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Mascot pepXML upload

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Mascot pepXML upload Alex  2006-07-06 07:32
Status: Closed
 
Hi,

I have troubles uploading pepXML files transformed using Mascot2XML from DAT files. I have the same error as already posted previously regarding the prevaa and nextaa issue. I'm using a modified version of Mascot2XML that contains a modified version of the "getmodificationtag" written by Matthias Schlesner that allows to do only one search with Mascot using light as static and heavy as variable and then run perfectly with Xpress or ASAPRatio. Thus I cannot use the windows binary that was present in the other message. Has this issue been updated in the CVS version of Mascotconverter.cxx so that I could upload the latest version and recompile the script so that the prevaa and nextaa attributes appears in the pepXML file. Then maybe CPAS would be fine with those files.

Thanks for any help or advice?

Alex
 
 
wongch responded:  2006-07-06 07:54
Brendanx has committed the earlier fix on prevaa and nextaa issue 3 weeks ago. You get can this fix from Sashimi CVS. Please let us know if the problem goes away. Thanks.
 
vensel responded:  2006-07-12 14:27
Hi,

I am also having trouble loading pep.xml files created from dat files using the Mascot2XML windows converter posted by Brendanx in a previous thread (Mascot2XML msun@bcgsc.ca 06/12/2006 10:26:56 ). I have attached an error log file from a failed attempt to load a .pep.xml file.

Thanks,

Bill
 
brendanx responded:  2006-07-18 15:14
Sorry for the delay on the reply. We are very near to dropping v1.5 on the web. That should fix this problem, and will contain significant perf improvements in the TPP and X!Tandem.

In the meantime, here is a new Mascot2XML.exe that can simply replace your existing version.
 
adam responded:  2007-01-04 09:39