With the advent of a new generation of high-resolution mass spectrometers, the fields of proteomics and metabolomics have gained powerful new tools. In this paper, we demonstrate a novel computational method that improves the mass accuracy of the {LTQ-Orbitrap} mass spectrometer from an initial ??1-2 ppm, obtained by the standard software, to an absolute median of 0.21 ppm {(SD} 0.21 ppm). With the increased mass accuracy it becomes much easier to match mass chromatograms in replicates and different sample types, even if compounds are detected at very low intensities. The proposed method exploits the ubiquitous presence of background ions in {LC-MS} profiles for accurate alignment and internal mass calibration, making it applicable for all types of {MS} equipment. The accuracy of this approach will facilitate many downstream systems biology applications, including mass-based molecule identification, ab initio metabolic network reconstruction, and untargeted metabolomics in general. ?? 2008 {Wiley-VCH} Verlag {GmbH} \& Co. {KGaA.}