Generates filtered and optimized assays using TraML files.

potential predecessor tools	→ OpenSwathAssayGenerator →	potential successor tools
	→ OpenSwathAssayGenerator →	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:

stty: 'standard input': Inappropriate ioctl for device

OpenSwathAssayGenerator -- Generates assays according to different models for a specific TraML
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenSwathAssayGenerator.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:
  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 content
                                         (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, C1H2N1O1) 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 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. (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 (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:

Legend:

required parameter

advanced parameter

+OpenSwathAssayGeneratorGenerates assays according to different models for a specific TraML

version3.4.0-pre-nightly-2024-12-16 Version of the tool that generated this parameters file.

++1Instance '1' section for 'OpenSwathAssayGenerator'

in Input fileinput file*.tsv, *.mrm, *.pqp, *.TraML

in_type Input file type -- default: determined from file extension or content
tsv, mrm, pqp, TraML

out Output fileoutput file*.tsv, *.pqp, *.TraML

out_type Output file type -- default: determined from file extension or content
tsv, pqp, 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

precursor_mz_threshold0.025 MZ threshold in Thomson for precursor ion selection

precursor_lower_mz_limit400.0 lower MZ limit for precursor ions

precursor_upper_mz_limit1200.0 upper MZ limit for precursor ions

product_mz_threshold0.025 MZ threshold in Thomson for fragment ion annotation

product_lower_mz_limit350.0 lower MZ limit for fragment ions

product_upper_mz_limit2000.0 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

unimod_file (Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml) describing residue modifiabilityinput file*.xml

enable_ipffalse IPF: set this flag if identification transitions should be generated for IPF. Note: Requires setting 'unimod_file'.true, false

max_num_alternative_localizations10000 IPF: maximum number of site-localization permutations

disable_identification_ms2_precursorsfalse IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level).true, false

disable_identification_specific_lossesfalse IPF: set this flag if specific neutral losses for identification fragment ions should not be allowedtrue, false

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

enable_swath_specifityfalse IPF: set this flag if identification transitions without precursor specificity (i.e. across whole precursor isolation window instead of precursor MZ) should be generated.true, false

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 Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false