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RTEvaluation

Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.

The method needs an idXML file with IDs and predicted RTs. The idXML must have been annotated with protein sequences (for the positive hits) using PeptideIndexer. This tool then evaluates the true positives, false positives, true negatives, and false negatives for the unfiltered IDs, for the IDs filtered in first RT dimension, for the IDs filtered in the second RT dimension as well as for the IDs filtered in both dimensions. The output is a table with either CSV format (can be imported by Excel) or LaTeX format (to include in your LaTeX manuscripts).

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:

INI file documentation of this tool: