OpenMS
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Generates decoys according to different models for a specific TraML
potential predecessor tools | → OpenSwathDecoyGenerator → | potential successor tools |
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OpenSwathAssayGenerator | OpenSwathAnalyzer | |
OpenSwathWorkflow |
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. The tool operates on TraML files, which can come from TargetedFileConverter or any other tool.
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 (excluding N-/C-terminal and K/R/P) and shuffles the fragment ion intensities accordingly. If the new sequence does not reach a threshold of identity within a set number of trials, a random amino acid (not N-/C-terminal or modified) is "mutated" to a random other amino acid.
The command line parameters of this tool are:
stty: 'standard input': Inappropriate ioctl for device OpenSwathDecoyGenerator -- Generates decoys according to different models for a specific TraML Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenSwathDecoyGenerator.html Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c To cite OpenMS: + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7. Usage: OpenSwathDecoyGenerator <options> Options (mandatory options marked with '*'): -in <file>* Input file (valid formats: 'tsv', 'mrm', 'pqp', 'TraML') -in_type <type> Input file type -- default: determined from file extension or content (valid: 'tsv', 'mrm', 'pqp', 'TraML') -out <file>* Output file (valid formats: 'tsv', 'pqp', 'TraML') -out_type <type> Output file type -- default: determined from file extension or content (valid: 'tsv', 'pqp', 'TraML') -method <type> Decoy generation method (default: 'shuffle') (valid: 'shuffle', 'pseudo-reverse', 'reverse', 'shift') -decoy_tag <type> Decoy tag (default: 'DECOY_') -switchKR <true/false> Whether to switch terminal K and R (to achieve different precursor mass) (default: 'true') (valid: 'true', 'false') 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)
INI file documentation of this tool: