Figure 2: The MS/MS CID spectra and ratios of isotopic pairs (quantification ratios) of the representative peptides TPDFESTGLYSAMPR for glycine amidinotransferase (A) and TTVLLADINDFNTVNEIYK for ribonuclease UK114 (B). Peptide quantification ratios (D/H) for RCC (deuterium labeling) and normal (hydrogen labeling) were calculated by Mascot Distiller program using the average area of the first three isotopic peaks across the elution profile. The program merged the Mascot search data and quantification results from each fraction, and peptide ratios for the same sequences obtained from different fractions or at different retention times and charge states were combined for further analysis.