OpenSwathDecoyGenerator

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 and shuffles the fragment ion intensities accordingly, however for this to work the fragment ions need to be matched to annotated before.

The command line parameters of this tool are:

OpenSwathDecoyGenerator -- Generates decoys according to different models for a specific TraML
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

Usage:
  OpenSwathDecoyGenerator <options>

Options (mandatory options marked with '*'):
  -in <file>*                           Input file ('traML') (valid formats: 'traML')
  -out <file>*                          Output file (valid formats: 'traML')
  -method <type>                        Decoy generation method ('shuffle','pseudo-reverse','reverse','shift'
                                        ) (default: 'shuffle')
  -decoy_tag <type>                     Decoy tag (default: 'DECOY_')
  -mz_threshold <double>                MZ threshold in Thomson for fragment ion annotation (default: '0.05')
  -exclude_similar                      Set this flag if decoy assays with similarity of the peptide sequence
                                        to the target assays higher than the identity_threshold should be
                                        excluded. If similarity_threshold is over 0, decoy assays with an
                                        absolute difference of the decoy and target product mz smaller than
                                        similarity_threshold are further excluded.
  -similarity_threshold <double>        Similarity threshold for absolute difference of the product mz of 
                                        target and decoy assays for exclusion in Dalton. Suggested value:
                                        0.05 (default: '-1')
  -append                               Set this flag if non-decoy TraML should be appended to the output.
  -remove_CNterm_mods                   Set this flag to remove decoy peptides with C/N terminal modification
                                        s (may be necessary depending on the decoy generation method).
  -remove_unannotated                   Set this flag if target assays with unannotated ions should be ignore
                                        d from decoy generation.
  -identity_threshold <double>          Shuffle: identity threshold for the shuffle algorithm (default: '0.7'
                                        )
  -max_attempts <int>                   Shuffle: maximum attempts to lower the sequence identity between targ
                                        et and decoy for the shuffle algorithm (default: '10')
  -mz_shift <double>                    Shift: MZ shift in Thomson for shift decoy method (default: '20')
  -precursor_mass_shift <double>        Mass shift to apply to the precursor ion (default: '0')
  -allowed_fragment_types <type>        Allowed fragment types (default: 'b,y')
  -allowed_fragment_charges <type>      Allowed fragment charge states (default: '1,2,3,4')
  -enable_detection_specific_losses     Set this flag if specific neutral losses for detection fragment ions 
                                        should be allowed
  -enable_detection_unspecific_losses   Set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N
                                        1O1) for detection fragment ions should be allowed
                                        
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 (defau
                                        lt: '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 file ('traML')input file*.traML

out output fileoutput file*.traML

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

decoy_tagDECOY_ decoy tag

mz_threshold0.05 MZ threshold in Thomson for fragment ion annotation

exclude_similarfalse set this flag if decoy assays with similarity of the peptide sequence to the target assays higher than the identity_threshold should be excluded. If similarity_threshold is over 0, decoy assays with an absolute difference of the decoy and target product mz smaller than similarity_threshold are further excluded.true,false

similarity_threshold-1 Similarity threshold for absolute difference of the product mz of target and decoy assays for exclusion in Dalton. Suggested value: 0.05

appendfalse set this flag if non-decoy TraML should be appended to the output.true,false

remove_CNterm_modsfalse set this flag to remove decoy peptides with C/N terminal modifications (may be necessary depending on the decoy generation method).true,false

remove_unannotatedfalse set this flag if target assays with unannotated ions should be ignored from decoy generation.true,false

identity_threshold0.7 shuffle: identity threshold for the shuffle algorithm

max_attempts10 shuffle: maximum attempts to lower the sequence identity between target and decoy for the shuffle algorithm

mz_shift20 shift: MZ shift in Thomson for shift decoy method

precursor_mass_shift0 Mass shift to apply to the precursor ion

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

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