It is of increasing interest and practical importance to develop convenient methods based on mass spectrometry for high-throughput analyses of biological samples. This is usually difficult because of the complex matrix and ion suppression effects. Generation of ions at ambient conditions is a promising solution to these problems because the sample is easily accessible and the ion suppression effect is reduced significantly. A new method for rapid on-line detection of metabolic markers in complex biological samples is described here. It combines atmospheric pressure desorption sampling by a gentle stream of air or nitrogen with extractive electrospray ionization (EESI) and mass spectrometric analysis. The resulting mass spectral fingerprints are shown to be able to detect spoilage of meat even in the frozen (-20 degrees C) state and the contamination of spinach by E. coli, and to identify metabolites and contaminants on human skin within seconds, in an on-line and high-throughput fashion. Typical molecular markers are identified using MS/MS data and by comparison with reference compounds. Differences between closely related samples are easily visualized by using principal component analysis (PCA) of the mass spectra data. The detection limit achieved is 10 fg/cm2 (S/N = 3) for histamine on the surface of frozen meat. The technique reported here shows potential for more advanced applications in multiple disciplines, including food regulation, homeland security, in vivo metabolomics, and clinical diagnosis.