Retention Time Window for Insert Transition List

Retention Time Window for Insert Transition List lparsons  2019-02-08

I am using Skyline to produce AUC values for specific ions observed in MS1-only acquisitions. Previously I would produce a two-column table (M/Z, charge - where charge is set to "1" for all lines) that I would import into Skyline via Edit -> Insert -> Transition List. This works really well though the chromatograms produced for each ion from the list goes across all time (and I presume therefore that the AUC does as well).

Therefore I wanted to try adding a time window in the interest of getting only AUC for a defined time window. I added "Explicit Retention Time" and "Explicit Retention Time Window" back to the list of columns in the Transition List. Then I imported a new list with those four columns through there (assuming that the two new columns are both in units of minutes).

This works fine, however the chromatograms that are drawn for each ion go across the full time of the MS file regardless of how wide or narrow the time window is. Does this mean that the AUC numbers are also produced for the full curve (rather than just the RT +/- the Time Window)? If so, is there something I can do so that only the window is considered?

thank you!

Nick Shulman responded:  2019-02-09
I believe that you can control the length of the chromatogram that gets extracted by going to:
Setting > Transition Settings > Full Scan
At the bottom of that page, there are some options related to whether the chromatogram should be truncated, and I believe choosing the one related to predicted retention time will result in a shorter chromatogram.

After the chromatogram is extracted, Skyline looks for something that is shaped like a peak. The explicit retention time that you specify is a very strong hint as to where Skyline should find that peak, but, I believe, if the chromatogram is completely flat at that point, Skyline might choose a peak somewhere else. (We are trying to think of a way to make "explicit retention time" more explicit so that this never happens).

The area that Skyline reports is always going to be the area between two integration boundaries, and is not dependent on anything that happens with the chromatogram outside of these boundaries. Thus, even if you specify the "Explicit Retention Time Window". Skyline will still look for a peak that overlaps with that window, and will not integrate beyond the boundaries of the peak-shaped thing that Skyline finds.

If you want to actually tell Skyline the real start and end times over which it should integrated, you can use the menu item:
File > Import > Peak Boundaries

-- Nick