Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, USA.
Department of Chemistry, University of Nevada, Reno, Reno, NV, USA.
Methods Mol Biol. 2022;2499:145-154. doi: 10.1007/978-1-0716-2317-6_7.
Posttranslational modifications (PTMs) are critical regulators of protein behavior, and over 200 different types of PTMs have been identified. Recent developments in mass spectrometry technology and sample enrichment approaches have led to a massive expansion in the number of identified PTM types and sites within eukaryotic proteins. As these types of data become increasingly available, it is important to develop additional analysis tools and data repositories to investigate PTM cross talk and larger networks of PTMs. Recently, we developed the Functional Analysis Tools for Post-translational Modifications (FAT-PTM) database, which supports data from publicly available proteomic analyses encompassing eight different types of PTMs and over 49,000 PTM sites. In this chapter, we describe the utility of FAT-PTM for analysis of posttranslationally modified proteins in three different contexts. First, a simple protein search tool is available that allows users to investigate proteins in the Arabidopsis proteome to identify types of PTMs that are associated with the query protein as well as quantitative phosphorylation site changes associated with ten different experimental conditions. Second, FAT-PTM contains a metabolic pathway analysis tool to investigate PTMs in the broader context of over 600 different metabolic pathways compiled from the Plant Metabolic Network. Finally, FAT-PTM contains a comodification tool that can be used to identify groups of proteins that are subject to two or more user-defined PTMs. Overall, FAT-PTM provides a user-friendly platform to visualize posttranslationally modified proteins at the individual, metabolic pathway, and PTM cross-talk levels.
翻译后修饰（PTMs）是蛋白质行为的关键调节因子，目前已鉴定出200多种不同类型的翻译后修饰。质谱技术和样品富集方法的最新进展使得真核生物蛋白质中已鉴定的翻译后修饰类型和位点数量大幅增加。随着这类数据越来越容易获取，开发更多的分析工具和数据存储库以研究翻译后修饰的相互作用和更大的翻译后修饰网络变得很重要。最近，我们开发了翻译后修饰功能分析工具（FAT-PTM）数据库，该数据库支持来自公开可用蛋白质组分析的数据，涵盖八种不同类型的翻译后修饰和超过49,000个翻译后修饰位点。在本章中，我们描述了FAT-PTM在三种不同情况下分析翻译后修饰蛋白质的效用。首先，有一个简单的蛋白质搜索工具，用户可以通过该工具研究拟南芥蛋白质组中的蛋白质，以确定与查询蛋白质相关的翻译后修饰类型以及与十种不同实验条件相关的定量磷酸化位点变化。其次，FAT-PTM包含一个代谢途径分析工具，用于在从植物代谢网络汇编的600多种不同代谢途径的更广泛背景下研究翻译后修饰。最后，FAT-PTM包含一个共修饰工具，可用于识别受到两种或更多种用户定义的翻译后修饰的蛋白质组。总体而言，FAT-PTM提供了一个用户友好的平台，可在个体、代谢途径和翻译后修饰相互作用水平上可视化翻译后修饰的蛋白质。
