simExTargId: An R package for real-time LC-MS metabolomic data analysis, instrument failure/drift notification and MS2 target identification

Abstract

The simExTargId R package provides real-time, autonomous, within-laboratory data analysis during a metabolomic LC-MS1-profiling experiment. Of concern to metabolomic investigators are instrumentation failure (especially for precious samples), outlier identification, instrument signal attenuation and pre-emptive feature identification for MS2 fragmentation.\n\nSimExTargId allows observation of an experiment in progress with PCA plot and peak table outputs and also two shiny applications targetId for MS2 target identification and peakMonitor for signal attenuation monitoring. SimExTargId is ideally utilised on a (temporarily) dedicated workstation or server which is networked to a LC-MS data directory. Features include: email notification for instrument stoppage/drift, file format conversion, peak-picking, pre-processing, PCA-based outlier identification and statistical analysis. Additional MS1/MS2 experiments can be concatenated to a worklist or cleaning/recalibration undertaken if instrument drift is observed.\n\nAll source code and a vignette with example data are available on GitHub https://github.com/WMBEdmands/simExTargId/.\n\nContact: edmandsw@berkeley.edu