The Nexus program is a database search program for crosslinking peptides for 
MS2 spectra on high accurate mass spectrometry. The Binary executable program can be 
run on any linux systems without installation of any other programs.  

To run the database search, it is recommended to convert the raw file into mzXML file by 
Rawconverter (http://fields.scripps.edu/rawconv/). 
You can directly copy these files:
    NexusSearch.exe, 
    ReportSearch.exe, and 
    nexus.params to the same directory.

 First run: chmod 775 NexusSearch.exe.
            chmod 775 ReportNexus.exe

     The parameter file is similar to and modified from comet.params. You need to specify the search parameters.

Then you can type: ./NexusSearch.exe <mzXML> and the search will begin for that mzXML file. Depends on your systems,
you can run the mzXML file one by one or in a batch mode. 

After all the search completed, you can then run: ./ReportSearch.exe <output name>. It will report the final search
results of crosslinked peptides in the file: output name.nexus.xls.

If you have any questions, please contact the Dr. Jie Luo at jluo@systemsbiology.org








Dr. Jie Luo 