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Getting smoother MS1 data while alternating with PRM

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Getting smoother MS1 data while alternating with PRM monica lane  2018-01-19 08:12
 
There are situations where we'd like to monitor both the MS1 and MS2 peaks in PRM (i.e. we alternate full scan with PRM during acquisition). We have issue where MS1 peak shape is very choppy in the Skyline profile (vendor software shows smoother profile). How should we optimize MS1 settings in Skyline - or instrument acquisition - so that peak shape is more comparable to transition peaks?

I've uploaded example case collected replicates of PRM-FullMS-SIM analysis of same sample over time (15 PRTC's spiked into ecoli digest) on QEHF-X. PRM settings: Res@60K/1e6 AGC/119ms for 15 scheduled precursors (+-2min), FullMS settings: Res@60K/ 3e6 AGC/30ms,375-1600 m/z
 
 
monica lane responded:  2018-01-19 09:45
I'm adding the library file attached. The version included in the .zip seems to be corrupt and won't load.
 
Brendan MacLean responded:  2018-01-19 16:15
Hi Monica,
Maybe try widening your mass accuracy to 20 ppm. You are extracting from centroided data with 10 ppm mass accuracy. Sometimes when you see abrupt signal drop-off like that it is because the mass accuracy is not stable enough and your MS1 peak of interest is coming and going within the extraction window.

The most extreme case I saw was a large peak in TASEFDSAIAQDK, but the jaggedness was less extreme in the picked peak. That might be just that the jagged peak is not the right peak and truly falls close to the edge of the extraction range, but m/z variance causes its signal to appear and disappear.

I often try a bit higher mass accuracy constraint (e.g. 20 ppm) when I see stuff like this. It would at least be interesting to see the impact of that.

Thanks for the library update. Not sure how you got what was in the ZIP file, it had no spectra at all, but was otherwise a well formed SQLite file, not corrupted on that level. If you can find a way of reproducing that, it is something we would be interested in fixing.

Thanks for your post to the Skyline support board.

--Brendan