RapidMass: A Graphical Data Processing Application for Automated Species Authentication in High-Throughput Mass Spectrometry

High-throughput mass spectrometry (HT-MS) facilitates rapid, large-scale data acquisition, providing a fast and efficient solution for various analytical challenges. However, the increasing volume of data generated by MS requires automation and easy-to-use processing tools. Currently, there is no freely available software that is compatible with most instruments for species authentication or classification. Here, we introduce RapidMass, a cutting-edge software platform designed to automate the handling, evaluation, presentation, and management of HT-MS data for species identification. Key features include a streamlined workflow for processing spectra from various instruments (e.g., DI-MS, ASAP-MS, DART-MS), three specialized algorithms for scoring unknown samples, peak annotation review, visualization of MS1 and MS2 spectra, and an expandable personal database for customized data management. Performance validation conducted on nine data sets covering diverse sample compositions, instrument types, suppliers, resolutions, and MS acquisition modes, demonstrated RapidMass’s excellent performance, with processing times of 12 to 20 s per sample and authentication accuracies ranging from 97% to 100% for easily confused plants. With its user-friendly interface, RapidMass empowers users to create and manage personalized databases, presenting significant prospects for broad applications across various fields.