Annotation of LC-MS metabolomics datasets by the “metaMS” package

metaMS is designed to perform the analysis of LC-MS and GC-MSbased metabolomics assays. For LC-MS data, its major function runLC() is a wrapper around the functions and classes of xcms and CAMERA and it is designed to process a series of data files producing a peak table with the intensity of each feature an mz,rt couple in each one of the samples. The functions and classes of xcms and CAMERA are used to perform the peak picking, grouping and retention correction, peak filling, and CAMERA annotation. The parameters required at each step are collected into a settings object which is passed as an argument to runLC. Three examples, fine-tuned for instruments in our own laboratory, are included: