Abstract: Covalent drugs offer significant therapeutic advantages, including enhanced potency and novel selectivity, making them valuable for tackling challenging diseases traditionally considered "undruggable." The identification of covalent binders to target proteins typically involves directly measuring protein covalent modifications using high-resolution mass spectrometry. As interest in this approach has grown, and with a continually expanding library of compounds, conventional mass spectrometry platforms such as LC-MS or SPE-MS have become limiting factors for high-throughput covalent ligand screening. Acoustic ejection mass spectrometry (AEMS) has emerged as a promising solution for a wide range of drug discovery assays, and in this study, we introduce a prototype high-resolution AEMS system for the rapid screening of a covalent modifier library comprising 10,000 compounds against a 50 kDa-sized target protein. The screening samples were arranged in a 1536-well format, each with a volume of 3 µL. The sample buffer, containing high-concentration salts, was directly analyzed without necessitating any cleanup steps. This allowed for direct analysis without the need for extensive cleanup, minimizing sample preparation efforts and ensuring protein stability. The entire screening process could be completed within a mere 17 hours. An automated data analysis tool facilitated batch quantitation of the protein samples and the assessment of the extent of formation of various covalent protein-ligand adducts. The screening results displayed a high degree of fidelity, with a Z' factor of 0.8 and a hit rate of 2.3%. These identified hits underwent orthogonal testing via the IC50 assay, revealing that 54% of them exhibited biological functionality. Notably, a comparative analysis with LC-MS showcased the AEMS platform's low risk of false positives or false negatives. This innovative platform has enabled robust high-throughput covalent modifier screening, featuring a 10-fold increase in library size and a 10- to 100-fold increase in throughput when compared to similar reports in the existing literature.