Vande Moortele Tibo, Verschaffelt Pieter, Huang Qingyao, Doncheva Nadezhda T, Holstein Tanja, Jachmann Caroline, Dawyndt Peter, Martens Lennart, Mesuere Bart, Van Den Bossche Tim
Department of Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.
Department of Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium; VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
Mol Cell Proteomics. 2025 Mar;24(3):100918. doi: 10.1016/j.mcpro.2025.100918. Epub 2025 Jan 27.
Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data. We here introduce PathwayPilot, a web-based application designed to improve metaproteomic data analysis by integrating pathway analysis with peptide- and protein-level data, filling a critical gap in current metaproteomics bioinformatics tools. By allowing users to compare functional annotations across different samples or multiple organisms within a sample, PathwayPilot provides valuable insights into microbial functions. In the re-analysis of a study examining the effects of caloric restriction on gut microbiota, the tool successfully identified shifts in enzyme expressions linked to short-chain fatty acid biosynthesis, aligning with its original findings. PathwayPilot's user-friendly interface and robust capabilities make it a significant advancement in metaproteomics, with the potential for widespread application in microbial ecology and health sciences. All code is open source under the Apache2 license and is available at https://pathwaypilot.ugent.be.
宏蛋白质组学是对环境群落中集体蛋白质组的研究，在理解影响生态系统和人类健康的微生物功能方面发挥着关键作用。通路分析为这些群落中的生化过程提供了结构化的见解。然而，现有的工具都无法有效地将通路分析与肽或蛋白质水平的数据结合起来。我们在此介绍PathwayPilot，这是一个基于网络的应用程序，旨在通过将通路分析与肽和蛋白质水平的数据相结合来改进宏蛋白质组学数据分析，填补当前宏蛋白质组学生物信息学工具中的一个关键空白。通过允许用户比较不同样本或样本内多种生物体之间的功能注释，PathwayPilot提供了有关微生物功能的宝贵见解。在重新分析一项研究热量限制对肠道微生物群影响的研究时，该工具成功地识别出与短链脂肪酸生物合成相关的酶表达变化，与原始研究结果一致。PathwayPilot用户友好的界面和强大功能使其成为宏蛋白质组学领域的一项重大进展，具有在微生物生态学和健康科学中广泛应用的潜力。所有代码根据Apache2许可开源，可在https://pathwaypilot.ugent.be获取。
