Matrix Effect on Chemical Isotope Labeling and Its Implication in Metabolomic Sample Preparation for Quantitative Metabolomics

Matrix effect from various constituents in biological samples can reduce the accuracy of quantitative metabolomics. Differential chemical isotope labeling liquid chromatography mass spectrometry (CIL LC-MS) can overcome the matrix effect on MS detection based on measuring the intensity ratios of metabolite peak pairs detected in a mixture of a light-isotope labeled sample and a heavy-isotope labeled reference sample. However, the chemical labeling process itself may encounter matrix effect which can influence the overall quantitative results. In this work, we report the effects of salts and buffers commonly present in metabolomic samples on dansylation labeling. It is shown that high concentrations of NaCl and phosphate buffer (>50 mM) or PBS can reduce or enhance the labeling efficiencies of metabolites. By maintaining similar matrix contents in an individual sample vs. a reference sample, relative quantification of metabolites can be performed without compromising the metabolomic profiling results. For samples containing varying amounts of high salts such as urine, we demonstrate that the matrix effect can be largely overcome by diluting the original sample before dansylation labeling (e.g., 4-fold dilution for urine).