Byonic to Proxl XML Converter

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

Notes

1. The results must be saved by Byonic in mzIdentML (mzId) format.
2. Currently, only the following cross-linkers are supported. If you are using a different cross-linker, please email us at mriffle .at. uw.edu and we will work with you to support your cross-linker.
   1. Disulfied
   2. Trisulfied
   3. Disulfied x 2
3. The Disulfied x 2 cross-link reports a crosslink between 1 position in peptide 1 to 2 positions in peptide 2. This type of link is not currently supported by proxl or proxl XML. In proxl XML this is represented as a single cross-link between the two peptides with a linker mass equal to Disulfied x 2's delta mass. The site of the 2nd cross-link in peptide two is marked as having a modification of mass 0.
4. Static mods are not currently fully supported. If you have static mods in your search, please email us at mriffle .at. uw.edu.

How To Run

1. Download the byonic2ProxlXML.jar from the latest release.
2. Run the program java -jar byonic2ProxlXML.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 http://proxl-ms.org/.

Command line documentation

java -jar byonic2ProxlXML.jar [-hvV] -m=<mzidFile> -o=<outFile>

Description:

Convert the results of a Byonic XL analysis to a ProXL XML file suitable for
import into ProXL.

More info at: https://github.com/yeastrc/proxl-import-byonic

Options:
  -m, --mzid=<mzidFile>      Full path to the mzID (mzIdentML) file output by Byonic.
  -o, --out-file=<outFile>   Full path to use for the ProXL XML output file
                               (including file name).
  -v, --verbose              If present, complete error messages will be printed.
                               Useful for debugging errors.
  -h, --help                 Show this help message and exit.
  -V, --version              Print version information and exit.