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Originally published In Press as doi:10.1074/mcp.T500030-MCP200 on October 24, 2005.
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Molecular & Cellular Proteomics 4:2010-2021, 2005.
© 2005 by The American Society for Biochemistry and Molecular Biology, Inc.

Technology

Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap*,S

Jesper V. Olsen{ddagger},§, Lyris M. F. de Godoy§, Guoqing Li§,¶, Boris Macek§, Peter Mortensen{ddagger}, Reinhold Pesch||, Alexander Makarov||, Oliver Lange||, Stevan Horning|| and Matthias Mann{ddagger},§,**

From the {ddagger} Center for Experimental BioInformatics (CEBI), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark, § Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China, and || Thermo Electron (Bremen) GmbH, Hanna-Kunath-Strasse 11, 28199 Bremen, Germany

Mass accuracy is a key parameter of mass spectrometric performance. TOF instruments can reach low parts per million, and FT-ICR instruments are capable of even greater accuracy provided ion numbers are well controlled. Here we demonstrate sub-ppm mass accuracy on a linear ion trap coupled via a radio frequency-only storage trap (C-trap) to the orbitrap mass spectrometer (LTQ Orbitrap). Prior to acquisition of a spectrum, a background ion originating from ambient air is first transferred to the C-trap. Ions forming the MS or MSn spectrum are then added to this species, and all ions are injected into the orbitrap for analysis. Real time recalibration on the "lock mass" by corrections of mass shift removes mass error associated with calibration of the mass scale. The remaining mass error is mainly due to imperfect peaks caused by weak signals and is addressed by averaging the mass measurement over the LC peak, weighted by signal intensity. For peptide database searches in proteomics, we introduce a variable mass tolerance and achieve average absolute mass deviations of 0.48 ppm (standard deviation 0.38 ppm) and maximal deviations of less than 2 ppm. For tandem mass spectra we demonstrate similarly high mass accuracy and discuss its impact on database searching. High and routine mass accuracy in a compact instrument will dramatically improve certainty of peptide and small molecule identification.

** To whom correspondence should be addressed: Dept. of Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz 18, D-82512 Martinsried, Germany. E-mail: mmann{at}biochem.mpg.de


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