Propionic Acid Outperforms Formic and Acetic Acid in MS Sensitivity for High-Flow Reversed-Phase LC-MS Bottom-Up Proteomics

Formic acid has long been the default acidic additive in reversed-phase LC-MS-based bottom-up proteomics, offering a practical balance between chromatographic performance and electrospray ionization (ESI) efficiency. Here, we evaluate propionic acid as an alternative mobile phase acidifier, a candidate that has been largely overlooked in efforts to improve ESI efficiency without compromising chromatography. By reducing both the ionic strength and surface tension of the mobile phase, propionic acid markedly enhanced ESI efficiency, yielding an average 39% increase in peptide identifications compared to formic acid and even a 12% increase relative to the recently revived acetic acid. These gains were consistent across interlaboratory data sets encompassing analytical- and microflow LC-MS configurations, diverse column chemistries, and varying sample complexities. Importantly, chromatographic performance remained virtually unaffected, with only a minor reduction in peptide retention. The mobile phase containing propionic acid was stable, instrument-compatible, and introduced a negligible background signal. Collectively, these findings challenge the long-standing reliance on formic acid and establish propionic acid as a robust, drop-in alternative for high-flow LC-MS workflows prioritizing MS sensitivity and proteome depth.