Base Peak not showing in but visible in

Base Peak not showing in but visible in H.Schmidt  2020-07-20

Dear Skyline community,

I have FullScan-PRM data from a QExactive.
Importing those to Skyline let me see the TIC but give me back a "No base peak chromatogram found" when selecting Transitions-->Base Peak.
However, Skyline version shows me the Base Peak of the very same data with Transitions-->Base Peak.
MS1 filtering is setup for both Skyline files in the same way.

I would like to know how I receive the Base Peak in the actual Skyline version.

Best regards.

Nick Shulman responded:  2020-07-20
Skyline 4.2 would extract the Base Peak and TIC chromatograms by looking at each spectrum and finding the highest intensity.

Starting in Skyline 19.1, a change was made so that instead of extracting these chromatograms from spectra, Skyline would use the TIC chromatogram that can usually be found in the raw file. This change was made as an optimization so that Skyline did not have to read every spectrum in the raw file.

One side effect of this change is that the base peak chromatogram is no longer available.

I suppose we could an option to Skyline to tell it to extract the base peak chromatogram in the way that it used to, but so far nobody has asked for that feature. Is it important to you to be able to see the base peak chromatogram in Skyline?
-- Nick
Brendan MacLean responded:  2020-07-20
Matt Chambers is looking into adding this feature back for our Thermo reader. This is the first request we have seen. Thanks for posting to the Skyline support board. It really helps to get user feedback on what seems important before we expend effort on it.