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

startProgress(self, begin: int, end: int, label: bytes | str | String) → None#