Comparative glycomic profiling of isotopically permethylated N‐glycans by liquid chromatography/electrospray ionization mass spectrometry

RATIONALE Mass spectrometry based comparative glycomics is essential for disease biomarker discovery. However, developing a reliable quantification method is still a challenging task. METHODS We here report an isotopic labeling strategy employing stable isotopic iodomethane for comparative glycomic profiling by liquid chromatography/electrospray ionization mass spectrometry (LC/ESI‐MS). N‐Glycans released from model glycoproteins and blood serum samples were permethylated with iodomethane ('light') and iodomethane‐ d 1 or ‐ d 3 ('heavy') reagents. Permethylated samples were then mixed at equal volumes prior to LC/ESI‐MS analysis. RESULTS Peak intensity ratios of N‐glycans isotopically permethylated (Heavy/Light, H/L) were almost equal to the theoretical values. Observed differences were mainly related to the purity of 'heavy' iodomethane reagents (iodomethane‐ d 1 or ‐ d 3 ). The data suggested the efficacy of this strategy to simultaneously quantify N‐glycans derived from biological samples representing different cohorts. Accordingly, this strategy is effective in comparing multiple samples in a single LC/ESI‐MS analysis. The potential of this strategy for defining glycomic differences in blood serum samples representing different esophageal diseases was explored. CONCLUSIONS LC/ESI‐MS comparative glycomic profiling of isotopically permethylated N‐glycans derived from biological samples and glycoproteins reliably defined glycan changes associated with biological conditions or glycoproteins expression. As a biological application, this strategy permitted the reliable quantification of glycomic changes associated with different esophageal diseases, including high grade dysplasia, Barrett's disease, and esophageal adenocarcinoma. Copyright © 2013 John Wiley & Sons, Ltd.