AUTHOR=Mao Yonghong , Su Tao , Lin Tianhai , Yang Hao , Zhao Yang , Zhang Yong , Dai Xinhua 

TITLE=Comprehensive Plasma N-Glycoproteome Profiling Based on EThcD-sceHCD-MS/MS

JOURNAL=Frontiers in Chemistry

VOLUME=Volume 10 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/chemistry/articles/10.3389/fchem.2022.920009

DOI=10.3389/fchem.2022.920009

ISSN=2296-2646

ABSTRACT=Glycoproteins are involved in a variety of biological processes. More than one-third of the plasma protein biomarkers of tumors approved by the FDA are glycoproteins, which could improve the diagnostic specificity and/or sensitivity. Therefore, it is of great significance to perform the systematic characterization of plasma N-glycoproteome. In previous studies, an integrated method based on combinatorial peptide ligands library (CPLL) and stepped collision energy/higher-energy collisional dissociation (sceHCD) was developed by us for comprehensive plasma N‑glycoproteome profiling. Recently, we presented a new fragmentation method, EThcD-sceHCD, which outperformed sceHCD in the accuracy of identification. Herein, we integrated CPLL into EThcD-sceHCD, and compared the performance of different mass spectrometry dissociation methods (EThcD-sceHCD, EThcD and sceHCD) in the intact N-glycopeptides analysis of prostate cancer plasma. The results illustrated that EThcD-sceHCD was better than EThcd and sceHCD in the numbers of identified intact N-glycopeptides (two folds). A combination of sceHCD and EThcD-sceHCD methods can cover almost all glycoproteins (96.4%) and intact N-glycopeptides (93.6%), indicating the good complementarity between the two. Our study has a great potential for the medium- and low-abundance plasma glycoprotein biomarker discovery.