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OpenMS
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Generates filtered and optimized assays using TraML files.
| potential predecessor tools | → OpenSwathAssayGenerator → | 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 TargetedFileConverter or any other tool. In a first step, the tool will annotate all transitions according to the predefined criteria. In a second step, the transitions will be filtered to improve sensitivity for detection of peptides.
Optionally, theoretical identification transitions can be generated when the TraML will be used for IPF scoring in OpenSWATH, see MRMAssay for more information on the algorithm. This is recommended if post-translational modifications are scored with OpenSWATH.
The command line parameters of this tool are:
OpenSwathAssayGenerator -- Generates assays according to different models for a specific TraML
Full documentation: http://www.openms.de/doxygen/release/3.2.0/html/TOPP_OpenSwathAssayGenerator.html
Version: 3.2.0 Nov 26 2024, 13:16:38, Revision: 962e60f
To cite OpenMS:
+ Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.
Usage:
OpenSwathAssayGenerator <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 conten
t
(valid: 'tsv', 'pqp', '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, C1H2N
1O1) for detection 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: '400.0')
-precursor_upper_mz_limit <double> Upper MZ limit for precursor ions (default: '1200.0')
-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: '350.0')
-product_upper_mz_limit <double> Upper MZ limit for fragment ions (default: '2000.0')
-swath_windows_file <file> Tab separated file containing the SWATH windows for exclusion of frag
ment 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. (valid formats: 'txt')
-unimod_file <file> (Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml)
describing residue modifiability (valid formats: 'xml')
-enable_ipf IPF: set this flag if identification transitions should be generated
for IPF. Note: Requires setting 'unimod_file'.
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 (defau
lt: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
INI file documentation of this tool:
1.9.1