MargheRita: an R package for LC-MS/MS SWATH metabolomics data analysis and confident metabolite identification based on a spectral library of reference standards

In the field of untargeted metabolomics, the deployment of high-resolution mass spectrometry technologies generates an immense volume of complex metabolite signals. This data density necessitates sophisticated computational frameworks for post-acquisition processing and the integration of specialized databases for accurate metabolite identification. Currently, many web-based data processing solutions offer fragmented workflows, covering only specific stages of the analysis and frequently requiring researchers to migrate data across multiple, often incompatible, platforms. To address these challenges, we introduced margheRita, an R package designed to streamline the workflow for untargeted metabolomic profiling. Developed to work seamlessly with MS-DIAL output, margheRita provides a comprehensive pipeline for liquid chromatography-tandem mass spectrometry (LC-MS/MS) data. This tool is particularly effective for Data-Independent Acquisition (DIA) experiments, where the high-resolution acquisition of all MS/MS spectra demands rigorous and integrated processing capabilities. A key innovation of margheRita is its ability to significantly enhance fragment matching accuracy. It achieves this by utilizing an original, curated high-quality spectral library from authentic reference standards. This library includes data acquired in both positive and negative ionization polarities using various chromatographic columns, ensuring high versatility. By bridging the gap between initial MS-DIAL processing and final biological insights, margheRita offers a holistic solution from metabolite identification to the functional interpretation of complex biological datasets.