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required parameter

advanced parameter

+RTPredictPredicts retention times for peptides using a model trained by RTModel.

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'RTPredict'

in_id peptides with precursor informationinput file*.idXML

in_text peptides as text-based fileinput file*.txt

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

total_gradient_time1 the time (in seconds) of the gradient (peptide RT prediction)1e-05:∞

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

testfalse Enables the test mode (needed for internal use only)true,false

+++out_idOutput files in idXML format

file Output file with peptide RT predictionoutput file*.idXML

positive Output file in idXML format containing positive predictions (peptide separation prediction - requires negative file to be present as well)
output file*.idXML

negative Output file in idXML format containing negative predictions (peptide separation prediction - requires positive file to be present as well)
output file*.idXML

rewrite_peptideidentification_rtmzfalse rewrites each peptideidentification's rt and mz from prediction and calculation (according to the best hit)true,false

+++out_textOutput files in text format

file Output file with predicted RT valuesoutput file*.csv