OpenMS
2.6.0
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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 Full documentation: http://www.openms.de/documentation/TOPP_PTPredict.html Version: 2.6.0 Sep 30 2020, 12:54:34, Revision: c26f752 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: