Ultra-High Mass Resolution MALDI-TOFMS System

JMS-S3000 SpiralTOF™-plus 2.0

The JMS-S3000 SpiralTOF™-plus Ultra-High Mass Resolution MALDI-TOFMS* System is a MALDI-TOFMS that incorporates the innovative SpiralTOF ion optics. The JMS-S3000 has evolved into SpiralTOF™-plus 2.0 with much wider dynamic range. The JMS-S3000 defines a new standard in MALDI-TOFMS performance and provides state-of-the-art analytical solutions for a wide range of research areas such as functional synthetic polymers, materials science, and biomolecules.

*Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometer

Revolutionary, Ultra-High Performance TOF Ion Optics

JMS-S3000 SpiralTOF™-plus

Setting the new standard in MALDI-TOFMS performance

To improve the mass resolving power and mass accuracy of a time-of-flight mass spectrometer, the flight distance must be extended while keeping a group of ions having the same m/z (an ion packet) from diverging in space.
The innovative SpiralTOF ion optics was developed by JEOL based on the "Perfect focusing" and "Multi-turn" principles. The ion packets are focused back in space at every fixed distance (i.e., each figure-eight trajectory) during the flight. Thus, even after the extended flight distance, the ion packets do not diverge at the detection plane, achieving high mass resolving power, high mass accuracy, and high ion transmission.
innovative SpiralTOF ion optics developed by JEOL
achieving high mass resolving power, high mass accuracy, and high ion transmission

Key Features

  • SpiralTOF, TOF/TOF and Linear TOF analyzers
  • Ultra-high resolving power of >75,000 over wide mass range
  • Sub-ppm mass accuracy with internal standard
  • Mono isotopic precursor selection
  • True high-energy (20 keV) CID
  • Free of artifacts from post-source decay (PSD)


The topographic effect of the matrix crystal leads to a difference in flight start position for the ions, resulting in a difference in flight time. In the conventional ion optical system, this time difference degrades the mass resolving power and also the mass accuracy obtained with external mass calibration. With its extended flight distance, the JMS-S3000 reduces this effect to the minimum and achieves highly reproducible mass resolving power and high mass accuracy with an external mass calibration. High mass-resolution and mass accuracy can be maintained for imaging analysis of a biological specimen in which a large number of mass spectra are acquired across a large area and the specimen surface is likely to be uneven.
The SpiralTOF™-plus 2.0 has realized a wide dynamic range by greatly improving the detection system. This makes it possible to simultaneously detect peaks with ion intensity differences of about 4 orders of magnitude. Also, the analysis of trace components has become easy in mass spectrometry imaging measurements, in addition to the conventional bulk sample measurements. Below is the measurement example of a mixture of polyethylene oxide and polypropylene oxide in the ratio of 1,000:1. In the case of polymer analysis, when combined with the Kendrick Mass Defect (KMD) analysis, it is possible to analyze trace components that are otherwise difficult to detect.
The mass spectrum of a mixture of polyethylene oxide and polypropylene oxide in the ratio of 1,000:1
The SpiralTOF™-plus 2.0 can realize a wide dynamic range and calculate the molecular weight distribution of trace components.
The mass spectrum of a mixture of polyethylene oxide and polypropylene oxide in the ratio of 1,000:1
Features and usages of TOF-TOF option and linear TOF option


  • By adopting the SpiralTOF ion optics as the first MS, the high precursor ion selectivity can be realized. The monoisotopic peak of precursor ions can be properly selected.
  • High-energy collision-induced dissociation (HE-CID) allows for the acquisition of product ion mass spectrum rich with structural information.
  • Off set parabolic reflectron, JEOL's patented technology, enables acquisition of all product ion information from m/z 5 to the precursor ion, and facilitates to obtain structural information of high reliability.


  • In structural analysis of organic compounds, the accuracy of composition determination using accurate mass in Spiral mode can be improved by determining the adduct ion, in addition to the structural information obtained by HE-CID.
  • In elucidation of amino acid sequences of a peptide, distinguishing structural isomers such as leucine and isoleucine is possible, as a feature of HE-CID. It is also possible to confirm the presence / absence of amino acids in a peptide by the presence / absence of immonium ions.
  • For the analysis of additives, surfactants, and lipids, the structural analysis of alkyl chains is important. With HE-CID, it is possible to estimate the alkyl chain length and the positions of double bonds.
  • For structural analysis of polymers, it is possible to confirm the ion type (adduct ion) and the mass of the end groups from the product ion mass spectrum. It is possible to improve the accuracy in structure elucidation in combination with the elemental composition estimation result with the Spiral mode.
Mass spectra of poly(styrene) 40K, 100K, and 200K
Mass spectra of poly(styrene) 40K, 100K, and 200K

SpiralTOF™-plus 2.0 is Ideal for Polymer Analysis

Industrial polymeric materials based on mixtures of polymers with different end groups or copolymers contain a wide variety of compounds. It is necessary to detect all the components in order to grasp the whole picture, which requires ultra-high mass resolution in a wide mass range. In addition, it is important to detect not only the base material but also trace components because multiple types of polymers and trace additives are blended for higher functionality.
With its wide dynamic range and ultra-high mass resolution over a wide mass range, SpiralTOF™-plus 2.0 is the solution that meets these requirements. Elimination of post source decay (PSD) derived ions, which is a major feature of SpiralTOF ion optics, also contributes significantly to clear mass spectrum analysis.
We provide the most effective and unique solution for polymer analysis with our msRepeatFinder Polymer Analysis Software.
MALDI MS imaging was initially developed to focus on high molecular weight compounds such as proteins and peptides. However, with the expanding applications of MALDI MS imaging, the interests have shifted to include smaller molecules such as lipids, pharmaceuticals, and pharmaceutical metabolites. Conventional MALDI - reflectron TOFMS has difficulty discerning small molecule signals from those of matrix. In the case of MALDI MS imaging, signals from unwanted molecules on the specimen surface will often interfere with signals from the target analytes. High selectivity by means of high mass-resolving power is essential for obtaining reliable target analyte spatial distributions. It is also important to maintain high mass-resolution and mass-accuracy for a long time even when measuring a sample surface with a large area and non-uniformity. SpiralTOF™-plus 2.0 is the only MALDI-TOFMS that meets imaging requirements with ultra-high mass-resolution and long flight distance to minimize loss of mass resolution due to sample surface non-uniformity. In addition, it also supports high-speed mass imaging analysis.

Mass Spectrometry Imaging Analysis of Lipids in Mouse Brain Tissue Section

Averaged mass spectrum of a mouse brain tissue section
PE: Phosphatidyl ethanolamine, PC: Phosphatidyl Choline, GalCer: Galactosylceramide
The data were acquired in a joint research project with the Mass Spectrometry Group, Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University.
The tissue section specimen was provided by Awazu laboratory, Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University.

Mass spectrometry imaging of polymers

Mass spectrometry imaging can be applied to polymers. Two spots are prepared by adding two antioxidants - Irgafos 168 (BASF) and Irganox 1010 (BASF) - to polymethylmethacrylate (PMMA). The ultraviolet irradiation was performed to the right spot only and its degradation was visualized by using mass spectrometry imaging. For polymers, it is possible to visualize the quantitative change in both polymers and additives. It is also possible to capture the changes in the average molecular weight and polydispersity.
MS imaging of PMMA, Irgafos 168, and Irganox 1010
MS imaging of PMMA, Irgafos 168, and Irganox 1010
For the detailed analysis of a protein, not only the intact protein but also enzymatic digest of the protein can be analyzed. Peptide mass fingerprinting allows identification of a protein.

Mass spectrum of the tryptic digest of bovine serum albumin (BSA) and the results of the peptide mass fingerprinting

Mass spectrum of BSA tryptic digest standard (equivalent to 500 amol)
Mass spectrum of BSA tryptic digest standard (equivalent to 500 amol)
Amount (fmol) Number of peptides matched/searched Sequence coverage (%) MASCOT score
50 52 / 81 75 570
10 41 / 79 64 390
5 36 / 77 54 351
1 28 / 57 43 255
0.5 31 / 52 46 306
0.1 12 / 34 18 92
* 3D-structure of RCSB PDB (www.rcsb.org) ID 1IGY (Harris, L.J., et al. (1998) J.Mol.Biol.
275: 861-872) created with Protein Workshop (Moreland, et al. (2005) BMC Bioinformatics 6:21).
Previously, MALDI-TOFMS systems were not suitable for the analysis of small molecules as matrix-derived peaks and continuous chemical noise interfere with the signal from analyte molecules. The SpiralTOF ion optics have solved these problems.

Analysis of a common cold medicine

Analysis of a common cold medicine

Application Notes

Published Papers

  1. MALDI-SpiralTOF technology for assessment of triacylglycerols in Croatian olive oils
  2. Structural Characterization of Polymers by MALDI Spiral-TOF Mass Spectrometry Combined with Kendrick Mass Defect Analysis
  3. Satoh, T., Analytical Capability of a High Performance Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometer for Peptide Mass Fingerprinting. Journal of the Mass Spectrometry Society of Japan, 2007. 55(3): p. 173-181. 
  4. Satoh, T., T. Sato, and J. Tamura, Development of a High-Performance MALDI-TOF Mass Spectrometer Utilizing a Spiral Ion Trajectory. Journal of the American Society for Mass Spectrometry, 2007. 18(7): p. 1318-1323.
  5. Satoh, T., Development of a time-of-flight mass spectrometer utilizing a spiral ion trajectory. Journal of the Mass Spectrometry Society of Japan, 2009. 57(5): p. 363-369.
  6. Ishii, Y., et al., Fusing Treatment of Pentacenes: Toward Giant Graphene-Like Molecule. Materials Express, 2011. 1(1): p. 36-42.
  7. Naka, T., et al., Lipid Phenotype of Two Distinct Subpopulations of Mycobacterium bovis Bacillus Calmette-Guerin Tokyo 172 Substrain. Journal of Biological Chemistry, 2011. 286(51): p. 44153-44161.
  8. Satoh, T., Development of Tandem Time-of-Flight Mass Spectrometer Using a Spiral Ion Trajectory and Its Application. Bunseki, 2011: p. 532-536.
  9. Satoh, T., et al., Tandem Time-of-Flight Mass Spectrometer with High Precursor Ion Selectivity Employing Spiral Ion Trajectory and Improved Offset Parabolic Reflectron. Journal of the American Society for Mass Spectrometry, 2011. 22(5): p. 797-803.
  10. Tsujita, T., et al., Purification and Characterization of Polyphenols from Chestnut Astringent Skin. Journal of Agricultural and Food Chemistry, 2011. 59(16): p. 8646-8654.
  11. Degawa, T., S. Shimme, and M. Toyoda, EJMS Protocol: Rapid sequencing of a peptide containing a single disulfide bondusing high-energy collision-induced dissociation. European Journal of Mass Spectrometry, 2012. 18: p. 345-348.
  12. Hamamoto, Y., et al., Brevisulcenal-F: A Polycyclic Ether Toxin Associated with Massive Fish-kills in New Zealand. Journal of the American Chemical Society, 2012. 134(10): p. 4963-4968.
  13. Holland, P.T., et al., Novel toxins produced by the dinoflagellate Karenia brevisulcata. Harmful Algae, 2012. 13: p. 47-57.
  14. JEOL Ltd., Mass Spectrometer Joint Development by Dr. Hisashi Matsuda & JEOL Ltd. Journal of the Mass Spectrometry Society of Japan, 2012. 60(6): p. 77-81.
  15. Li, K., et al., A Rheological and Chemical Investigation of Canadian Heavy Oils From the McMurray Formation. Energy & Fuels, 2012. 26(7): p. 4445-4453.
  16. Mukosaka, S., K. Teramoto, and H. Koike, Visual Analytics of Repeating Structures Using Mass Spectrometry. Journal of the Mass Spectrometry Society of Japan, 2012. 60(2): p. 27-32.
  17. Satoh, T., et al., Mass Spectrometry Imaging and Structural Analysis of Lipids Directly on Tissue Specimens by Using a Spiral Orbit Type Tandem Time-of-Flight Mass Spectrometer, SpiralTOF-TOF. Mass Spectrometry, 2012. 1(2): p. A0013 (1-6).
  18. Shimma, S., et al., Detailed Structural Analysis of Lipids Directly on Tissue Specimens Using a MALDI-SpiralTOF-Reflectron TOF Mass Spectrometer. PLoS ONE, 2012. 7(5): p. e37107.
  19. Voorhees, K.J., C.R. McAlpin, and C.R. Cox, Lipid profiling using catalytic pyrolysis/metal oxide laser ionization-mass spectrometry. Journal of Analytical and Applied Pyrolysis, 2012. 98(0): p. 201-206.
  20. Yamazaki, M., et al., Origins of Oxygen Atoms in a Marine Ladder-Frame Polyether: Evidence of Monooxygenation by 18O-Labeling and Using Tandem Mass Spectrometry. The Journal of Organic Chemistry, 2012. 77(11): p. 4902-4906.
  21. Kubo, A., et al., Structural analysis of triacylglycerols by using a MALDI-TOF/TOF system with monoisotopic precursor selection. Journal of the American Society for Mass Spectrometry, 2013. 24(5): p. 684-689.
  22. Matsumori, N., et al., A Novel Sperm-Activating and Attracting Factor from the Ascidian Ascidia sydneiensis. Organic Letters, 2013. 15(2): p. 294-297.
  23. Teramoto, K., et al., Simple and rapid characterization of mycolic acids from Dietzia strains by using MALDI spiral-TOFMS with ultra high mass-resolving power. The Journal of Antibiotics, 2013: p. 1-5.
  24. Voorhees, K.J., et al., Modified MALDI MS fatty acid profiling for bacterial identification. Journal of Mass Spectrometry, 2013. 48(7): p. 850-855.
  25. msMicroimager Data Analysis Software for Ultrahigh-mass Mass Resolution MALDI MS Imaging
  26. Application of High-Resolution MALDI-TOFMS with a Spiral Ion Trajectory for the Structural Characterization of Free Radical Polymerized Methacrylate Ester Copolymers; H. Sato, Ishii, Momose, T. Sato, and Teramoto; Mass Spectrometry; 2013.
  27. Fouquet, T., Cody, R.B., Sato, H. Capabilities of the remainders of nominal Kendrick masses and the referenced Kendrick mass defects for copolymer ions. J. of Mass Spectrometry; 2017; Vol. 59, Issue 9; p. 618-624.


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