Proteome Integral Solubility Alteration (PISA) for High-Throughput Ligand Target Deconvolution with Increased Statistical Significance and Reduced Sample Amount

Abstract

Proteome Integral Solubility Alteration (PISA) is a recently developed mass spectrometry-based, deep proteomics method for unbiased, proteome-wide target deconvolution of ligands, requiring no chemical ligand modification. PISA can be applied to living cells for studying target engagement in vivo or alternatively to protein extracts to identify in vitro ligand-interacting proteins. Here we describe the PISA workflow optimized in our lab. PISA improves the target discovery throughput 10-100 folds compared to the previously used proteomics methods and provides higher statistical significance for target candidates by enabling several biological replicates. Sample multiplexing makes all-in-one analysis of multiple ligands simultaneously possible. PISA dramatically reduces analysis costs, allowing many research questions in need of target deconvolution to be addressed, and unlocks the potential of miniaturizing biological models, including primary cells.

Keywords: Chemoproteomics; Ligand; Ligand target deconvolution; PISA; Protein–metabolite interactions; Solubility alteration.