The Role of Data-Independent Acquisition for Glycoproteomics
| Autor: | Sergey Y. Vakhrushev, Zilu Ye |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Proteomics
RT retention time Swath ms Special Issue: Glycoproteomics Glycosylation Proteome FDR false discovery rate SA sialic acid Computer science GLYCOPEPTIDES DIA data-independent acquisition Peptide N-Glycosidase F Review PTMs post-translational modifications COMPUTATIONAL FRAMEWORK Biochemistry Analytical Chemistry ETD electron transfer dissociation 03 medical and health sciences CORE 2 data-independent acquisition SWATH-MS sequential window acquisition of all theoretical mass spectra Animals Humans glycoproteomics Data-independent acquisition LINKED GLYCOSYLATION SRM selected reaction monitoring COLLISION-INDUCED DISSOCIATION Molecular Biology 030304 developmental biology Glycoproteins 0303 health sciences IDENTIFICATION 030302 biochemistry & molecular biology QUANTITATIVE-ANALYSIS Data science Glycoproteomics LC-MS post-translational modification HCD higher-energy collisional dissociation Posttranslational modification DDA data-dependent acquisition PROTEOMICS PNGase F peptide-N-glycosidase F RESOLUTION MASS-SPECTROMETRY Retention time SWAT-MS sequential window acquisition of targeted fragment ions |
| Zdroj: | Ye, Z & Vakhrushev, S Y 2021, ' The Role of Data-Independent Acquisition for Glycoproteomics ', Molecular & Cellular Proteomics, vol. 20, 100042 . https://doi.org/10.1074/mcp.R120.002204 Molecular & Cellular Proteomics : MCP |
| DOI: | 10.1074/mcp.R120.002204 |
| Popis: | 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. Graphical Abstract Highlights • 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. In Brief 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|