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PEP_ISOTOPE_ERROR in mascot

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PEP_ISOTOPE_ERROR in mascot mmetod  2010-08-03 04:33
Status: Closed
 
Hi guys,
How do you set the isotope error in mascot.xml? I am trying to search orbitrap data on Labkey 10.2 using mascot. It gives me very large errors. The data is with low to sub ppm accuracy for peptide precursors and X!Tandem searches show this correctly. Mascot does not. I tried to include various lines with PEP_ISOTOPE_ERROR in the xml but it doesn't work.
Thanks,
Metodi
 
 
Brian Connolly responded:  2010-08-05 14:48
Metodi,

I apologize for the delay in getting back to you with a response.

I am sorry to say, that in LabKey 10.2 you will not be able to set the PEP_ISOTOPE_ERROR search parameter for your mascot searches. Currently LabKey only supports a subset of all available search parameters for the MASCOT search engine. The list of supported search parameters is available in the table at https://www.labkey.org/wiki/home/Documentation/page.view?name=pipelineMascot

A possible work around for this problem will be to

  1. Perform these searches outside of LabKey (ie using the MASCOT interface)
  2. Move the search results files back into your Pipeline directories
  3. In the Data Pipeline web part, click on the Process and Import button
  4. Select the search results files and click on the Import Search Results button.
I have opened a bug, in our bug database, to add support for this search parameter. (See https://www.labkey.org/issues/home/Developer/issues/details.view?issueId=10718 if you would like to track it's progress.)