Can skyline do manual integration if no peak detected

Can skyline do manual integration if no peak detected xue shi  2021-12-16

Dear Skyline team,
Can skyline integrate baseline if no peak detected?
Please see attachment, at retention time 3.1, there is no peak detected in this sample. Can skyline integrate the baseline or does it offer manual integration? we need a number instead 0 for other data process purpose.
Thank you,
Xue Shi

Nick Shulman responded:  2021-12-16
You can always choose a new peak by clicking at a point below the X-axis and dragging the mouse horizontally to select the new peak boundaries.

By the way, another user also asked a similar question about how to integrate a peak manually when Skyline had not found any peaks:
For this other user, the reason that Skyline was not finding any peaks was that the "Explicit Retention Time Window" value that they had set in the Document Grid was much too small a number, so Skyline was only looking for candidate peaks in a very small time window around the explicit retention time.
I suspect the same thing might be going wrong for you. In your screenshot, I would have expected Skyline to detect a candidate peak at 3.75 minutes, so it must be that a small Explicit Retention Time Window is preventing Skyline from looking for peaks at that time. If the Explicit Retention Time Window has been specified for a molecule, it would usually be displayed on the chromatogram graph as a yellow rectangle centered around the Explicit Retention Time line on the graph. The fact that I do not see any yellow rectangle there makes me think that you have specified a very small value for the Explicit Retention Time Window.
You should probably change to a higher number of blank out the Explicit Retention Time values that you may have specified for your molecules in the Document Grid.
-- Nick
xue shi responded:  2021-12-17
Hi Nick,
But even, I add the retention time window to 2 minutes. it showed the yellow rectangle. but still not integrate peaks.
I tried to manual integrate it, but it only let me zoom the peak instead of manual integrate peak. Please find attachment what I have tried.
Could you please let me know how I can manual integrate it?
Nick Shulman responded:  2021-12-17
You should point the mouse at a point below the X-axis on the graph and drag the mouse horizontally. When you release the mouse, Skyline will choose a peak which extends from where you started the drag to where you released it.

Clicking and dragging underneath the X-axis is the way to manually integrate a peak when there are no peaks available to click on.
-- Nick