Skyline won't import PD result files

Skyline won't import PD result files sa825  2019-09-24

Good afternoon,

I am trying to import some DDA files that have been processed in Proteome Discoverer (PD) using the Import --> Peptide Search format.
However, when I do this, I get the following error: "This file does not contain q-values. You can set a cut-off score of 0 in order to build a library from it, but this may cause your library to include a lot of false-positives."

If I reduce the cut off score to 0, it works but then as it says, such results are unreliable.

I have attached a screenshot of the error.



Brendan MacLean responded:  2019-09-24

Hi Shimon,
Ideally, you would want to use PD in a way that it uses Percolator to assing q values (FDR estimates) to each peptide. Skyline is telling you that you have run your search in a way that has not produced any known probability score that it can use to test against a cut-off. Using zero for the cut-off is really only appropriate, if your workflow included some way of filtering the results prior to it reaching Skyline and, therefore, already contains a known FDR as is.

You need to examine your workflow and decide whether:

  1. You can adjust it to produce a probability value (e.g. introducing Percolator)
  2. You believe it already has a probability value other than a Percolator q value that Skyline is just not recognizing (we would need your example data and a clear explanation to fix this)
  3. You believe you have already filtered your result set to a known FDR and, therefore, do not need a cut-off, in which case zero is an acceptable value to use in the Skyline library building form.

Hope this helps. Good luck with importing your DDA results into Skyline.