rtmsEcho: An Open-Source R Package for Automated Analysis of Acoustic Ejection Mass Spectrometry Data.

Mass spectrometry (MS) is a well-established technology in biological research, enabling the sensitive and precise quantitative analysis of complex samples. While traditional LC-MS systems provide robust performance for targeted analyses, their reliance on chromatographic separation limits throughput, rendering large-scale studies inefficient. The emergence of Acoustic Ejection Mass Spectrometry (AEMS) has revolutionized high-throughput workflows by eliminating chromatography and enabling direct nanoliter-scale sampling, achieving hundreds to thousands of measurements per hour. However, AEMS's full potential remains constrained by software limitations─existing tools lack robust automated processing capabilities for critical tasks such as peak detection, integration, and multimodal data analysis (e.g., multiple reaction monitoring, precursor ion, and neutral loss scans). To address this gap, we developed rtmsEcho, an open-source R package that extends our previously published rtms framework. This specialized solution provides direct access to AEMS data, enabling customizable processing of both MRM and full-scan acquisitions (precursor ion and neutral loss modes) while automating shot-to-peak association and spectral analysis. By streamlining data extraction and quantification, rtmsEcho enhances efficiency and reproducibility in high-throughput applications, including drug discovery, quality control, and clinical diagnostics. This innovation bridges a critical gap in AEMS data analysis, allowing researchers to fully leverage the speed and precision of next-generation mass spectrometry.