Hello! As the title states I'm having trouble doing PRM on small molecule targets when the data was collected with an inclusion list. When collecting data with an inclusion list the precursor targets get "shuffled" into the available MS2 events on the fly. On my Sciex qTOF they don't always get put into the same experiment (sciex terminology for ms events per duty cycle), where the 1st experiment is a TOFMS scan, followed by several experiments for the MS2 events.

This is an issue when trying to integrate with the vendor software, since I have to choose one of the numbered ms2 events to quantitate from across the entire chromatogram and samples, yet it will not necessarily fall into the same experiment.

When attempting to integrate with skyline, I could not tell if it was operating in the same way.

Can skyline pull out any ms2 events that are from a particular precusor, since I know those well, and look for the transitions I tell it? Or does it also use the same ordered ms2 event across the entire chromatogram?