DDA search hangs on "Running percolater..." with a specific FASTA file

DDA search hangs on "Running percolater..." with a specific FASTA file Remco van Soest  2022-09-20

Skyline (64 bit) (c99206313)

When using the "Import DDA Peptide Search" workflow Skyline hangs on "Running percolator..." after the search has successfully finished. I have to manually end the "percolator.exe" task in order to make the software respond again.

The issue seems related to the FASTA file (attached; downloaded from NCBI; sequence is correct). If I manually remove line 11 and 12 everything works just fine. It is not the length, as everything works fine as well if I replace line 11 and 12 with A's.

Why does the percolator task hang when using a specific FASTA file? I don't see anything wrong with the file, and obviously want to be able to use the full sequence for my search.


Nick Shulman responded:  2022-09-21
I think we will need to get more files from you in order to reproduce this bug.
Can you send us the raw files or mzML files that you were searching?

It sounds like you did "File > Import > Peptide Search" and told Skyline to perform a peptide search.
Can you send us screenshots of the pages of the Import Peptide Search wizard so that we can see what settings you used?

It might also be helpful if you could send us the Skyline document that you were importing the search into. That might be a blank Skyline document, but it might still be helpful for us to see it in case any of the settings in the document impact the reproducibility of this bug.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including spectral libraries, ion mobility libraries, extracted chromatograms, etc.

If that .zip file, your raw files, and your screenshots are less than 50MB you can attach them to this support request.
If those files are larger than that, it might be easiest if you could package them all into a zip file and upload them here:

-- Nick
Remco van Soest responded:  2022-09-21
See attached PPT for the settings used. We prefer not to make the data publicly available, but if you contact me directly, I can make it available through box.

I tried again today, and found that the search works fine with the unmodified FASTA file as long as I use "0" for "Max missed cleavages" in the "Import FASTA (required)" screen.

Nick Shulman responded:  2022-09-22
I will send you an email.
-- Nick