Generates decoys according to different models for a specific TraML

potential predecessor tools	$\longrightarrow$ OpenSwathDecoyGenerator $\longrightarrow$	potential successor tools
FileFilter	$\longrightarrow$ OpenSwathDecoyGenerator $\longrightarrow$	OpenSwathAnalyzer

This module generates "decoy" transitions from a set of real or "target" transitions. The idea is to use the decoy transitions in a statistical scoring process to estimate the false hits in an SRM / SWATH experiment.

There are multiple methods to create the decoy transitions, the simplest ones are reverse and pseudo-reverse which reverse the sequence either completely or leaving the last (tryptic) AA untouched respectively.

Another decoy generation method is "shuffle" which uses an algorithm similar to the one described in Lam, Henry, et al. (2010). "Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics". Journal of Proteome Research 9, 605-610. It shuffles the amino acid sequence (excluding N-/C-terminal and K/R/P) and shuffles the fragment ion intensities accordingly. If the new sequence does not reach a threshold of identity within a set number of trials, a random amino acid (not N-/C-terminal or modified) is "mutated" to a random other amino acid.

The command line parameters of this tool are:

OpenSwathDecoyGenerator -- Generates decoys according to different models for a specific TraML
Version: 2.3.0 Apr 18 2018, 18:59:40, Revision: 2cda6bd
To cite OpenMS:
  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

Usage:
  OpenSwathDecoyGenerator <options>

Options (mandatory options marked with '*'):
  -in <file>*        Input file (valid formats: 'tsv', 'mrm', 'pqp', 'TraML')
  -in_type <type>    Input file type -- default: determined from file extension or content
                     (valid: 'tsv', 'mrm', 'pqp', 'TraML')
  -out <file>*       Output file (valid formats: 'tsv', 'pqp', 'TraML')
  -out_type <type>   Output file type -- default: determined from file extension or content
                     (valid: 'tsv', 'pqp', 'TraML')
  -method <type>     Decoy generation method ('shuffle','pseudo-reverse','reverse','shift') (default: 'shuffl
                     e' valid: 'shuffle', 'pseudo-reverse', 'reverse', 'shift')
  -decoy_tag <type>  Decoy tag (default: 'DECOY_')
                     
Common TOPP options:
  -ini <file>        Use the given TOPP INI file
  -threads <n>       Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>  Writes the default configuration file
  --help             Shows options
  --helphelp         Shows all options (including advanced)

The algorithm parameters for the Analyzer filter are:

Legend:

required parameter

advanced parameter

+OpenSwathDecoyGeneratorGenerates decoys according to different models for a specific TraML

version2.3.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'OpenSwathDecoyGenerator'

in Input fileinput file*.tsv,*.mrm,*.pqp,*.TraML

in_type Input file type -- default: determined from file extension or content
tsv,mrm,pqp,TraML

out Output fileoutput file*.tsv,*.pqp,*.TraML

out_type Output file type -- default: determined from file extension or content
tsv,pqp,TraML

methodshuffle decoy generation method ('shuffle','pseudo-reverse','reverse','shift')shuffle,pseudo-reverse,reverse,shift

decoy_tagDECOY_ decoy tag

min_decoy_fraction0.8 Minimum fraction of decoy / target peptides and proteins

shuffle_max_attempts30 shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm

shuffle_sequence_identity_threshold0.5 shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm

shift_precursor_mz_shift0 shift: precursor ion MZ shift in Thomson for shift decoy method

shift_product_mz_shift20 shift: fragment ion MZ shift in Thomson for shift decoy method

product_mz_threshold0.025 MZ threshold in Thomson for fragment ion annotation

allowed_fragment_typesb,y allowed fragment types

allowed_fragment_charges1,2,3,4 allowed fragment charge states

enable_detection_specific_lossesfalse set this flag if specific neutral losses for detection fragment ions should be allowedtrue,false

enable_detection_unspecific_lossesfalse set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowedtrue,false

separatefalse set this flag if decoys should not be appended to targets.true,false

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

forcefalse Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false