On the proper use of mass accuracy in proteomics
MCP Papers in Press. Published on December 12, 2006 as Manuscript M600380-MCP200
Roman Zubarev1 and Matthias Mann2
1) Laboratory for Biological and Medical Mass Spectrometry, Uppsala University, Box
583, Uppsala S-751 23, Sweden. Roman.Zubarev@bmms.uu.se
2) Department of Proteomics and Signal Transduction, Max-Planck-Institute of
Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
Mass measurement is the main outcome of mass spectrometry based proteomics yet the potential of recent advances in accurate mass measurements remains largely unexploited. There is even no clear definition of mass accuracy in the proteomic literature and we identify at least three uses of this term: anecdotal mass accuracy, statistical mass accuracy and the maximum mass deviation (MMD) allowed in a database search. We suggest using the second of these terms as the generic one. To make the best use of the mass precision offered by modern instruments we propose a series of simple steps involving recalibration of the data on ‘internal standards’ contained in every proteomic data set. Each data set should be accompanied by a plot of mass errors from which the appropriate MMD can be chosen. More advanced uses of high mass accuracy include an MMD that depends on the signal abundance of each peptide. Adapting search engines to high mass accuracy in the MS/MS data is also a high priority. Proper use of high mass accuracy data can make MS-based proteomics one of the most ‘digital’ and accurate post genomic disciplines.