OpenSwathAssayGenerator

Generates filtered and optimized assays using TraML files.

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

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 TargetedFileConverter 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 TargetedFileConverter 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: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

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_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, 
                                             C1H2N1O1) for detection fragment ions should be allowed
  -enable_identification_specific_losses     Set this flag if specific neutral losses for identification frag
                                             ment ions should be allowed
  -enable_identification_unspecific_losses   Set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, 
                                             C1H2N1O1) for identification fragment ions should be allowed
  -enable_identification_ms2_precursors      Set this flag if MS2-level precursor ions for identification 
                                             should be allowed to enable extraction of the precursor signal
                                             from the fragment ion data (MS2-level). This may help in identif
                                             ication if the MS1 signal is weak.
  -enable_ms1_uis_scoring                    Set this flag if MS1-UIS assays for UIS scoring should be genera
                                             ted
  -enable_ms2_uis_scoring                    Set this flag if MS2-UIS assays for UIS scoring should be genera
                                             ted
  -max_num_alternative_localizations <int>   Maximum number of site-localization permutations (default: '20')
  -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: 
                                             '0.025')
  -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: 
                                             '0.025')
  -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

version2.3.0 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_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

enable_identification_specific_lossesfalse set this flag if specific neutral losses for identification fragment ions should be allowedtrue,false

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

enable_identification_ms2_precursorsfalse set this flag if MS2-level precursor ions for identification should be allowed to enable extraction of the precursor signal from the fragment ion data (MS2-level). This may help in identification if the MS1 signal is weak.true,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

max_num_alternative_localizations20 maximum number of site-localization permutations

enable_reannotationfalse set this flag if reannotation of fragment ions should be allowed.true,false

precursor_mz_threshold0.025 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_threshold0.025 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