Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
VIB-Center for Plant Systems Biology, Ghent, Belgium.
Methods Mol Biol. 2022;2447:285-296. doi: 10.1007/978-1-0716-2079-3_23.
An increasing numbed and diversity of protein posttranslational modifications are mapped by proteomics. Knowledge of modified protein sites can be of direct relevance to steer downstream functional studies, but such information can be difficult to distill from the numerous individual studies that often report modified sites in supplementary data files. In this chapter, we provide basic instructions and use cases to browse and collect plant protein modifications from over 100 studies in a user-friendly manner with the Plant PTM Viewer. The Plant PTM Viewer ( https://www.psb.ugent.be/PlantPTMViewer ) is a central resource compiling currently 24 modifications types for ten thousands of plant proteins. Next to viewing modifications for a protein of interest, we demonstrate how evolutionary conserved modifications can be retrieved using PTM Blast. In addition, modifications themselves located in a motif or sequence context of interest can be retrieved by PTM search. Altogether, these operations can be performed, are intuitive, and open for non-bioinformatic experts.
蛋白质翻译后修饰的数量和种类不断增加，通过蛋白质组学可以对其进行映射。对修饰蛋白位点的了解可以直接指导下游功能研究，但这些信息很难从经常在补充数据文件中报告修饰位点的众多单独研究中提取出来。在本章中，我们将提供基本说明和用例，以便使用 Plant PTM Viewer 以用户友好的方式从 100 多项研究中浏览和收集植物蛋白修饰。Plant PTM Viewer（https://www.psb.ugent.be/PlantPTMViewer）是一个集中资源，为成千上万的植物蛋白编译了目前 24 种修饰类型。除了查看感兴趣的蛋白质的修饰外，我们还展示了如何使用 PTM Blast 检索进化保守修饰。此外，还可以通过 PTM 搜索检索位于感兴趣的模体或序列上下文内的修饰。总之，这些操作直观且易于操作，即使是非生物信息学专家也可以使用。
