OpenMS
2.4.0
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This application is used to predict retention times for peptides or peptide separation.
This methods and applications of this model are described in several publications:
Nico Pfeifer, Andreas Leinenbach, Christian G. Huber and Oliver Kohlbacher Statistical learning of peptide retention behavior in chromatographic separations: A new kernel-based approach for computational proteomics. BMC Bioinformatics 2007, 8:468
Nico Pfeifer, Andreas Leinenbach, Christian G. Huber and Oliver Kohlbacher Improving Peptide Identification in Proteome Analysis by a Two-Dimensional Retention Time Filtering Approach J. Proteome Res. 2009, 8(8):4109-15
The input of this application is an svm model and a file with peptide identifications (idXML or text). 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 RTModel application.
For retention time prediction the peptide sequences are extracted from the idXML/text inputfile and passed to the svm. The svm then predicts retention times according to the trained model. The predicted retention times are stored as
inside the peptide entities in the idXML output file.
For separation prediction you have to specify two output file names. 'out_id:positive' is the filename of the peptides which are predicted to be collected by the column and 'out_id:negative' is the file of the predicted flowthrough peptides.
Retention time prediction and separation prediction cannot be combined!
The command line parameters of this tool are:
RTPredict -- Predicts retention times for peptides using a model trained by RTModel. Version: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06 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: RTPredict <options> Options (mandatory options marked with '*'): -in_id <file> Peptides with precursor information (valid formats: 'idXML') -in_text <file> Peptides as text-based file (valid formats: 'txt') -in_oligo_params <file> Input file with additional model parameters when using the OLIGO kernel (valid formats: 'paramXML') -in_oligo_trainset <file> Input file with the used training dataset when using the OLIGO kernel (valid formats: 'txt') -svm_model <file>* Svm model in libsvm format (can be produced by RTModel) (valid formats: 'txt') -total_gradient_time <time> The time (in seconds) of the gradient (peptide RT prediction) (default: '1' min: '1e-05') Output files in idXML format: -out_id:file <file> Output file with peptide RT prediction (valid formats: 'idXML') -out_id:positive <file> Output file in idXML format containing positive predictions for peptide separa tion prediction - requires 'out_id:negative' to be present as well. (valid formats: 'idXML') -out_id:negative <file> Output file in idXML format containing negative predictions for peptide separa tion prediction - requires 'out_id:positive' to be present as well. (valid formats: 'idXML') Output files in text format: -out_text:file <file> Output file with predicted RT values (valid formats: 'csv') 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: