Straightforward and Highly Efficient Strategy for Hepatocellular Carcinoma Glycoprotein Biomarker Discovery Using a Nonglycopeptide-Based Mass Spectrometry Pipeline

Efficient detection of aberrant glycoproteins in serum is particularly important for biomarker discovery. However, direct quantitation of glycoproteins in serum remains technically challenging because of the extraordinary complexity of the serum proteome. In the current work, we proposed a straightforward and highly efficient strategy by using the nonglycopeptides releasing from the specifically enriched glycoproteins for targeted glycoprotein quantification. With this so-called nonglycopeptide-based mass spectrometry (NGP-MS) strategy, a powerful and nondiscriminatory pipeline for hepatocellular carcinoma (HCC) glycoprotein biomarker discovery, verification, and validation has been developed. First, a data set of 234 NGPs was strictly established for multiple-reaction monitoring (MRM) quantification in serum. Second, the NGPs enriched from 20 HCC serum mixtures and 20 normal serum mixtures were labeled with mTRAQ reagents (Delta 0 and Delta 8, respectively) to find the differentially expressed glycoproteins in HCC. A total of 97 glycoprotein candidates were preliminarily screened and submitted for absolute quantitation with NGP-based stable-isotope-labeled (SID)-MRM in the individual samples of 38 HCC serum and 24 normal controls. Finally, 21 glycoproteins were absolutely quantified with high quality. The diagnostic sensitivity results showed that three glycoproteins, beta-2-glycoprotein 1 (APOH), alpha-1-acid glycoprotein 2 (ORM2), and complement C3 (C3), could be used for the discrimination between HCC patients and healthy people. A novel glycoprotein biomarker panel [APOH, ORM2, C3, and alpha-fetoprotein (AFP)] has proven to outperform AFP, the known HCC serum biomarker, alone, in this study. We believe that this strategy and the panel of glycoproteins might hold great clinical value for HCC detection in the future.