Here is a thread where Brendan talks about the relationship between the resolution and the extraction width:
https://skyline.gs.washington.edu/labkey/announcements/home/support/thread.view?rowId=22685

Here is a thread where I give the formula for converting the resolving power number (which I might be erroneously calling "resolution") to ppm for a particular m/z for the Orbitrap here:
https://skyline.gs.washington.edu/labkey/announcements/home/support/thread.view?entityId=a6ebc95f-05ec-1033-bad2-da202582f4ca&_anchor=22458#row:22458

If you are using a different type of mass analyzer than the Orbitrap, let me know, and I will figure out what the formula is that Skyline uses to convert from the resolving power to extraction width.

In our field, people frequently talk about "resolution" when they mean "resolving power". Resolution is the FHWM in m/z units of a peak. If instead, you are talking about a unitless number in the 10,000s for most modern mass spectrometers (e.g. 17,500 or 20,000 or 40,000) then you are actually talking about a resolving power, from which the resolution can be calculated. Anyway, Nick's references should help.

Ok, much more clear now!
For example in my case I defined a resolving power of 15000. This represents an extraction width of 133.33 ppm (2 x 66.66 ppm). And this is what I see in Skyline.
Thanks very much :)
Gauthier

One last note that it can be extremely useful to view the extraction widths in the Full-Scan graph, which you can get to after extraction by clicking on any point in the chromatogram graph. I usually do this for some representative chromatograms (standards if possible) after importing data for which I am unsure about the resolving power of the instrument.

Also, I will note that in complex samples we have been finding that actually using a single FWHM (i.e. resolution) for extraction produces better results than the 2xFWHM Skyline is currently using by default. The 2xFWHM was originally designed to cover 95% of the peaks in the m/z dimension to their base. Recent empirical assessment has shown us that the reduced selectivity causes more harm than the added ion selection can make up for. So, you should actually be targeting extraction of about 1 FWHM or using 2 x resolving power in the Skyline settings, i.e. if your mass spectrometer achieved 15,000 resolving power, you will likely do better using 30,000 resolving power in the Skyline settings.

See the attached PDF for Full-Scan graph visualization of the extraction windows recently tested in a thorough quantitative study, showing 20,000 rp v. 40,000 rp for 5600 TripleTOF data, where 20,000 was the actual resolving power in the data, but a setting of 40,000 in Skyline produced better results in a complex sample.

I intend to add a check box in the Skyline Transition Settings - Full-Scan for "High selectivity extraction", which causes this change from 2xFWHM to 1xFWHM.

Good luck with your data analysis.

--Brendan

One more question, Brendan. What should I use for the resolving power for MS and MS/MS in the Full Scan section if my 5600 was ran at 30,000 and 15,000 resolving power for MS and MS/MS modes, respectively? As per your last reply here, should I double the 15,000 and insert 30,000 for both?

Thanks a lot!
Kaspar

Hi Kaspar,
You should use Skyline 3.7 and check the "Use high selectivity extraction" checkbox. This will have the effect of doubling the resolving power or instructing Skyline to use only 1 FWHM (resolution width) for extraction. That is, assuming you have a complex sample prep like a cell lysate. This may not be necessary for a low complexity sample, e.g. immunoprecipitation.

This checkbox was added explicitly for the purpose of not having to tell everyone to double the resolving power for these settings. Though, that would have the same effect, if you did not also check this checkbox.

Thanks for asking.

--Brendan