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OpenSwathAssayGenerator

Generates filtered and optimized assays using TraML files.

potential predecessor tools $ \longrightarrow $ OpenSwathAssayGenerator $ \longrightarrow $ potential successor tools
OpenSwathDecoyGenerator

This module generates assays for targeted proteomics using a set of rules that was found to improve the sensitivity and selectivity for detection of typical peptides (Schubert et al., 2015). The tool operates on TraML files, which can come from ConvertTSVToTraML or any other tool. If the TraML is annotated with the CV terms for fragment ion annotation, it can directly filter the transitions according to the set rules. If this is not the case (e.g. if an older version of ConvertTSVToTraML was used), the option -enable_reannotation can do the reannotation.

The command line parameters of this tool are:

OpenSwathAssayGenerator -- Generates assays according to different models for a specific TraML
Version: 2.0.0 Aug 19 2015, 22:19:33, Revision: GIT-NOTFOUND

Usage:
  OpenSwathAssayGenerator <options>

Options (mandatory options marked with '*'):
  -in <file>*                         Input file ('traML') (valid formats: 'traML')
  -out <file>*                        Output file (valid formats: 'traML')
  -min_transitions <int>              Minimal number of transitions (default: '6')
  -max_transitions <int>              Maximal number of transitions (default: '6')
  -allowed_fragment_types <type>      Allowed fragment types (default: 'b,y')
  -allowed_fragment_charges <type>    Allowed fragment charge states (default: '1,2,3,4')
  -enable_losses                      Set this flag if neutral losses for fragment ions should be allowed
  -enable_ms1_uis_scoring             Set this flag if MS1-UIS assays for UIS scoring should be generated
  -enable_ms2_uis_scoring             Set this flag if MS2-UIS assays for UIS scoring should be generated
  -enable_site_scoring                Set this flag if site-specific assays for site-specific scoring should 
                                      be generated
  -enable_alternative_localizations   Set this flag if hypotheses for alternative modification localizations 
                                      should be generated
  -enable_insilico                    Set this flag if insilico fragment ions for UIS / site-specific scoring
                                      should be generated
  -enable_reannotation                Set this flag if reannotation of fragment ions should be allowed.
  -precursor_mz_threshold <double>    MZ threshold in Thomson for precursor ion selection (default: '0.1')
  -precursor_lower_mz_limit <double>  Lower MZ limit for precursor ions (default: '400')
  -precursor_upper_mz_limit <double>  Upper MZ limit for precursor ions (default: '1200')
  -product_mz_threshold <double>      MZ threshold in Thomson for fragment ion annotation (default: '0.05')
  -product_lower_mz_limit <double>    Lower MZ limit for fragment ions (default: '350')
  -product_upper_mz_limit <double>    Upper MZ limit for fragment ions (default: '2000')
                                      
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
+OpenSwathAssayGeneratorGenerates assays according to different models for a specific TraML
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'OpenSwathAssayGenerator'
in input file ('traML')input file*.traML
out output fileoutput file*.traML
min_transitions6 minimal number of transitions
max_transitions6 maximal number of transitions
allowed_fragment_typesb,y allowed fragment types
allowed_fragment_charges1,2,3,4 allowed fragment charge states
enable_lossesfalse set this flag if neutral losses for fragment ions should be allowedtrue,false
enable_ms1_uis_scoringfalse set this flag if MS1-UIS assays for UIS scoring should be generatedtrue,false
enable_ms2_uis_scoringfalse set this flag if MS2-UIS assays for UIS scoring should be generatedtrue,false
enable_site_scoringfalse set this flag if site-specific assays for site-specific scoring should be generatedtrue,false
enable_alternative_localizationsfalse set this flag if hypotheses for alternative modification localizations should be generatedtrue,false
enable_insilicofalse set this flag if insilico fragment ions for UIS / site-specific scoring should be generatedtrue,false
enable_reannotationfalse set this flag if reannotation of fragment ions should be allowed.true,false
precursor_mz_threshold0.1 MZ threshold in Thomson for precursor ion selection
precursor_lower_mz_limit400 lower MZ limit for precursor ions
precursor_upper_mz_limit1200 upper MZ limit for precursor ions
product_mz_threshold0.05 MZ threshold in Thomson for fragment ion annotation
product_lower_mz_limit350 lower MZ limit for fragment ions
product_upper_mz_limit2000 upper MZ limit for fragment ions
swath_windows_file Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline ... Note that the first line is a header and will be skipped.input file*.txt
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

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:31 using doxygen 1.8.9.1