"Not Responding" after MS1 filtering

"Not Responding" after MS1 filtering y nishimura  2024-04-25 04:39

I imported 32 interact.pep files from FragPipe closed search output, 32 mzML files, and 1% FDR filtered FASTA generated by FragPipe with 2 missed cleavages into Skyline-daily. After MS1 filtering is completed, Skyline does not respond as soon as I click anything. Checking my PC memory and CPU performance, it does not look like they are the reason. Do you have any suggestions to fix this?

Nick Shulman responded:  2024-04-25 06:09
What exactly do you mean by "not responding"? Are you saying that Task Manager says that Skyline is "Not Responding"?
Can you send us a screenshot of what the Skyline window looks like when it is in this state?

If Task Manager does not say that Skyline is "Not Responding" but clicking on anything in Skyline does not do anything, the problem might be that Skyline is trying to show a message box, but, for some reason, the message box appeared behind the Skyline window instead of in front of it. We have had a few bugs like that. I am not sure exactly what you can do to be able to see the message box if you are in that state. You might be able to press the Windows key and the letter "D" at the same time, which will minimize all of the windows on the screen. Sometimes after you do that you might be able see the message box that was hidden before.

It might be helpful if you could send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

Files which are less than than 50MB can be attached to this support request. You can always upload larger files here:

If Skyline is really stuck, you might not be able to use the "File > Share" menu item, and it's also possible that seeing your Skyline document might not be sufficient for us to figure out what is going wrong.

You might have to also send us all of your peptide search result files and mzML files.
You could package everything up into a zip file and upload it to that same spot:

-- Nick
y nishimura responded:  2024-04-26 05:12
Hi Nick,

Thank you for your response. Skyline is working in Task Manager, but it freezes as soon as I open the Skyline document saying "Nor Responding". Please see the attached screenshot. I also tried to press the Windows key and the letter "D" at the same time, but I did not see any error messages. I will share search results and mzML files with you, but I'd prefer send them to you directory. Could you provide your email please?

Thank you in advance for your support.
Nick Shulman responded:  2024-04-26 07:59
I will send you an email message directly.

-- Nick