Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Maximus-von-Imhof Forum 3, 85354 Freising, Germany.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W459-64. doi: 10.1093/nar/gkt436. Epub 2013 May 31.
Regulated intramembrane proteolysis (RIP) is a critical mechanism for intercellular communication and regulates the function of membrane proteins through sequential proteolysis. RIP typically starts with ectodomain shedding of membrane proteins by extracellular membrane-bound proteases followed by intramembrane proteolysis of the resulting membrane-tethered fragment. However, for the majority of RIP proteases the corresponding substrates and thus, their functions, remain unknown. Proteome-wide identification of RIP protease substrates is possible by mass spectrometry-based quantitative comparison of RIP substrates or their cleavage products between different biological states. However, this requires quantification of peptides from only the ectodomain or cytoplasmic domain. Current analysis software does not allow matching peptides to either domain. Here we present the QARIP (Quantitative Analysis of Regulated Intramembrane Proteolysis) web server which matches identified peptides to the protein transmembrane topology. QARIP allows determination of quantitative ratios separately for the topological domains (cytoplasmic, ectodomain) of a given protein and is thus a powerful tool for quality control, improvement of quantitative ratios and identification of novel substrates in proteomic RIP datasets. To our knowledge, the QARIP web server is the first tool directly addressing the phenomenon of RIP. The web server is available at http://webclu.bio.wzw.tum.de/qarip/. This website is free and open to all users and there is no login requirement.
调控的膜内蛋白水解（RIP）是细胞间通讯的关键机制，通过顺序蛋白水解调节膜蛋白的功能。RIP 通常从细胞膜结合蛋白酶对膜蛋白的外切结构域脱落开始，随后是产生的膜连接片段的跨膜蛋白水解。然而，对于大多数 RIP 蛋白酶，其相应的底物，因此它们的功能，仍然未知。通过基于质谱的定量比较不同生物学状态下的 RIP 底物或其切割产物，可以在蛋白质组范围内鉴定 RIP 蛋白酶底物。然而，这需要仅对胞外域或胞质域的肽进行定量。当前的分析软件不允许将肽与任一个域匹配。这里我们介绍了 QARIP（调控的跨膜蛋白水解的定量分析）网络服务器，它将鉴定的肽与蛋白质的跨膜拓扑结构匹配。QARIP 允许分别确定给定蛋白质的拓扑结构域（胞质、胞外）的定量比值，因此是蛋白质组 RIP 数据集的质量控制、定量比值的改进和新底物鉴定的有力工具。据我们所知，QARIP 网络服务器是第一个直接针对 RIP 现象的工具。该网络服务器可在 http://webclu.bio.wzw.tum.de/qarip/ 获得。该网站是免费的，对所有用户开放，无需登录。
