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