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


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.

SUBMITTER: Edmands WMB 

PROVIDER: S-EPMC6184452 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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

Edmands William M B WMB   Hayes Josie J   Rappaport Stephen M SM  

Bioinformatics (Oxford, England) 20181001 20


<h4>Summary</h4>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 pr  ...[more]

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