SimExTargId: a comprehensive package for real‐time LC‐MS data acquisition and analysis

Summary: Liquid chromatography mass spectrometry (LC‐MS) is the favored method for untargeted metabolomic analysis of small molecules in biofluids. Here we present SimExTargId, an open‐source R package for autonomous analysis of metabolomic data and real‐time observation of experimental runs. This simultaneous, fully automated and multi‐threaded (optional) package is a wrapper for vendor‐independent format conversion (ProteoWizard), xcms‐ and CAMERA‐ based peak‐picking, MetMSLine‐based pre‐processing and covariate‐based statistical analysis. Users are notified of detrimental instrument drift or errors by email. Also included are two shiny applications, targetId for real‐time MS2 target identification, and peakMonitor to monitor targeted metabolites. Availability and implementation: SimExTargId is publicly available under GNU LGPL v3.0 license at https://github.com/JosieLHayes/simExTargId, which includes a vignette with example data. SimExTargId should be installed on a dedicated data‐processing workstation or server that is networked to the LC‐MS platform to facilitate MS1 profiling of metabolomic data. Supplementary information: Supplementary data are available at Bioinformatics online.