Improving the Depth and Reliability of Glycopeptide Identification Using Protein Prospector.

IF 6.1 2区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Molecular & Cellular Proteomics Pub Date : 2025-02-01 Epub Date: 2025-01-07 DOI:10.1016/j.mcpro.2025.100903

Robert J Chalkley, Peter R Baker

引用次数: 0

Abstract

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.

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利用蛋白质探矿器提高糖肽鉴定的深度和可靠性。

糖基化是蛋白质最常见和最多样化的修饰。它可以影响蛋白质的功能和稳定性，并与许多疾病有关。虽然目前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个挑战，特别是从数据分析方面。在过去的几年中，已经开发了几个软件包，旨在支持组学水平的n链糖肽分析。本研究介绍了用于分析n -糖肽数据的Protein Prospector的发展。结果与其他软件进行了比较，表明Protein Prospector报告的糖肽糖型比竞争软件多。考虑聚糖加合物的优点和缺点也进行了评估，显示考虑它们如何可以纠正以前的错误分配。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Molecular & Cellular Proteomics 生物-生化研究方法

CiteScore

11.50

自引率

4.30%

发文量

131

审稿时长

84 days

期刊介绍： The mission of MCP is to foster the development and applications of proteomics in both basic and translational research. MCP will publish manuscripts that report significant new biological or clinical discoveries underpinned by proteomic observations across all kingdoms of life. Manuscripts must define the biological roles played by the proteins investigated or their mechanisms of action. The journal also emphasizes articles that describe innovative new computational methods and technological advancements that will enable future discoveries. Manuscripts describing such approaches do not have to include a solution to a biological problem, but must demonstrate that the technology works as described, is reproducible and is appropriate to uncover yet unknown protein/proteome function or properties using relevant model systems or publicly available data. Scope: -Fundamental studies in biology, including integrative "omics" studies, that provide mechanistic insights -Novel experimental and computational technologies -Proteogenomic data integration and analysis that enable greater understanding of physiology and disease processes -Pathway and network analyses of signaling that focus on the roles of post-translational modifications -Studies of proteome dynamics and quality controls, and their roles in disease -Studies of evolutionary processes effecting proteome dynamics, quality and regulation -Chemical proteomics, including mechanisms of drug action -Proteomics of the immune system and antigen presentation/recognition -Microbiome proteomics, host-microbe and host-pathogen interactions, and their roles in health and disease -Clinical and translational studies of human diseases -Metabolomics to understand functional connections between genes, proteins and phenotypes