The user has areas with "ugly peaks" that Skyline sees as noise, so explicit retention times don't help. They'd like to be able to force Skyline to integrate the signal in those windows even if Skyline doesn't see a peak there. One challenge here is Skyline's insistence on background subtraction, since to us it all looks like background.
and this related internal email thread:
Brian Pratt <email@example.com>
Nov 10, 2020, 11:59 AM (3 days ago)
to Brendan, Skyline
Yes, I was imagining that this would have to be explicitly requested by the user.
On Tue, Nov 10, 2020 at 11:54 AM Brendan MacLean <firstname.lastname@example.org> wrote:
Absolutely, we get into trouble, because we do background subtraction. Without a peak-like shape that can be close to zero even if there is a great deal of signal. Though, Nick has recently done some work to avoid background subtraction for SureQuant. So, it might be possible to apply that mode to this case. We do probably need some kind of indicator ("checkbox") that the user truly wants to do this, as we already have for SureQuant. We don't want to just go integrating the entire Explicit Retention Time range just because we can't find a peak as a default behavior.
On Mon, Nov 9, 2020 at 9:57 AM Brian Pratt <email@example.com> wrote:
It seems like it wouldn't be that hard to add a flag that tells chromatogram extraction to integrate the entire explicit RT window when it doesn't see a proper peak, or are there subtleties I'm missing that make this difficult to pull off? That is, do we get into trouble with a signal that doesn't have a peak-like shape?