Analytical and Bioanalytical Chemistry

, Volume 405, Issue 1, pp 51–61 | Cite as

Towards analytically useful two-dimensional Fourier transform ion cyclotron resonance mass spectrometry

  • Maria A. van Agthoven
  • Marc-André Delsuc
  • Geoffrey Bodenhausen
  • Christian Rolando


Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) achieves high resolution and mass accuracy, allowing the identification of the raw chemical formulae of ions in complex samples. Using ion isolation and fragmentation (MS/MS), we can obtain more structural information, but MS/MS is time- and sample-consuming because each ion must be isolated before fragmentation. In 1987, Pfändler et al. proposed an experiment for 2D FT-ICR MS in order to fragment ions without isolating them and to visualize the fragmentations of complex samples in a single 2D mass spectrum, like 2D NMR spectroscopy. Because of limitations of electronics and computers, few studies have been conducted with this technique. The improvement of modern computers and the use of digital electronics for FT-ICR hardware now make it possible to acquire 2D mass spectra over a broad mass range. The original experiments used in-cell collision-induced dissociation, which caused a loss of resolution. Gas-free fragmentation modes such as infrared multiphoton dissociation and electron capture dissociation allow one to measure high-resolution 2D mass spectra. Consequently, there is renewed interest to develop 2D FT-ICR MS into an efficient analytical method. Improvements introduced in 2D NMR spectroscopy can also be transposed to 2D FT-ICR MS. We describe the history of 2D FT-ICR MS, introduce recent improvements, and present analytical applications to map the fragmentation of peptides. Finally, we provide a glossary which defines a few keywords for the 2D FT-ICR MS field.


Mass spectrometry Fourier transform ion cyclotron resonance Two-dimensional FT-ICR 



The FT-ICR mass spectrometer and the proteomics platform used for this study are funded by the European Community (FEDER), the Région Nord–Pas-de-Calais (France), the IBISA network, the CNRS, and Université Lille 1, Sciences et Technologies, and this funding is gratefully acknowledged. Computational resources were provided by the Centre de Ressources Informatiques of Université Lille 1 supported by the CNRS and Université Lille 1. M.v.A. thanks the Région Nord–Pas-de-Calais for postdoctoral funding. The authors gratefully acknowledge funding of this project by the Agence Nationale de la Recherche (grant 2010 FT-ICR 2D). Financial support from the TGE FT-ICR for conducting the research is also gratefully acknowledged. The authors thank the referees for their very careful reading of the manuscript and their suggested corrections.


Autocorrelation line

Line with a y = x equation in the 2D mass spectrum, which shows the modulation of the relative ICR signal magnitude of the precursor ions with their own cyclotron frequency. The autocorrelation line is the equivalent of the MS spectrum of the precursor ions.

Encoding pulse

Second pulse (designated P2) of the pulse sequence, which excites or de-excites precursor ions according to their cyclotron frequency and the value of t1.

Encoding sequence

The sequence which encodes the frequencies of the precusor ions prior to fragmention and normally composed of a excitation pulse, an encoding period and an encoding pulse.

Excitation pulse

First pulse (designated P1) of the pulse sequence, which excites all precursor ions equally.

Frequency encoding period

Regularly incremented interval (designated t1) in between the two pulses of the encoding sequence, during which all precursor ions rotate at their cyclotron frequency.

Fragmentation period

Fixed period between the encoding sequence and the observe pulse during which precursor ions are fragmented.

Horizontal fragment ion spectrum

Horizontal cross section of the 2D mass spectrum. The horizontal fragment ion spectrum shows the fragment ion spectrum of the ion species with the m/z ratio where it intersects the autocorrelation line.

Observe pulse

Third pulse (designated P3) of the pulse sequence, which excites both precursor and fragment ions prior to detection.

Two-dimensional mass spectrum

Two-dimensional spectrum obtained from the time transients acquired using the pulse sequence presented in Fig. 2 with regularly incremented delay t 1, followed by Fourier transformation in two dimensions and conversion of cyclotron frequencies into m/z ratios. By convention 2D mass spectra are plotted with the Fourier transform which corresponds to the transient obtained during time t 2 in the horizontal dimension, whereas the Fourier transform which corresponds to the signal measured with incremental values of t 1 is plotted vertically. This convention respects the usual convention in MS [66].

Vertical precursor ion spectrum

Vertical cross section of the 2D mass spectrum. The vertical precursor ion spectrum shows the precursor ion spectrum of the ion species with the m/z ratio where it intersects the autocorrelation line.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Maria A. van Agthoven
    • 1
  • Marc-André Delsuc
    • 2
  • Geoffrey Bodenhausen
    • 3
  • Christian Rolando
    • 1
  1. 1.Miniaturisation pour la Synthèse l’Analyse et la Protéomique, USR CNRS 3290, Institut Michel-Eugène Chevreul, FR CNRS 2638 and Protéomique, Modifications Post-Traductionnelles et Glycobiologie, IFR 147 Université de Lille 1, Sciences et TechnologieVilleneuve d’Ascq CedexFrance
  2. 2.U 596 and UMR CNRS 7104, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERMUniversité de StrasbourgIllkirch-GraffenstadenFrance
  3. 3.UMR 7203, Département de ChimieÉcole Normale SupérieureParis Cedex 05France

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