OpenSwathDecoyGenerator

Generates decoys according to different models for a specific TraML

potential predecessor tools	→ OpenSwathDecoyGenerator →	potential successor tools
OpenSwathAssayGenerator		OpenSwathAnalyzer
		OpenSwathWorkflow

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. The tool operates on TraML files, which can come from TargetedFileConverter or any other tool.

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
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenSwathDecoyGenerator.html
Version: 3.3.0-pre-nightly-2024-11-20 Nov 21 2024, 02:34:56, Revision: decb5c8
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

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 (default: 'shuffle') (valid: 'shuffle', 'pseudo-reverse', 
                          'reverse', 'shift')
  -decoy_tag <type>       Decoy tag (default: 'DECOY_')
  -switchKR <true/false>  Whether to switch terminal K and R (to achieve different precursor mass) (default: 
                          'true') (valid: 'true', 'false')
                          
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)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+OpenSwathDecoyGeneratorGenerates decoys according to different models for a specific TraML

version3.3.0-pre-nightly-2024-11-20 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 methodshuffle, pseudo-reverse, reverse, shift

decoy_tagDECOY_ decoy tag

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

aim_decoy_fraction1.0 Number of decoys the algorithm should generate (if unequal to 1, the algorithm will randomly select N peptides for decoy generation)

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_shift0.0 shift: precursor ion MZ shift in Thomson for shift decoy method

shift_product_mz_shift20.0 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

switchKRtrue Whether to switch terminal K and R (to achieve different precursor mass)true, 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 Overrides tool-specific checkstrue, false

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