Introducing a CATALYST to Accelerate Native Affinity Selection Mass Spectrometry

In recent publications, we have demonstrated applications of multiplexed affinity selection electrospray mass spectrometry based on three different principles: size-exclusion chromatography, flow-induced dispersion analysis, and Taylor/non-Taylor dispersion. To enable this multiplexing─i.e., simultaneous measurement of pools of ligands, with their masses acting as selective labels─higher resolving power was required than is typically achievable in native MS; therefore, we worked under conditions that promoted gas-phase ejection of protein-bound ligands, allowing their detection with high mass accuracy in the low-m/z region of the spectrum. Subsequent data analysis required correlation of the extracted ion chromatograms (EICs) of candidate ligands with the EIC of the target protein. Even when relying on simple visual inspection, generating these EICs manually is laborious even for only a few dozen ligand candidates, and a quantitative correlation based on statistical tests quickly becomes very time-consuming. Performing such an experiment for a larger compound library or even without a defined target list, but by instead extracting the chromatogram for every low-m/z signal present, is entirely impractical. Here, we present CATALYST (Computer-Assisted Time Alignment for Ligand Yield and Screening Tool), an open-source software package that can perform this type of analysis─in either targeted or untargeted mode─in a matter of seconds. CATALYST performs several statistical tests to correlate EICs and identify protein-binding ligands and then visualizes the results, greatly accelerating affinity selection mass spectrometry workflows.