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import problem tobias.kockmann  2014-04-14 09:24
 
Dear Brendan,

I am having the following issue regarding re-import of DIA (SWATH-MS) results into the latest skyline-daily release:

Initially I imported fragment ion chromatogram for a few hundred target peptides into a skyline document. After manual inspection of the chromatograms I added decoy peptides using the random mass shift method. When I now re-import the results using Manage Results -> Reimport I see lots of activity in the import window, but decoy peptide chromatograms remain empty. In contrast to the initial import the chromatogram in the import window do not "grow" from low to high RTs. Instead peaks rise simultaniously all along the RT axis. To me it looks like the data gets reimported from some kind of cached data, but not from the originial .wif and wif.scan files.

Any idea what might be the problem and how to solve it?

Removing all current results is of course an option, but then I would also need to import all the target peptide related data a second time.

Best,
Tobi
 
 
Brendan MacLean responded:  2014-04-14 12:19
Hi Tobi,
Could you have possibly clicked the Re-score button rather than the Re-import button? What you are describing sounds a lot more like a re-score than a re-import.

When you click Re-import, it should only add an asterisk beside the name(s) of the selected replicate(s), and not actually do anything until you click the OK button. When you click Re-score, however, you will be immediately presented with a message box asking whether you want to re-score in place or save as to a new location before re-scoring.

I have tried several re-import tests, but don't see them acting as you describe. If you are sure you have clicked re-import, followed by the OK button, then I may need to look at this myself over WebEx.

Let me know. Thanks.

--Brendan