This document describes how to use xcms for the analysis of direct injection mass spec data, including peak detection, calibration and correspondence (grouping of peaks across samples). Prior to any other analysis step, peaks have to be identified in the mass spec data. In contrast to the typical metabolomics workflow, in which peaks are identified in the chromatographic (time) dimension, in direct injection mass spec data sets peaks are identified in the m/z dimension. xcms uses functionality from the MassSpecWavelet package to identify such peaks.
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