MRMDecoy

class pyopenms.MRMDecoy

Bases: object

Cython implementation of _MRMDecoy

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1MRMDecoy.html

– Inherits from [‘ProgressLogger’]

__init__()

  • Cython signature: void MRMDecoy()

  • Cython signature: void MRMDecoy(MRMDecoy &)

Methods

__init__

  • Cython signature: void MRMDecoy()

endProgress

Cython signature: void endProgress() Ends the progress display

findFixedResidues

Cython signature: libcpp_vector[size_t] findFixedResidues(const String & sequence, bool keepN, bool keepC, const String & keep_const_pattern)

generateDecoys

Cython signature: void generateDecoys(TargetedExperiment & exp, TargetedExperiment & dec, String method, double aim_decoy_fraction, bool switchKR, String decoy_tag, int max_attempts, double identity_threshold, double precursor_mz_shift, double product_mz_shift, double product_mz_threshold, libcpp_vector[String] fragment_types, libcpp_vector[size_t] fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, int round_decPow)

getLogType

Cython signature: LogType getLogType() Returns the type of progress log being used

nextProgress

Cython signature: void nextProgress() Increment progress by 1 (according to range begin-end)

setLogType

Cython signature: void setLogType(LogType) Sets the progress log that should be used.

setProgress

Cython signature: void setProgress(ptrdiff_t value) Sets the current progress

startProgress

Cython signature: void startProgress(ptrdiff_t begin, ptrdiff_t end, String label)
endProgress()

Cython signature: void endProgress() Ends the progress display

findFixedResidues()

Cython signature: libcpp_vector[size_t] findFixedResidues(const String & sequence, bool keepN, bool keepC, const String & keep_const_pattern)

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()

Cython signature: void generateDecoys(TargetedExperiment & exp, TargetedExperiment & dec, String method, double aim_decoy_fraction, bool switchKR, String decoy_tag, int max_attempts, double identity_threshold, double precursor_mz_shift, double product_mz_shift, double product_mz_threshold, libcpp_vector[String] fragment_types, libcpp_vector[size_t] fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, int round_decPow)

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()

Cython signature: LogType getLogType() Returns the type of progress log being used

nextProgress()

Cython signature: void nextProgress() Increment progress by 1 (according to range begin-end)

setLogType()

Cython signature: void setLogType(LogType) Sets the progress log that should be used. The default type is NONE!

setProgress()

Cython signature: void setProgress(ptrdiff_t value) Sets the current progress

startProgress()

Cython signature: void startProgress(ptrdiff_t begin, ptrdiff_t end, String label)