The experiment with low complexity sample matrix and well resolved peaks. A segment of a GC-MS experiment recorded on a control mix with 45 reference compounds. The total ion chromatogram (TIC) is shown in dotted line, and individual ion chromatograms (ICs) in the m/z range 50-550 are overlaid in full line. The true multi-component GC-MS peaks, identified manually by an experienced operator, are shown as filled triangles at the bottom of the graph. The peaks detected by four software packages are shown in the upper part of the Figure ('*'― AMDIS, ' + ' ― XCMS, 'x' ― PyMS, 'o' ― AnalyzerPro). The segment chosen for this analysis is sparsely populated with peaks, which are all well resolved. All four software packages performed comparably to the human operator. Clustering of individual single ion peaks around true multi-component GC-MS peaks is evident from the peak detected by XCMS. For the list of detected signals see Additional file 1.