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 |