The experiment with complex biological matrix and moderate peak overlap. A GC-MS experiment was recorded on foetal calf serum spiked with a mix of 17 known 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 shown region includes two of the spiked compounds, aspartic acid (the large peak near 524 s) and malic acid (the large peak near 540 s). Two smaller peaks are closely eluting with malic acid providing a good test for deconvolution. Both PyMS and AnalyzerPro performed similarly to an experienced operator in the identification of peaks. For the list of detected signals see Additional file 3.