Abstract The challenges of data management and interpretation for purveyors of capillary chromatography instrumentation with mass spectrometric detection are reviewed. Techniques to succeed are detailed within the context of standard analytical targeted, nontargeted, and hybrid targeted/nontargeted work flows. The processes are divided into the common elements of preprocessing, comparative analysis, deconvolution (i.e., mathematical resolution), result analysis, and statistical presentation. Time-honored techniques are discussed throughout with a focus on the added complications created by the data size and density in modern experiments where the samples are analyzed by chromatographic instruments with mass spectrometric detection. Multidimensional and multivariate options are included throughout and the focus constantly returns to harvesting useful information from the windfall of data created by these technologies.