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
+SpecLibCreatorCreates an MSP formatted spectral library.
version2.5.0-GIT-NOTFOUND-GIT-NOTFOUND 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 Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false