Gas-Phase Chemistry in the GC Orbitrap Mass Spectrometer

  • Tim U. H. Baumeister
  • Nico Ueberschaar
  • Georg PohnertEmail author
Research Article


Gas-phase reactions of temporally stored ions play a significant role in trapped ion mass spectrometry. Especially highly labile ion species generated through electron ionization (EI) are prone to undergo gas-phase reactions after relaxation to a low vibrational state. Here, we show that in the C-Trap of the Q Exactive GC Orbitrap mass spectrometer, gaseous water reacts with radical cations of various compound classes. High-resolution accurate mass spectrometry of the resulting ions provides a key to the mechanistic understanding of the chemistry of high energetic species generated during EI. We systematically addressed water adduct formation by use of H2O and D218O in the C-Trap. Mass spectra of halogen cyanides XCN (X=Cl, Br, I) showed the formation of HXCN+ species, indicating hydrogen atomic transfer reactions. Relative ratios of HXCN+/XCN+• increased as the electronegativity of the halide increased. The common internal calibrant perfluorotributylamine forms oxygenated products from water reactive fragment ions. These can be explained by the addition of water to an initial cation followed by elimination of two HF molecules. This addition/elimination chemistry can also explain [M+2]+ and [M+3]+ ions that commonly occur in mass spectra of silylated analytes. High-resolution accurate mass spectra of trimethylsilyl (TMS) derivatives revealed these as [M−CH3+H2O]+ and [M−CH4+H2O]•+, respectively. This study explains common fragment ions in ion trap mass spectrometry. It also opens up perspectives for the systematic mechanistic and kinetic investigation of high-energy ion reactivity.

Graphical Abstract


Orbitrap C-Trap Gas-phase reactions Gas chromatography mass spectrometry Water adducts High-resolution mass spectrometry Cyanogen halides 



The authors thank the German Research Foundation (DFG) for funding within the framework of the CRC 1076 (AquaDiva) and the CRC 1127 (ChemBioSys). We acknowledge funding by the state of Thuringia 2015 FGI0021 co-supported by the EU EFRE program. Remington X. Poulin is acknowledged for helpful discussion and Marine Vallet for her active support during experiments.

Supplementary material

13361_2018_2117_MOESM1_ESM.docx (608 kb)
ESM 1 (DOCX 607 kb)


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Copyright information

© American Society for Mass Spectrometry 2018

Authors and Affiliations

  1. 1.Max Planck Fellow Group on Plankton Community InteractionMax Planck Institute for Chemical EcologyJenaGermany
  2. 2.Institute for Inorganic and Analytical Chemistry, Mass Spectrometry PlatformFriedrich Schiller University JenaJenaGermany
  3. 3.Institute for Inorganic and Analytical Chemistry, Department of Bioorganic AnalyticsFriedrich Schiller University JenaJenaGermany

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