Increasing the mass accuracy of high-resolution LC-MS data using background ions - A case study on the LTQ-Orbitrap

Richard A. Scheltema, Anas Kamleh, David Wildridge, Charles Ebikeme, David G. Watson, Michael P. Barrett, Ritsert C. Jansen, Rainer Breitling

Research output: Contribution to journalArticleAcademicpeer-review


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.
Original languageEnglish
Pages (from-to)4647-4656
Number of pages10
Issue number22
Publication statusPublished - 1 Nov 2008
Externally publishedYes


  • Alignment and internal mass calibration
  • High resolution
  • Mass spectrometry
  • Metabolomics
  • Software
  • background ions
  • essential amino acid
  • ion
  • trypanothione
  • unclassified drug
  • accuracy
  • article
  • software
  • liquid chromatography
  • mass spectrometry
  • mathematical computing
  • metabolomics
  • priority journal
  • Trypanosoma


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