PTPredict

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.

Note

Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

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
Full documentation: http://www.openms.de/doxygen/release/3.0.0/html/TOPP_PTPredict.html
Version: 3.0.0 Jul 14 2023, 11:57:33, Revision: be787e9
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:
  PTPredict <options>

Options (mandatory options marked with '*'):
  -in <file>*                    Input file  (valid formats: 'idXML')
  -in_oligo_params <file>        Input file with additional model parameters when using the OLIGO kernel (val
                                 id formats: 'paramXML')
  -in_oligo_trainset <file>      Input file with the used training dataset when using the OLIGO kernel (valid
                                  formats: 'txt')
  -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:

Legend:

required parameter

advanced parameter

+PTPredictpredicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel

version3.0.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'PTPredict'

in input file input file*.idXML

in_oligo_params input file with additional model parameters when using the OLIGO kernelinput file*.paramXML

in_oligo_trainset input file with the used training dataset when using the OLIGO kernelinput file*.txt

out output file
output file*.idXML

svm_model svm model in libsvm format (can be produced by PTModel)input file*.txt

max_number_of_peptides100000 the maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory).

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