Generates filtered and optimized assays using TraML files.
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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 25 2015, 00:02:58, 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:
OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Aug 25 2015 05:53:56 using doxygen 1.8.9.1 |