Updated project metadata. Complexome profiling is a rapidly spreading, powerful approach to gain insight into the nature of protein complexes. It identifies and quantifies protein complexes separated into multiple fractions of increasing molecular mass using mass spectrometry-based, label-free bottom-up proteomics. Complexome profiling enables a sophisticated and thorough characterization of the composition, molecular mass, assembly and interactions of protein complexes. However, in practice, its application is limited by the large number of samples it generates and the related time and costs of mass spectrometry analyses. Here we implemented tandem mass tags for multiplexing complexome profiling.