It has been pointed out that having the ability to limit extraction of chromatograms from MS1, in the same way we allow for MS/MS DIA isolation schemes, is desirable in some modern methods employing SIM scans, such as Boxcar.

https://skyline.ms/announcements/home/support/thread.view?rowId=37966

e.g. at least the ability to have a margin like the ones used in SWATH (0.5) to avoid extraction from regions with signal decline in quadrupole isolation.

Here is a related support request where the user ends up requesting the ability to specify MS1 type to avoid needing convert to mzML and filter either MS1 full-range spectra or SIM spectra in files that contain both.

https://skyline.ms/announcements/home/support/thread.view?rowId=37000

Clearly acquisition methods around MS1 are getting more complicated and Skyline hasn't kept up with these new methods.

I would really like to see Skyline support BoxCar MS1. Matt, can you take the lead on this?

https://www.ncbi.nlm.nih.gov/pubmed/29735998

You should be able to get data here:

http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD006109

I can certainly try. How deeply do you want this get into the Skyline UI? Is it just a matter of stitching up the MS1s so they can be treated as a single logical MS1?

It should not impact the Skyline UI. It should just impact how Skyline extracts chromatograms from MS1, making this more like multiple-isolation SIM, from which we only extract isolated ions, than MS1 survey scans, from which we try to extract everything.

Well, reviewing the methods from the paper:

https://static-content-springer-com.offcampus.lib.washington.edu/esm/art%3A10.1038%2Fs41592-018-0003-5/MediaObjects/41592_2018_3_MOESM3_ESM.pdf

It seems like you would need some way to exclude some portion of the isolated range from having ions extracted from it, as is currently possible with our DIA isolation schemes.

Though, even more than DIA, I can imagine the need for these excluded "margins" to be asymmetric, because we really want to extract the entire isotope distribution, which currently means -1 DA to as many as +6 for a triply charged ion, but even assuming we only support +2 (our default - 3 ions - M, M+1, M+2) then we need 1 m/z on the left and 2 m/z on the right for a 3 m/z total of overlap to support full isolation of the ions we currently inspect, since the 0.5 m/z margins are meant only to keep the monoisotopic peak quantitatively isolated.

So, I think this means supporting new UI that allows setting of margins on SIM scans. I think this could be supported with just 2 new values: left margin and right margin.

Maybe add an "Isolation scheme:" field to the Transition Settings - Full-Scan tab in the MS1 filtering section that contains:
All Ions (or Survey?)
SIM (i.e. SIM without margins)
<Add...>

Where Add gives you a form:

Edit SIM Isolation

Name:
[ ]

Margins:
Left: Right:
[ ] [ ]

[OK][Cancel]