mProphet missing decoys error dkueltz  2019-01-02

Hi Brendan, Nat,

Using the newest version of Skyline (4.2) an error pops up from mProphet that no decoy peptides are present in the document even though they had been generated (Refine - Add decoys) and are clearly present. This behavior is different from previous Skyline versions we have used in my lab. I just updated to the latest Skyline daily and the problem is the same. A screenshot with the error message is attached. Thanks for looking into this!


Brendan MacLean responded:  2019-01-02

Hi Dietmar,
Nothing changed here. You are mistakenly attributing this error to 4.2. You must just never have made this mistake before.

Your decoy peptides do not have chromatograms. You may be able to solve this by re-importing your data files, if they are DIA or DDA, or even PRM if you collected data for your decoy precursors.

Hope this helps. Thanks for the helpful screenshot.


dkueltz responded:  2019-01-02

Hi Brendan,
Sorry for that oversight! Of course, you are right! I did not reload the sample files after generating the decoys. How could I forget that? I am glad this was an easy solution. Thanks for your great work re: Skyline and the quick response and Happy New Year!