Comparison of label-free quantification methods for the determination of protein complexes subunits stoichiometry

•Label-free quantification methods are straightforward and reasonably precise tools.•They are suitable to study the stoichiometry of subunits within protein complexes.•The spectral counting approach tends to flatten the measured stoichiometries.

Protein complexes are the main molecular machines that support all major cellular pathways and their in-depth characterization are essential to understand their functions. Determining the stoichiometry of the different subunits of a protein complex still remains challenging. Recently, many label-free quantitative proteomic approaches have been developed to study the composition of protein complexes. It is therefore of great interest to evaluate these different methods in a stoichiometry oriented objective. Here we compare the ability of four absolute quantitative label-free methods currently used in proteomic studies to determine the stoichiometry of a well-characterized protein complex, the 26S proteasome.

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