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

William M. B. Edmands | Zendy; Josie Hayes | Zendy; Stephen M. Rappaport | Zendy

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

Author(s) -

William M. B. Edmands,

Josie Hayes,

Stephen M. Rappaport

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty218

Subject(s) - computer science , r package , profiling (computer programming) , vendor , metabolomics , identification (biology) , data mining , database , operating system , chromatography , chemistry , botany , computational science , biology , marketing , business

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.

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