瑞士苏黎世联邦理工学院Matthias Gstaiger等研究人员，合作开发出用于解构蛋白质复合物的超深度相互作用蛋白质组学。相关论文于2024年3月26日在线发表于国际学术期刊《自然—方法学》。

研究人员表示，大多数蛋白质都以大分子组合的形式存在，它们是调节和催化大多数细胞过程的关键功能单元。亲和纯化感兴趣的蛋白质并结合液相色谱-串联质谱法（AP-MS），是鉴定相互作用蛋白质的首选方法。然而，AP样品中同时存在的复杂亚型的组成不能通过一次AP-MS实验来解决，而需要通过多次时间和资源密集型的相互AP-MS实验进行计算推断。

研究人员介绍了质谱深度相互作用组剖析（DIP-MS），它结合了AP与blue-native-PAGE分离、质谱数据独立采集和基于深度学习的信号处理，可在一次实验中解析共享相同诱饵蛋白的复杂亚型。研究人员应用DIP-MS探测了人类预折叠蛋白家族复合物的组织结构，解析了不同的预折叠蛋白整体和亚复合物变体、复合物与复合物之间的相互作用以及具有实验验证的新亚基的复合物亚型。这些研究结果表明，DIP-MS能以前所未有的深度和分辨率揭示蛋白质组的模块性。

附：英文原文

Title: DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes

Author: Frommelt, Fabian, Fossati, Andrea, Uliana, Federico, Wendt, Fabian, Xue, Peng, Heusel, Moritz, Wollscheid, Bernd, Aebersold, Ruedi, Ciuffa, Rodolfo, Gstaiger, Matthias

Issue&Volume: 2024-03-26

Abstract: Most proteins are organized in macromolecular assemblies, which represent key functional units regulating and catalyzing most cellular processes. Affinity purification of the protein of interest combined with liquid chromatography coupled to tandem mass spectrometry (AP–MS) represents the method of choice to identify interacting proteins. The composition of complex isoforms concurrently present in the AP sample can, however, not be resolved from a single AP–MS experiment but requires computational inference from multiple time- and resource-intensive reciprocal AP–MS experiments. Here we introduce deep interactome profiling by mass spectrometry (DIP-MS), which combines AP with blue-native-PAGE separation, data-independent acquisition with mass spectrometry and deep-learning-based signal processing to resolve complex isoforms sharing the same bait protein in a single experiment. We applied DIP-MS to probe the organization of the human prefoldin family of complexes, resolving distinct prefoldin holo- and subcomplex variants, complex–complex interactions and complex isoforms with new subunits that were experimentally validated. Our results demonstrate that DIP-MS can reveal proteome modularity at unprecedented depth and resolution.

DOI: 10.1038/s41592-024-02211-y

Source: https://www.nature.com/articles/s41592-024-02211-y