The Role of Data-Independent Acquisition for Glycoproteomics

• Published in: Molecular & cellular proteomics 2021-01, Vol.20, p.100042-100042, Article 100042
• Main Authors: Ye, Zilu, Vakhrushev, Sergey Y.
• Format: Article
• Language: English
• Subjects: Animals; data-independent acquisition; Glycoproteins; glycoproteomics; Glycosylation; Humans; post-translational modification; Proteome; Proteomics - methods; Review
• ISSN: 1535-9476; 1535-9484
• DOI: 10.1074/mcp.R120.002204

Data-independent acquisition (DIA) is now an emerging method in bottom–up proteomics and capable of achieving deep proteome coverage and accurate label-free quantification. However, for post-translational modifications, such as glycosylation, DIA methodology is still in the early stage of development. The full characterization of glycoproteins requires site-specific glycan identification as well as subsequent quantification of glycan structures at each site. The tremendous complexity of glycosylation represents a significant analytical challenge in glycoproteomics. This review focuses on the development and perspectives of DIA methodology for N- and O-linked glycoproteomics and posits that DIA-based glycoproteomics could be a method of choice to address some of the challenging aspects of glycoproteomics. First, the current challenges in glycoproteomics and the basic principles of DIA are briefly introduced. DIA-based glycoproteomics is then summarized and described into four aspects based on the actual samples. Finally, we discussed the important challenges and future perspectives in the field. We believe that DIA can significantly facilitate glycoproteomic studies and contribute to the development of future advanced tools and approaches in the field of glycoproteomics. [Display omitted] •Protein glycosylation and challenges in glycoproteomics.•Data-independent acquisition for deglycosylated and intact N-linked glycopeptides.•Unbiased screening of oxonium ions from all glycopeptide precursors.•Glyco–data-independent acquisition on mucin-type O-glycopeptides. As a highly abundant and diverse post-translational modification, protein glycosylation is challenging to characterize in various approaches including MS. In MS-based proteomics, data-independent acquisition (DIA) has been advanced rapidly and showed outstanding analytical performances. DIA now started to be applied in different facets of glycoproteomics, including deglycosylated and intact N-linked and O-linked glycopeptides, and screening of oxonium ions. We summarized current applications of DIA in glycoproteomics and discussed its limitations and perspectives.