Complexome Profiling: Assembly and Remodeling of Protein Complexes

Abstract

Many proteins have been found to operate in a complex with various biomolecules such as proteins, nucleic acids, carbohydrates, or lipids. Protein complexes can be transient, stable or dynamic and their association is controlled under variable cellular conditions. Complexome profiling is a recently developed mass spectrometry-based method that combines mild separation techniques, native gel electrophoresis, and density gradient centrifugation with quantitative mass spectrometry to generate inventories of protein assemblies within a cell or subcellular fraction. This review summarizes applications of complexome profiling with respect to assembly ranging from single subunits to large macromolecular complexes, as well as their stability, and remodeling in health and disease.

Complexome Profiling—Exploring Mitochondrial Protein Complexes in Health and Disease

“…Icons of the most popular tools used for CP studies are shown (see Section 2.1 for details). Protein abundance profiles are further obtained by (Continued ) Frontiers in Cell and Developmental Biology | www.frontiersin.org January 2022 | Volume 9 | Article 796128 intensity-based absolute quantification (iBAQ) (Schwanhausser et al, 2011;Tyanova et al, 2016a) et al (2014) and Wittig and Malacarne (2021). Ultimately, the list of hundreds or even thousands of identified proteins is mainly sorted based on similarities of the abundance patterns across fractions by hierarchical clustering analysis (Figure 1).…”

“…It is thus not surprising that the majority of CP studies use iBAQ since it enables a fair comparison between different protein groups in the same and multiple samples. Additional information regarding LFQ and other alternative methods have been reviewed in Fabre et al (2014) and Wittig and Malacarne (2021) . Ultimately, the list of hundreds or even thousands of identified proteins is mainly sorted based on similarities of the abundance patterns across fractions by hierarchical clustering analysis ( Figure 1 ).…”

“…The most used CP workflow, currently referred to as “classic CP” ( Wittig and Malacarne, 2021 ), uses Blue Native-polyacrylamide gel electrophoresis (BN-PAGE) followed by MS identification. The main advantages of BN-PAGE are the relatively low amounts of biological material required and high-resolution separation of native proteins.…”

“…Resultant data are clustered to visualize the inventory, abundance and arrangement of multi-protein complexes in a biological sample. Since its formal introduction a decade ago, CP has been primarily used in mitochondrial research ( Kiirika et al, 2013 ; Senkler et al, 2017 ; Giese et al, 2021 ; Guerrero-Castillo et al, 2021b ; Wittig and Malacarne, 2021 ); albeit CP can be applied to any kind of cellular fraction.…”

Aging of Podospora anserina Leads to Alterations of OXPHOS and the Induction of Non-Mitochondrial Salvage Pathways

“…Here we report results from a complexome profiling analysis, in which high molecular weight protein complexes were separated using BN-PAGE, subsequently sliced into even fractions, and analyzed by quantitative mass spectrometry [ 60 , 61 , 62 ]. The identified proteins were quantified and their appearance in high molecular weight regions could be visualized as interaction profiles, using heatmaps [ 63 ]. Here, the comparison of the resulting profiles of two mitochondrial samples, from two different age stages of the P. anserina wild type, uncovered detailed age-dependent alterations of the mitochondrial complexome.…”