Proteome Integral Solubility Alteration (PISA): a high-throughput proteomics assay for target deconvolution

Various agents, including drugs as well as non-molecular influences, induce alterations in the physic-chemical properties of proteins in cell lysates, living cells and organisms. These alterations can be probed by applying a stability-modifying factor, such as elevated temperature, to a varying degree. As a second dimension of variation, drug concentration or agent intensity/concentration can be used. A typical example is the thermal stability assay. However, the conventional analysis scheme has a low throughput and high cost. Additionally, since traditional data analysis employs curve fitting, proteins with unusual behavior are frequently ignored. The novel Proteome Integral Stability Alteration (PISA) assay avoids these issues altogether, increasing the analysis throughput by one to two orders of magnitude for unlimited number of factor variation points. The consumption of the compound and biological material decreases by the same factor. As an example, an analogue of a two-dimensional thermal stability assay can be performed in three replicates using a single 10-plex proteome analysis. We envision widespread use of the PISA approach in chemical biology and drug development.