Chalkley Robert J, Baker Peter R
Department of Pharmaceutical Chemistry, University of California, San Francisco, USA.
Department of Pharmaceutical Chemistry, University of California, San Francisco, USA.
Mol Cell Proteomics. 2025 Feb;24(2):100903. doi: 10.1016/j.mcpro.2025.100903. Epub 2025 Jan 7.
Glycosylation is the most common and diverse modification of proteins. It can affect protein function and stability and is associated with many diseases. While proteomic methods to study most post-translational modifications are now quite mature, glycopeptide analysis is still a challenge, particularly from the aspect of data analysis. Several software packages have been developed in the last few years that aim to support omic-level N-linked glycopeptide analysis. This study presents developments of Protein Prospector for the analysis of N-glycopeptide data. Results are compared to other software, showing that Protein Prospector reports many more glycoforms of glycopeptides than competing software. The advantages and disadvantages of considering glycan adducts are also evaluated, showing how considering them can correct previously wrong assignments.
糖基化是蛋白质最常见且最多样化的修饰。它会影响蛋白质的功能和稳定性，并与许多疾病相关。虽然目前用于研究大多数翻译后修饰的蛋白质组学方法已经相当成熟，但糖肽分析仍然是一项挑战，特别是在数据分析方面。在过去几年中已经开发了几个软件包，旨在支持组学水平的N-连接糖肽分析。本研究展示了用于分析N-糖肽数据的Protein Prospector的进展。将结果与其他软件进行比较，表明Protein Prospector报告的糖肽糖型比竞争软件多得多。还评估了考虑聚糖加合物的优缺点，展示了考虑它们如何能够纠正以前错误的归属。
