Target identification, selectivity profiling and binding site mapping of small molecule & peptide drugs by LiP-MS

Target identification in the cellular context is a critical step for both target-based and phenotypic drug discovery. Limited proteolysis coupled with mass spectrometry (LiP-MS) has emerged as a powerful technique for target deconvolution of small molecules or peptides in cell lysate without compound modification or genetic manipulation of cell lines [1,2,3]. Utilizing a non-specific protease under well-controlled conditions, LiP-MS exploits drug-induced structural alteration or steric hindrance on protein targets and utilizes quantitative mass spectrometry to probe over 250’000 peptides representing up to 9000 proteins in the proteome (Fig. 1). To aid target identification (ID), this workflow incorporates a 7-concentration dose response experiment and a machine-learning framework [1] to compute a LiP-score to rank identified target proteins, as well as predict potential binding site (Fig. 2)