The experiment with low complexity sample matrix and moderate peak overlap. 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). This elution segment includes few closely eluting peaks in the retention time range 1895-1920 s. For example, the range 1910-1920 s contains three distinct co-eluting compounds to give appearance of two TIC peaks. Both PyMS and AnalyzerPro deconvoluted these three peaks successfully, and also detected the other peaks in the chromatogram comparably to the human operator. AMDIS significantly overestimated the number of peaks on this segment. By default, XCMS looks for single ion peaks and not GC-MS type multi-ion peaks, and therefore in this segment detected many such peaks. For the list of detected signals see Additional file 2.