If any of the support crew is around during the holidays, I was wondering if someone could post a XTandem output file that that is known to work on CPAS- as a check to see if my XTandem output is not properly formatted.

Holiday Cheers,

S.

Your MS2 upload log doesn't show any errors, though based on the elapsed time (0.02 seconds) it appears to have stopped very early on. Hard to tell what the problem is from the log (we are adding more verbose MS2 upload logging in the next release), so you should probably just post a copy of your pepXML file. I've attached a small sample file you can upload as well. Note: I'm not including the FASTA file, so the loader will warn you that it can't find the file… just ignore the warning.

You can configure CPAS to load MS2 results from anywhere in the file system. You want to add a "Data Pipeline" webpart to a portal page and set it up with the root path you want. See the documentation here: https://cpas.fhcrc.org/Wiki/home/help/page.view?name=bioModules%2Fpipeline

Adam

I tried your mini pepXML, but it runs into the same errors. I've attached the log file below.

Can you make any sense of it?

EDIT:

Nevermind, your pepXML works fine. After setting up the pipeline, the file got loaded. I think I just goofed on the path to my pepXML files before.