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iProphet (TPP) to Proxl XML Converter

Use this program to convert the results of a Kojak + iProphet (Trans Proteomic Pipeline or TPP) cross-linking analysis to Proxl XML suitable for import into the proxl web application.

How To Run

  1. Download the latest release.
  2. Run the program java -jar iProphet2ProxlXML.jar with no arguments to see the possible parameters.

For more information on importing data into Proxl, please see the Proxl Import Documentation.

More Information About Proxl

For more information about Proxl, visit

Command line documentation

Usage: java -jar iProphet2Proxl.jar -x pepXML file path -o output file path -f fasta file path -l linker name -k kojak conf file [-k kojak conf file...] -d decoy string [-d decoy string...]


 -x or --pepxml       : Required. The full path to the pepXML file
 -o or --out-file     : Required. Full path (including file name) to which
                        to write the Proxl XML

 -k or --kojak-conf   : Required. Full path to kojak configuration files
                        used to generate the Kojak results. More than one
                        may be specified using multiple -k paramters.
 -f or --fasta-file   : Required. Full path to the fasta file used in
                        the search.
 -l or --linker-name  : Required. The name of the linker (e.g., edc or dss)
                        used in the experiment.
 -d or --decoy-string : Optional. The string to use to identify decoy
                        protein matches. For example decoy, random,
                        or reversed. If option is not present, all hits
                        are assumed to be targets. May be specified
                        multiple times with multiple -d parameters.
                        All protein names containing any of the
                        given decoy strings will be considered
                        decoy hits.


java -jar iProphet2Proxl.jar -x ./results.pep.xml -o ./results.proxl.xml -f /data/mass_spec/yeast.fa -l dss -k ./kojak1.conf -k ./kojak2.conf -d random -d rand1 -d rand0

More information: