Differential analysis of combinatorial protein complexes with CompleXChange

Abstract

Although a considerable number of proteins operate as multiprotein complexes and not on their own, organism-wide studies so far are only able to quantify individual proteins or protein-coding genes in a condition-specific manner for a sizeable number of samples, but not their assemblies. Consequently, there exist large amounts of transcriptomic data and an increasing amount of data on proteome abundance, but quantitative knowledge on complexomes is missing. This deficiency impedes the applicability of the powerful tool of differential analysis in the realm of macromolecular complexes. Here, we present a pipeline for differential analysis of protein complexes based on predicted or manually assigned complexes and inferred complex abundances, which can be easily applied on a whole-genome scale.