A need exists for technologies that allow direct quantification of differences in protein expression levels. There is a strategy for absolute quantification (termed AQUA) of proteins and their modification states. AQUA, enabling absolute protein quantitation using stable isotope-labeled peptides and HPLC-MS. By applying a common principle, a labeled molecule as an internal standard, to protein analysis, AQUA has enhanced the abilities of protein researchers to study complex biological samples quantitatively and provided a valuable new tool for proteomics. For proteomics researchers, it facilitates targeted, quantitative studies of not only specific protein expression, but specific amino acid modification as well.