Multiplex measurement of protein-peptide dissociation constants using dialysis and mass spectrometry

We propose a high-throughput method for quantitatively measuring hundreds of protein-peptide binding affinities in parallel. In this assay, a solution of protein is dialyzed into a buffer containing a pool of potential binding peptides, such that upon equilibration the relative abundance of a peptide species is mathematically related to that peptide's dissociation constant, K-d. We use isobaric multiplexed quantitative proteomics to simultaneously determine the relative abundance, and hence the K-d and its associated error, for an entire peptide library. We apply this technique, which we call PEDAL (parallel equilibrium dialysis for affinity learning), to determine accurate K-d's between a PDZ domain and hundreds of peptides, spanning an affinity range of multiple orders of magnitude in a single experiment. PEDAL is a convenient, fast, and low-cost method for measuring large numbers of protein-peptide affinities in parallel, providing a rare combination of true in-solution binding equilibria with the ability to multiplex.