Generates decoys according to different models for a specific TraML
potential predecessor tools | ![]() ![]() | potential successor tools |
FileFilter | 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: 2.0.0 Aug 25 2015, 00:02:58, Revision: GIT-NOTFOUND 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') (def ault: 'shuffle') -decoy_tag <type> Decoy tag (default: 'DECOY_') -theoretical Set this flag if only annotated transitions should be used and be corrected to the theoretical mz. -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 modifications (may be necessary depending on the decoy generation method). -remove_unannotated Set this flag if target assays with unannotated ions should be ignored from decoy generation. -enable_losses Set this flag if fragment ions should also be annotated with neutral losses . -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 target 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') 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 |