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GproDIA enables data-independent acquisition glycoproteomics with comprehensive statistical control
- Source :
- Nature Communications, Nature Communications, Vol 12, Iss 1, Pp 1-15 (2021)
- Publication Year :
- 2021
- Publisher :
- Springer Science and Business Media LLC, 2021.
-
Abstract
- Large-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. Data independent acquisition (DIA) is an emerging technology with deep proteome coverage and accurate quantitative capability in proteomics studies, but is still in the early stage of development in the field of glycoproteomics. We propose GproDIA, a framework for the proteome-wide characterization of intact glycopeptides from DIA data with comprehensive statistical control by a 2-dimentional false discovery rate approach and a glycoform inference algorithm, enabling accurate identification of intact glycopeptides using wide isolation windows. We further utilize a semi-empirical spectrum prediction strategy to expand the coverage of spectral libraries of glycopeptides. We benchmark our method for N-glycopeptide profiling on DIA data of yeast and human serum samples, demonstrating that DIA with GproDIA outperforms the data-dependent acquisition-based methods for glycoproteomics in terms of capacity and data completeness of identification, as well as accuracy and precision of quantification. We expect that this work can provide a powerful tool for glycoproteomic studies.<br />Data independent acquisition (DIA) proteomics provides deep coverage and high quantitative accuracy, but is not yet well established in glycoproteomics. Here, the authors develop a DIA-based glycoproteomics workflow with stringent statistical controls to enable accurate glycopeptide identification.
- Subjects :
- Proteomics
False discovery rate
Proteome
Computer science
Science
Glycobiology
General Physics and Astronomy
Inference
Proteome informatics
computer.software_genre
Article
General Biochemistry, Genetics and Molecular Biology
Workflow
Polysaccharides
Humans
Data-independent acquisition
Glycoproteins
Profiling (computer programming)
Multidisciplinary
Mass spectrometry
Glycopeptides
Blood Proteins
General Chemistry
Statistical process control
Glycoproteomics
Identification (information)
Benchmark (computing)
Schizosaccharomyces pombe Proteins
Data mining
computer
Algorithms
Subjects
Details
- ISSN :
- 20411723
- Volume :
- 12
- Database :
- OpenAIRE
- Journal :
- Nature Communications
- Accession number :
- edsair.doi.dedup.....4e2cad76149dc0750f708238d9a7df7e