Peak picking MS1-only data

Peak picking MS1-only data lparsons  2019-01-31

Is there a way that I can import MS1-only data to skyline for peak picking? Previously I have used other software to do the peak picking and then taken the results from that in as a list for Skyline, is there a way that Skyline can pick peaks for me? I have ~12 files in a current data set, I would like for Skyline to pick peaks from them and then produce a consensus list of peaks and intensities across the files (functions I would normally do in OpenMS). I was looking at the "Skyline MS1 Full-Scan Filtering" tutorial though it seems to expect that I have a list of peaks ready to go to give to Skyline.

thank you

Brian Pratt responded:  2019-01-31

Hi Lee,

Skyline is for targeted mass spec - it assumes that you have some sense of what you're looking for in your experiment, and will work to confirm that there are indeed peaks for your targets. So it does need targets before it looks for peaks, yes. It won't just look for peaks in the abstract sense.

Thanks for using the Skyline support board!

Brian Pratt