Cannot see peaks when data is imported, just shows as a flat line

ayacoob

2024-07-18 10:12

I saw this thread and it seemed similar to my issue: https://skyline.ms/announcements/home/support/thread.view?rowId=49486

I tried to follow the steps (changing filters, turning off filters, etc.), but my peaks still look the same (nonexistent lol). I do have one spectrum that does show data, and it's a 60-minute runtime whereas the others are 30-min. It doesn't seem to be an issue with the intensity. I feel it's some filtering issue, but I'm not experienced enough with Skyline.

Thanks for any help anyone can give me!

Nick Shulman responded:	2024-07-18 10:16
Can you send us your Skyline document and one or more of your raw files? 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. The "Share Skyline Document" dialog in Skyline gives you the option to include the raw files in the .zip or you can send them to us separately. Files which are less than 50MB can be attached to these support requests. You can always upload larger files here: https://skyline.ms/files.url -- Nick

ayacoob responded:	2024-07-18 11:20
Thanks for coming to the rescue again, Nick! I've attached the files here. Sorry for the delay; the files took a long time to compress.

Nick Shulman responded:	2024-07-18 12:21
Thank you for uploading that zip file. I see that the "Precursor mass analyzer" at "Settings > Transition Settings > Full Scan" is set to "Centroided". I think you should change that to something else such as "TOF". After you do that, you need to use the "Reimport" button at "Edit > Manage Results" so that Skyline will extract chromatograms again. There is a bug in the way that Skyline figures out the m/z range that was measured in centroided Agilent data. There is some information about how this impacts chromatogram extraction here: https://skyline.ms/announcements/home/support/thread.view?rowId=52933 I was supposed to fix this bug a few months ago but then I ran into some issues with the fix that I could not figure out: https://github.com/ProteoWizard/pwiz/pull/2957 Thank you for reminding me about this bug. I will try to fix this soon, but, for now, you should avoid using "Centroided" with Agilent data. -- Nick

ayacoob responded:	2024-07-18 12:43
Thanks, Nick! You rock. I appreciate your help. Have a nice weekend!