| OpenMS 2.5.0

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/documentation/UTILS_SpecLibCreator.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    To cite OpenMS:

      Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

    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 UTIL 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
+SpecLibCreator Creates an MSP formatted spectral library.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'SpecLibCreator'
info Holds id, peptide, retention time etc.input file*.csv
itemseperator, Separator between items. e.g. ,
itemenclosed false 'true' or 'false' if true every item is enclosed e.g. '$peptide$,$run$...true,false
spec spectra input file*.mzData,*.mzXML
out output MSP formatted spectra library output file*.msp
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false