Methods Mol Biol. 2023;2426:243-265. doi: 10.1007/978-1-0716-1967-4_11.
Immunoprecipitation mass spectrometry (IP-MS) is a popular method for the identification of protein-protein interactions. This approach is particularly powerful when information is collected without a priori knowledge and has been successively used as a first key step for the elucidation of many complex protein networks. IP-MS consists in the affinity purification of a protein of interest and of its interacting proteins followed by protein identification and quantification by mass spectrometry analysis. We developed an R package, named IPinquiry, dedicated to IP-MS analysis and based on the spectral count quantification method. The main purpose of this package is to provide a simple R pipeline with a limited number of processing steps to facilitate data exploration for biologists. This package allows to perform differential analysis of protein accumulation between two groups of IP experiments, to retrieve protein annotations, to export results, and to create different types of graphics. Here we describe the step-by-step procedure for an interactome analysis using IPinquiry from data loading to result export and plot production.