Pancreatic cysts are pockets of fluid containing proteins leached out of the pancreatic duct and pancreatic microenvironment. It is known from emerging data that pancreatic cyst fluid is rich with proteins that can serve as potential biomarkers for pancreatic cancer. However, not all pancreatic cysts are potential pancreatic cancer precursors; hence there is the need to properly differentiate the types of pancreatic cyst to enhance the discovery of potential biomarkers for pancreatic cancer. Our work focuses on targeting specific proteins and protein glycoforms to distinguish the different types of pancreatic cyst and investigate these proteins as potential biomarkers. An online automated sample fractionation platform designed in our laboratory that has an advantage of targeting specific protein glycoforms was applied in enriching for glycoproteins. The platform consists of abundant protein depletion followed by Multiple Lectin Affinity Chromatography (M-LAC) enrichment and sample desalting/concentration. Fractions collected were subject to digestion followed by LC-MS/MS analysis. Our experimental results show that 135 glycoproteins differentiate between the cyst types, and about 14 glycoproteins were observed to have significant fold change. These proteins may be targets for validation as biomarker candidates and are currently under investigations in our laboratory. Research funded by NCI.