Convert MetaMorpheus cross-linking search results to proxl XML suitable for import into proxl.
Switch branches/tags
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.

MetaMorpheus to Proxl XML Converter

Use this program to convert the results of a MetaMorpheus cross-linking analysis to proxl XML suitable for import into the proxl web application.

Note: When running MetaMorpheus, you must enable output as PepXML when defining your XL Search taslk.

How To Run

  1. Download the latest release.
  2. Run the program java -jar metaMorpheus2ProxlXML.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 metamorph2ProxlXML.jar -x pepXML file path -o output file path -f fasta file path -c conf file (toml file)


 -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

 -c or --conf         : Required. Full path to  configuration file
                        used for the MetaMorpheus cross-linking search.
                        (e.g. XLSearchTaskconfig.toml)
 -f or --fasta-file   : Required. Full path to the fasta file used in
                        the search.
 -l or --linker       : Optional. If the linker was not set to the
                        built-in "DSS" or "DSSO" linkers using the GUI
                        and a user-defined linker was used in this search
                        (such as BS3 or EDC), use this to specify the
                        linker name that proxl will recognize. See below
                        for currently-supported values.


java -jar metamorph2ProxlXML.jar -x ./results.pep.xml -o ./results.proxl.xml
-f /data/mass_spec/yeast.fa -c ./XLSearchTaskconfig.toml

java -jar metamorph2ProxlXML.jar -x ./results.pep.xml -o ./results.proxl.xml
-f /data/mass_spec/yeast.fa -c ./XLSearchTaskconfig.toml -l edc

More information:

Currently-supported linkers:

  • dss
  • bs3
  • edc
  • bs2
  • sulfo-smcc
  • dsso
  • bs3.sty (supports links from K/nterm-K/S/T/Y/nterm)
  • dss.sty (supports links from K/nterm-K/S/T/Y/nterm)