OpenMS
SpecLibCreator

creates with given data a .MSP format spectral library.

Information file should have the following information: peptide, retention time, measured weight, charge state. Extra information is allowed.

Experimental classes:
This Utility is not well tested and some features might not work as expected.

The command line parameters of this tool are:

SpecLibCreator -- Creates an MSP formatted spectral library.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_SpecLibCreator.html
Version: 3.2.0-pre-nightly-2024-07-21 Jul 22 2024, 02:13:52, Revision: b650df0
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:
  SpecLibCreator <options>

Options (mandatory options marked with '*'):
  -info <file>*          Holds id, peptide, retention time etc. (valid formats: 'csv')
  -itemseperator <char>   Separator between items. e.g. , (default: ',')
  -itemenclosed <bool>   'true' or 'false' if true every item is enclosed e.g. '$peptide$,$run$... (default: 
                         'false') (valid: 'true', 'false')
  -spec <file>*          Spectra (valid formats: 'mzData', 'mzXML')
  -out <file>*           Output MSP formatted spectra library (valid formats: 'msp')
                         
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
+SpecLibCreatorCreates an MSP formatted spectral library.
version3.2.0-pre-nightly-2024-07-21 Version of the tool that generated this parameters file.
++1Instance '1' section for 'SpecLibCreator'
info Holds id, peptide, retention time etc.input file*.csv
itemseperator, Separator between items. e.g. ,
itemenclosedfalse 'true' or 'false' if true every item is enclosed e.g. '$peptide$,$run$...true, false
spec spectrainput file*.mzData, *.mzXML
out output MSP formatted spectra libraryoutput file*.msp
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