Advancing mass spectrometry–based glycoproteomic software tools for comprehensive site-specific glycoproteome analysis

Glycoproteome analysis at a site-specific level and proteome scale stands out as a highly promising approach for gaining insights into the intricate roles of glycans in biological systems. Recent years have witnessed an upsurge in the development of innovative methodologies tailored for precisely this purpose. Breakthroughs in mass spectrometry–based glycoproteomic techniques, enabling the identification, quantification, and systematic exploration of site-specific glycans, have significantly enhanced our capacity to comprehensively and thoroughly characterize glycoproteins. In this short review, we delve into novel tools in advancing site-specific glycoproteomic analysis and summarize pertinent studies published in the past two years. Lastly, we discuss the ongoing challenges and outline future prospects in the field, considering both the analytical strategies of mass spectrometry and the tools employed for data interpretation.