Peak Integration

Peak Integration muluneh  2021-06-10
Hi, I have been using Skyline for the last 8 months and I really liked the way it works. I am analyzing MRM data generated with the AB SCIEX instrument. Some of the proteins I work with are less abundant and have a high background. So I need to manually integrate the peaks. We use two fragment ions for each peptide we collect MS data for. Skyline displays the two peaks simultaneously and when I try to edit a peak (Peak B in the Figure) for one of the fragments by moving the vertical line, all the peaks (Peak A) are being affected. Are there any means that I can process the two fragments separately/independently? For now, I am manually deselecting the peak I don't edit, then export the data, and then process the second peak. I am working with several proteins, and this app[roach is taking too much time. Just looking for an efficient approach... Thanks! Muluneh
Nick Shulman responded:  2021-06-10
It is possible to adjust the peak boundaries for one transition. Skyline intentionally makes it difficult to do this, since nearly always you want to use the same integration boundaries for every transition.

To adjust the peak boundaries for a single transition:
1. Select the transition of interest in the Targets tree.
2. Right-click on the chromatogram graph and choose "Transitions > Single".
3. Adjust the peak boundaries on the chromatogram (which you can do either by moving either the start or end of the existing peak boundaries, or by dragging the mouse in the region below the X-axis.

-- Nick
muluneh responded:  2021-06-14
Hi Nick,

Thanks for the reply! It works.