This application is used to predict the likelihood of peptides to be proteotypic.
This method has been described in the publication
Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gröpl, Oliver Kohlbacher and Knut Reinert LC-MSsim - a simulation software for Liquid ChromatographyMass Spectrometry data BMC Bioinformatics 2008, 9:423.
The input of this application is an svm model and an idXML file with peptide identifications. The svm model file is specified by the svm_model parameter in the command line or the ini file. This file should have been produced by the PTModel application.
The command line parameters of this tool are:
PTPredict -- predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
  PTPredict <options>
Options (mandatory options marked with '*'):
  -in <file>*                    Input file  (valid formats: 'idXML')
  -out <file>                    Output file
                                 (valid formats: 'idXML')
  -svm_model <file>*             Svm model in libsvm format (can be produced by PTModel) (valid formats: 'txt
                                 ')
  -max_number_of_peptides <int>  The maximum number of peptides considered at once (bigger number will lead 
                                 to faster results but needs more memory).
                                 (default: '100000')
                                 
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:
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |