|Extracting precursor intensities from MS2 targeted scan||kentsisresearchgroup||2018-12-20|
Dear Skyline community,
we used a Thermo Fusion Orbitrap to collect targeted MS2 of peptides, with an isolation window including two isotopologues. We are now trying to use Skyline to quantify these peptides based on their precursor intensities, extracted from these MS2 scans (the precursors are indeed detected, based on inspection of the spectra). However, for most peptides the light isotopologue is not extracted at all by Skyline, despite being in the targets list.
Can this depend on the scan header? Does the software filter spectra in any way, for example based on the nominal target mass in the header? Is there anyway to force Skyline to use all scans covering a mass range containing both isotopologues?
Thank you very much in advance for your help,