|L/H Area Ratio Mismatch||germolus||2021-05-17|
I am working on the same data which I mentioned in this earlier post but now a bit further down the pipeline. I'm quantifying small derivatized metabolites, and using internal standard additions (13C6) to make ratios.
Skyline does this, as well as a cal curve and quantification, but I'm working with an external (MATLAB) pipeline to process the exports. Upon checking the peak area ratios that Skyline exported, and those which I calculate manually by using the ratio of light-to-heavy area, the two answers are slightly different. For example:
8/17 = 0.4705
This probably wouldn't be a big deal if the peak areas were really large, but what I'd like to know is if there's something I missed. I used glutamic acid because, unlike some of the other molecules, I only have the precursors for light and heavy in the doc. As far as I can tell, there isn't another molecule that would be incorporated as in cases where quantifying peptides via multiple transitions.
When Skyline exports peak areas, are they not the same as the ones it used to calculate the light/heavy ratios?