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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