|Is L/H ratio corrected for shift in isotope patterns?||Tobi||2018-12-05|
Dear skyline team,
reading this nice technical note ( http://www.isotope.com/userfiles/files/assetLibrary/PRT_MACCOSS.pdf ) brings me to ask if and which corrections skyline applies to SILAC ratios when quantification is not based on the whole isotope cluster but just on the precursor or fragments from isolating just the precursor. (want to make sure i dont accidentially apply correction twice)
The issue is well illustrated in figure 3 of the linked pdf, stating that the shape of the heavy peptide is shifted towards the precursor with the heavy precursor intensity beeing up to 10% higher in a 1:1 light:heavy mix (depending on the type of labeling). Adding up intensities of precursor plus isotopes before calculating the ratio evens out this shift, but this is not happening fully in PRM and quantification on the precursor level.
It would be great getting a short reply.