Create a ProXL XML file from StavroX cross-linking analyses.
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README.md

StavroX 3 to Proxl XML Converter

Use this program to convert the results of a StavroX 3 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 stavrox2ProxlXML.jar with no arguments to see the possible parameters.
  3. Run the program, e.g., java -jar stavrox2ProxlXML.jar -r ./results.zhrs -l dss -f FASTA yeast2016.fa -a 1 -o ./output.proxl.xml

In the above example, output.proxl.xml will be created and be suitable for import into ProXL.

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

Usage: java -jar stavrox2ProxlXML.jar -r /path/to/results.file -l linker -f FASTA file full path [-s scan file name] -o /path/to/output.proxl.xml

E.g.:

java -jar stavrox2ProxlXML.jar -r ./results.zhrs -l dss -f /path/to/yeast2016.fa -s mydata.mzML -o ./output.proxl.xml

java -jar stavrox2ProxlXML.jar -r ./results.zhrs -l dss -f /path/to/yeast2016.fa -o ./output.proxl.xml

java -jar stavrox2ProxlXML.jar -r ./results.zhrs -l dss -f FASTA /path/to/yeast2016.fa -a 1 -s mydata.mzML -o ./output.proxl.xml

Required parameters:

-r </path/to/results.zhrs> -- The full path to the results file from the
                              StavroX analysis.

-f </path/to/fasta.fa> -- The full path to the FASTA file used in the
                          StavroX analysis.

-l <name of cross-linker> -- The name of the cross-linker used. See
                             below for a list of valid linkers.

-o </path/to/output.xml> -- The full path to the desired output proxl
                            XML file.

Optional parameters:

-s <scan file name> -- The name of the scan file (e.g. mydata.mzML). Used to
                       annotate PSMs with the name of the scan file in which
                       the scan can be found.

-a <scan number adjustment> -- Adjust the reported scan number by this amount.

As of this writing, StavroX 3 has a bug in the parsing of mzML files that
causes incorrect scan numbers to be reported. It uses the spectrum index
instead of the scan number of the spectrum at that index. This causes
a mismatch when the ProXL XML importer attempts to find the referenced
scans. In testing, the true scan number appears to always be 1 higher
than the reported scan number when using mzML files. "-a 1" will adjust
the scan numbers appropriately.


-i <import FDR cutoff> -- PSMs with a FDR greater than this amount will not
                          be imported into ProXL. Default is 0.05. If set
                          to a value greater than or equal to 1, no import
                          FDR will be used.

Valid 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)