Issue 730: Peak MS1 integration with FAIMS

issues
Status:open
Assigned To:matt.chambers42@gmail.com
Type:Defect
Area:Skyline
Priority:2
Milestone: 
Opened:2020-05-15 by blaine roberts21202
Changed:2020-05-18 by matt.chambers42
Resolved:
Resolution:
Closed:
2020-05-15 blaine roberts21202
Title»Peak MS1 integration with FAIMS
Assigned ToGuest»Brendan MacLean
Type»Defect
Area»Skyline
Priority»2
I am working with FAIMS data collected on an Orbitrap. I am using a 2CV scheme and the issue is that integration is difficult because the peaks have both CV voltage data displayed (i.e. -50, -70V) which causes a large up and down between CV scans.

Is there a way to display only one CV scan?
Is there an automated way to display just the most abundant CV scan? Maybe something like selecting between charge states or the optimum CV maybe could be determined from the library spectra?

Attached is an image to show how the integration range was only between 2 points in the CV cycle. This is the typical integration range selected. Only in really high abundant peptides or peptides that appear in both CV scans does a normal peak integration occur.

I tried setting up an ion mobility predictor using the results but this does not populate with peptides as it does with drift tube ion mobility data.

Blaine
 
 Screen Shot 2020-05-15 at 6.34.30 PM.png

2020-05-17 Brendan MacLean
Assigned ToBrendan MacLean»matt.chambers42@gmail.com
Notify»Nick Shulman;Brian Pratt;Kaipo Tamura;Brendan MacLean
Wish this had started on the support board, but since it may lead to a fix in the software, I will leave it here and just make sure everyone gets email about it.

Starting with assigning to Matt. Is there a workaround here with MSConvert to generate mzML with just one FAIMS CoV?

Blaine, it would be best for you to post an example raw data file to:

https://skyline.ms/files.url

Also, ideally the Skyline document by using File > Share to create a .sky.zip.

2020-05-18 matt.chambers42
No there's currently no filter on ion mobility (of any kind) but it wouldn't be hard to add (at least on a scan-by-scan basis).

2020-05-18 matt.chambers42
Actually...since this is Thermo data, if the CV is specified in the scan filter, you can use the thermoScanFilter filter, something like:
--filter "thermoScanFilter contains include CV=-50"
which would accept spectra only if they include CV=-50 in their scan filter. This filter on the Thermo scan filter is not available in the GUI right now so you'll have to use command-line msconvert.exe.