Development of a Computational Tool for Automated Interpretation of Intact O-Glycopeptide Tandem Mass Spectra from Single Proteins.

Jiangming Huang, Biyun Jiang, Huanhuan Zhao, Mengxi Wu, Siyuan Kong, Mingqi Liu, Pengyuan Yang, Weiqian Cao

Analytical chemistry 2020 May 05

filter terms:

Precise and automated analysis of site-specific O-glycosylation on single proteins is crucial for comprehensive characterization of some important glycoproteins, such as tumor biomarkers and recombinant drug proteins. Mass spectrometry has been proven to be a powerful technique for protein sequencing and N-glycosylation analysis. However, challenges remain in developing computational tools for intact O-glycopeptide analysis, which has greatly hindered the development of mass-spectrometry-based O-glycosylation analysis. Herein, an integrated strategy together with a dedicated automated computational tool termed AOGP was developed for intact O-glycopeptide analysis on single proteins. AOGP utilized de novo sequencing for O-glycans and a database search strategy for peptide backbones. The false discovery rate (FDR) of the identification results was controlled and validated by a mixed Gaussian distribution estimation method. AOGP exhibited superior performance in identifying intact O-glycopeptides of the human erythropoietin with a total of 188 O-glycopeptide spectra reported under 1% FDR. AOGP is developed in Python, is fully open-sourced, and is equipped with a user-friendly interface. Such an easy-operating and robust tool would greatly facilitate O-glycosylation analysis on single proteins in tumor biomarker and recombinant drug protein development.

Citation

Jiangming Huang, Biyun Jiang, Huanhuan Zhao, Mengxi Wu, Siyuan Kong, Mingqi Liu, Pengyuan Yang, Weiqian Cao. Development of a Computational Tool for Automated Interpretation of Intact O-Glycopeptide Tandem Mass Spectra from Single Proteins. Analytical chemistry. 2020 May 05;92(9):6777-6784