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Publication Detail

Title: SimExTargId: a comprehensive package for real-time LC-MS data acquisition and analysis.

Authors: Edmands, William M B; Hayes, Josie; Rappaport, Stephen M

Published In Bioinformatics, (2018 10 15)

Abstract: 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.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 data are available at Bioinformatics online.

PubMed ID: 29790936 Exiting the NIEHS site

MeSH Terms: Chromatography, Liquid/methods*; Metabolomics; Software*; Tandem Mass Spectrometry/methods*; Time Factors

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