Importing daughter scan data from a Xevo TQ-S

Importing daughter scan data from a Xevo TQ-S matthew daly-3  2021-05-11

Hello. I was hoping there was a way of importing daughter scan data acquired on a Xevo TQ-S? My precursors are selected for but then all product ions are monitored. I notice there was a similar question posted in 2017 but I wasn't sure if it had been resolved. Many thanks.

matt.chambers42 responded:  2021-05-14

Hi Matthew,

The easiest way to tell how your spectra looks to Skyline is to open the file in SeeMS. You'll need to install ProteoWizard for that if you haven't already:

Then you'll have an "Open with SeeMS" option in your right-click menu in Windows explorer, which should work with your Waters .raw directories. Give us a screenshot or something of what you see in SeeMS. If your data isn't showing spectra or chromatograms that make sense, then you'll probably have to upload the file so we can take a look.

matthew daly-3 responded:  2021-05-17

Thanks for the quick reply.

I've attached a screenshot of the data opened in SeeMS. It seems like each of my 25 precursors are recorded in different channels and it has recorded the precursor m/z properly.

Thanks, Matt.

matt.chambers42 responded:  2021-05-18

It's hard to tell from that screenshot. Anything on the chromatograms tab?

From what I can tell, a "daughter ion" scan in Waters parlance refers to product ion scans (IUPAC term), aka fragment ion scans. So basically just plain MS2 full scan spectra. Since your precursor ions are preselected rather than data-dependent, your method sounds basically like PRM. As long as you have your precursors in Skyline's target list and the full scan settings set properly, Skyline should your MS2s without a problem.

matthew daly-3 responded:  2021-05-20

Hi Matt.

I've attached another screenshot from SeeMS with the chromatogram tab showing. I have also attached a screenshot of my transition settings - please could you tell me if these look correct? I'm actually having an issue where Skyline is crashing while attempting to import the data now. There are no error messages, the application just closes.

Many thanks, Matt

matt.chambers42 responded:  2021-05-20

Try setting the product mass analyzer to TOF instead of centroided. The Waters reader has an issue with some files crashing when we try to centroid them.

matthew daly-3 responded:  2021-05-25

Changing the analyzer to TOF solved my problem. Thank you.