Analysis of the diﬀerence in protein glycosylation between patients and healthy subjects provides a better understanding of disease progression. Importantly, the comparative analyses of aberrant glycosylation in proteins are known to be useful for diagnosing diseases in clinical practice, where the glycopeptides can be used as analytes to obtain information of different type of glycoforms and glycosylated sites. These glycoproteomic studies need optimal platforms to enrich glycoproteins from complex protein mixtures followed by qualitative and quantitative analysis to determine which proteins are glycosylated, where the glycosylation sites are, and how much the glycoproteins are changed in disease progression.
Recently, mass spectrometry (MS) is widely used to discover glycoprotein biomarkers for their clinical applications. A signiﬁcant advantage of MS is its ability for direct identification and quantification of glycoproteins. Analytical advances of LC-MS/MS have now facilitated bottom-up analysis of glycoproteins to identify hundreds of unique intact glycopeptides from a single experiment in clinical laboratories.
In this presentation, we will show an LC-MS/MS-based platform with GlycoProteomeAnalyzer (GPA) software for high throughput analysis of intact N-and O-linked glycopeptides in proteomics scale. It combines tandem mass spectrometry with database search for glycopeptides and algorithmic suite for accurate annotation of the large-scale MS/MS spectral data from complementary fragmentation modes such as collision-induced dissociation (CID), high-energy collision dissociation (HCD), and electron transfer dissociation (ETD). It shows promise for confident identification less than one percent false discovery rate (FDR) and automated quantification of tryptic glycopeptides of glycoproteins in human blood, urine and tissue samples.