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  • Title: SimExTargId: a comprehensive package for real-time LC-MS data acquisition and analysis.
    Author: Edmands WMB, Hayes J, Rappaport SM.
    Journal: Bioinformatics; 2018 Oct 15; 34(20):3589-3590. PubMed ID: 29790936.
    Abstract:
    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.
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