Principal component analysis of comprehensive three-dimensional gas chromatography time-of-flight mass spectrometry data

•The first application of PCA to GC3-TOFMS data is provided using a jet fuel dataset.•Vacant 3D modulations are subtracted to re-register the data prior to PCA.•An additional band of compounds is resolved using GC3 relative to GC × GC.•3D PCA loadings are highly useful for visualizing fine chemical differences.•“Pairwise” PCA reveals differences which are drowned out in multi-class model.