Hello,

I ran three different m/z from a compound as shown in the transition list attached on Agilent QQQ. I can see the peaks fine at retention time around 4min for two transitions and less than 1min for one transition from Agilent Quantitative Analysis software. However, when I load the same raw files onto Skyline, I do not see any peaks and the retention time window is shown only up to 1.2min for the chromatograms which does not cover where the peaks are supposed to be in. Even after changing the explicit retention time and window, the chromatograms stay the same and I do not see anything.
I have attached the transition list, raw files, and Skyline template.

Please let me know how I can go about resolving this problem.

Thank you.