PGlycoQuant with a deep residual network for quantitative glycoproteomics at intact glycopeptide level enabling the functional exploration of site-specific glycosylation

ABSTRACT: Interpreting large-scale glycoproteomic data for intact glycopeptide identification has been tremendously advanced by software tools. However, software tools for quantitative analysis of intact glycopeptides remain lagging behind, which greatly hinders exploring the differential expression and functions of site-specific glycosylation in organisms. Here, we report pGlycoQuant, a generic software tool for quantitative intact glycopeptide analysis, supporting both primary and tandem mass spectrometry quantitation for multiple quantitative strategies. pGlycoQuant advances in glycopeptide evidence matching through applying a deep learning model that reduces missing values for glycopeptide quantification by over 60% compared with Byologic, MSFragger-Glyco and Skyline, as well as an optional function of Match-In-Run (MIR) algorithm for more quantitative coverage of glycopeptides, thus greatly expanding the quantitative function of several powerful search engines, currently including pGlyco 2.0, pGlyco3, Byonic and MSFragger-Glyco. The pGlycoQuant-based site-specific N-glycoproteomic study conducted here quantifies 6435 intact N-glycopeptides in three hepatocellular carcinoma cell lines with different metastatic potentials and, together with in vitro molecular biology experiments, illustrates core fucosylation at site 979 of the L1 cell adhesion molecule (L1CAM) as a potential regulator of HCC metastasis. pGlycoQuant is freely available at https://github.com/Power-Quant/pGlycoQuant/releases. We have demonstrated pGlycoQuant to be a powerful tool for the quantitative analysis of site-specific glycosylation and the exploration of potential glycosylation-related biomarker candidates, and we expect further applications in glycoproteomic studies.

INSTRUMENT(S): Orbitrap Fusion ETD

ORGANISM(S): Saccharomycetales (ncbitaxon:4892) Homo Sapiens (ncbitaxon:9606) Schizosaccharomyces Pombe (ncbitaxon:4896)

SUBMITTER: Weiqian Cao  

PROVIDER: MSV000089484 | MassIVE | Mon May 16 13:47:00 BST 2022

REPOSITORIES: MassIVE