Hello,

I am currently setting up a PRM method, but I am having some issues with one of my files. I have 42 peptides and set up a PRM run on a QExactive without full-scan or scheduling.
The first time the sample was loaded in to Skyline I was only able to detect peaks for 3 peptides. I was not sure if it is an instrument method setup issue, so I repeated the run this time only including 13 peptides in the inclusion list (with two detected in the previous run included), but this time I have no chromatograms for any of the peptides. Looking at the raw file there is no visible problem and the two runs look very similar. I also did a DDA run to see if I made a mistake with the setup, but it does not seem to be the case.

I must be missing something in the setup but I am not able to find where the problem is.

Please find attached the raw files as well as the Skyline document (Skyline version: 64-bit, 20.1.0.155).

Thank you very much for the help in advance!

Best,
Anna