Functional Proteomics aims to the identification of in vivo protein-protein interaction (PPI) in order to piece together protein complexes, and therefore, cell pathways involved in biological processes of interest. Over the years, proteomic approaches used for protein-protein interaction investigation have relied on classical biochemical protocols adapted to a global overview of protein-protein interactions, within so-called “interactomics” investigation. In particular, their coupling with advanced mass spectrometry instruments and innovative analytical methods led to make great strides in the PPIs investigation in proteomics. In this review, an overview of protein complexes purification strategies, from affinity purification approaches, including proximity-dependent labeling techniques and cross-linking strategy for the identification of transient interactions, to Blue Native Gel Electrophoresis (BN-PAGE) and Size Exclusion Chromatography (SEC) employed in the “complexome profiling”, has been reported, giving a look to their developments, strengths and weakness and providing to readers several recent applications of each strategy. Moreover, a section dedicated to bioinformatic databases and platforms employed for protein networks analyses was also included.

功能蛋白质组学的目的是鉴定体内蛋白质-蛋白质相互作用（PPI），以便将蛋白质复合物和涉及的生物学过程中涉及的细胞途径拼凑在一起。多年来，用于蛋白质-蛋白质相互作用研究的蛋白质组学方法一直依赖于经典的生化方案，该方案适用于所谓的“蛋白质组学”研究中的蛋白质-蛋白质相互作用的全球概览。特别是，它们与先进的质谱仪和创新的分析方法相结合，在蛋白质组学的PPI研究中取得了长足的进步。在这篇综述中，对蛋白质复合物的纯化策略进行了概述，包括亲和纯化方法，据报道，包括邻近依赖性标记技术和用于鉴定瞬时相互作用的交联策略，以及“复杂组分析”中采用的蓝色天然凝胶电泳（BN-PAGE）和尺寸排阻色谱（SEC），他们的发展，优势和劣势，并为读者提供每种策略的几种最新应用。此外，还包括专门用于蛋白质网络分析的生物信息数据库和平台的部分。