Metabolomics (defined as comprehensive small molecule chemical analysis), together with genomics, transcriptomics, proteomics and phenomics, now plays a fundamental role in system biological studies. Chromatography- mass spectrometry machines, which have the characteristics of high resolution and high sensitivity, are widely used for metabolomics analysis, both qualitatively and quantitatively. With the fast development of the chromatography-mass spectrometry technology, metabolomics analysis has been successfully applied in various biological research fields. Here, we introduce the different chromatography-mass spectrum machines used for metabolomics analysis and their applications to various biological issues by mainly using the metabolomics platform in Institute of Genetics and Developmental Biology as a case study.