OpenMS  3.0.0
OpenSwathDecoyGenerator

Generates decoys according to different models for a specific TraML

potential predecessor tools $ \longrightarrow $ OpenSwathDecoyGenerator $ \longrightarrow $ 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: 3.0.0-pre-nightly-2022-07-20 Jul 21 2022, 00:07:28, Revision: ea0316e
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 (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
version3.0.0-pre-nightly-2022-07-20 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