Hi all,
A colleague has performed a scheduled PRM, including a full ms scan in each cycle. Then he has created a Skyline project to analyze the targets both at the precursor and fragment level. Now we have a question about the y-axis values displayed when the EIC chromatograms of multiple peptides are displayed (when you highight a peptide list or a protein) as in the image attached. Are the values the summed intensity of all transitions? Precursor or fragment transitions? Is it only the intensity of the highest transition?
I hope all is going well and hope to hear back from you.
Sincerely,
JC