Coping with the trade-off between comprehensive identification and accurate quantitation using stable isotope dimethyl labeling

摘要

LC/MS-based proteomics is now a mature technology to a great extent, and often applied for practical evaluations in both basic and clinical sciences. Stable isotope dilution methods are quite necessary and generally used for the accurate relative quantitation. However, identification rate is decreased because sample complexity is artificially increased by mixing different isotopes. In order to avoid this effect, non-labeled samples were analyzed as the reference samples for both identification and quantitation. To match peaks between runs, non-labeled peptide peaks were computationally assigned to isotope-labeled ones by using m/z, retention time, and some physicochemical parameters, leading to comprehensive identification and quantitation, even when retention times were shifted by chemical labeling. This strategy will successfully achieve complete identification and accurate quantitation.