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RTPredict

This application is used to predict retention times for peptides or peptide separation.

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 RTModel application.
For retention time prediction the peptide sequences are extracted from the IdXML inputfile and passed to the svm. The svm then predicts retention times according to the trained model. The predicted retention times are stored as

 <userParam name="predicted_retention_time" value="<predicted retention time>" /> 
inside the peptide entities in the IdXML output file. For separation prediction you have to specify two output file names. 'out_positive' is the filename of the peptides which are predicted to be collected by the coloumn and 'out_negative' is the file of the predicted flowthrough peptides.
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