Unscheduled MS raw file

Unscheduled MS raw file aqassab  2019-07-31

I have uploaded a a raw MS files that was created using unscheduled SRM extending from 0-90 minutes. After I uploaded my file to Skyline I noticed that Skyline is showing my peptide in a scheduled time frame (for instance: 10 minutes or 20 minutes) instead of the whole 90 minutes. I tried to figure out whether it was some setting issue but I still couldn't make Skyline display the unscheduled run. I uploaded a zip file named "16 Glycopeptides" for that purpose. Could you please assist me to solve the issue?


Nick Shulman responded:  2019-07-31
Can you send us that file "Glyco_Ref_Plasma_B_Corning_072619.raw"?

The simplest explanation would that those are the time ranges over which there were matching MS2 scans in that .raw file.

Another possibility is that it has something to do with the setting you have "Use only scans within 5 minutes of MS/MS IDs" selected at:
Settings > Transition Settings > Full Scan > Retention Time Filtering

For a PRM experiment, you would normally set that to "Use all matching scans" since all of the scans that you have told the mass spectrometer to correct should probably be used.

Your Skyline document does not have a spectral library, so I would not expect the Retention Time Filtering setting to have any effect. Did you maybe used to have a spectral library in this document when you extracted chromatograms and afterwards you removed it at "Settings > Peptide Settings > Library"?

It's also not likely to be the retention time filtering settings since some of your chromatograms ended up being 15 or 20 minutes long.

-- Nick