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

Untargeted metabolomics studies by mass spectrometry technologies generate huge numbers of metabolite signals, requiring computational analyses for post-acquisition processing and dedicated databases for metabolite identification. Web-based data processing solutions frequently include only a part of the entire workflow thus implying the use of different platforms. The R package margheRita addresses the complete workflow for metabolomic profiling in untargeted studies based on liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS). This pipeline is especially advantageous in the case of data-independent acquisition (DIA), where all MS/MS spectra are acquired with high resolution. Interestingly, the R package margheRita enhances fragment matching accuracy by providing an original metabolite spectral library acquired in both polarities using different chromatographic columns. This R package provides a comprehensive solution for metabolomics, covering the entire analysis workflow from raw data processing to biological interpretation.