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

Untargeted metabolomics by mass spectrometry technologies generates huge numbers of metabolite signals, requiring computational analyses for post-acquisition processing and databases for metabolite identification. Web-based data processing solutions frequently include only a part of the entire workflow thus requiring the use of different platforms. The R package "margheRita" enhances fragment matching accuracy and addresses the complete workflow for metabolomic profiling in untargeted studies based on liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS), especially in the case of data-independent acquisition, where all MS/MS spectra are acquired with high quantitative accuracy. Availability and Implementation: source code and documentation are available at https://github.com/emosca-cnr/margheRita.