An investigation on the mechanism of sublimed DHB matrix on molecular ion yields in SIMS imaging of brain tissue


We have characterized the use of sublimation to deposit matrix-assisted laser desorption/ionization (MALDI) matrices in secondary ion mass spectrometry (SIMS) analysis, i.e. matrix-enhanced SIMS (ME-SIMS), a common surface modification method to enhance sensitivity for larger molecules and to increase the production of intact molecular ions. We use sublimation to apply a thin layer of a conventional MALDI matrix, 2,5-dihydroxybenzoic acid (DHB), onto rat brain cerebellum tissue to show how this technique can be used to enhance molecular yields in SIMS while still retaining a lateral resolution around 2 μm and also to investigate the mechanism of this enhancement. The results here illustrate that cholesterol, which is a dominant lipid species in the brain, is decreased on the tissue surface after deposition of matrix, particularly in white matter. The decrease of cholesterol is followed by an increased ion yield of several other lipid species. Depth profiling of the sublimed rat brain reveals that the lipid species are de facto extracted by the DHB matrix and concentrated in the top most layers of the sublimed matrix. This extraction/concentration of lipids directly leads to an increase of higher mass lipid ion yield. It is also possible that the decrease of cholesterol decreases the potential suppression of ion yield caused by cholesterol migration to the tissue surface. This result provides us with significant insights into the possible mechanisms involved when using sublimation to deposit this matrix in ME-SIMS.

Schematic representation of the enhancement on the molecular ion yields in SIMS by deposition of DHB matrix on the brain tissue using sublimation

This is a preview of subscription content, log in to check access.

Access options

Buy single article

Instant unlimited access to the full article PDF.

US$ 39.95

Price includes VAT for USA

Subscribe to journal

Immediate online access to all issues from 2019. Subscription will auto renew annually.

US$ 157

This is the net price. Taxes to be calculated in checkout.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5


  1. 1.

    McDonnell LA, Piersma SR, MaartenAltelaar AF, Mize TH, Luxembourg SL, Verhaert PD, et al. Subcellular imaging mass spectrometry of brain tissue. J Mass Spectrom. 2005;40(2):160–8.

  2. 2.

    Chughtai K, Heeren RM. Mass spectrometric imaging for biomedical tissue analysis. Chem Rev. 2010;110(5):3237–77.

  3. 3.

    McDonnell LA, Heeren RM. Imaging mass spectrometry. Mass Spectrom Rev. 2007;26(4):606–43.

  4. 4.

    Hanrieder J, Phan NT, Kurczy ME, Ewing AG. Imaging mass spectrometry in neuroscience. ACS Chem Neurosci. 2013;4(5):666–79.

  5. 5.

    Lanni EJ, Dunham SJ, Nemes P, Rubakhin SS, Sweedler JV. Biomolecular imaging with a C60-SIMS/MALDI dual ion source hybrid mass spectrometer: instrumentation, matrix enhancement, and single cell analysis. J Am Soc Mass Spectrom. 2014;25(11):1897–907.

  6. 6.

    Brunelle A, Touboul D, Laprevote O. Biological tissue imaging with time-of-flight secondary ion mass spectrometry and cluster ion sources. J Mass Spectrom. 2005;40(8):985–99.

  7. 7.

    Rubakhin SS, Jurchen JC, Monroe EB, Sweedler JV. Imaging mass spectrometry: fundamentals and applications to drug discovery. Drug Discov Today. 2005;10(12):823–37.

  8. 8.

    McDonnell LA, Heeren RM, de Lange RP, Fletcher IW. Higher sensitivity secondary ion mass spectrometry of biological molecules for high resolution, chemically specific imaging. J Am Soc Mass Spectrom. 2006;17(9):1195–202.

  9. 9.

    Passarelli MK, Winograd N. Lipid imaging with time-of-flight secondary ion mass spectrometry (ToF-SIMS). Biochim Biophys Acta. 2011;1811(11):976–90.

  10. 10.

    Murphy RC, Hankin JA, Barkley RM. Imaging of lipid species by MALDI mass spectrometry. J Lipid Res. 2009;50(Suppl):S317–22.

  11. 11.

    Woods AS, Jackson SN. Brain tissue lipidomics: direct probing using matrix-assisted laser desorption/ionization mass spectrometry. AAPS J. 2006;8:E391–5.

  12. 12.

    Wang J, Qiu S, Chen S, Xiong C, Liu H, Wang J, et al. MALDI-TOF MS imaging of metabolites with a N-(1-naphthyl) ethylenediamine dihydrochloride matrix and its application to colorectal cancer liver metastasis. Anal Chem. 2015;87(1):422–30.

  13. 13.

    Yang J, Caprioli RM. Matrix sublimation/recrystallization for imaging proteins by mass spectrometry at high spatial resolution. Anal Chem. 2011;83(14):5728–34.

  14. 14.

    Guenther S, Römpp A, Kummer W, Spengler B. AP-MALDI imaging of neuropeptides in mouse pituitary gland with 5μm spatial resolution and high mass accuracy. Int J Mass Spectrom. 2011;305(2-3):228–37.

  15. 15.

    Schober Y, Guenther S, Spengler B, Rompp A. Single cell matrix-assisted laser desorption/ionization mass spectrometry imaging. Anal Chem. 2012;84(15):6293–7.

  16. 16.

    Fletcher JS, Vickerman JC. A new SIMS paradigm for 2D and 3D molecular imaging of bio-systems. Anal Bioanal Chem. 2010;396(1):85–104.

  17. 17.

    Sjovall P, Lausmaa J, Johansson B. Mass spectrometric imaging of lipids in brain tissue. Anal Chem. 2004;76(15):4271–8.

  18. 18.

    Svara FN, Kiss A, Jaskolla TW, Karas M, Heeren RM. High-reactivity matrices increase the sensitivity of matrix enhanced secondary ion mass spectrometry. Anal Chem. 2011;83(21):8308–13.

  19. 19.

    Sheraz nee Rabbani S, Barber A, Fletcher JS, Lockyer NP, Vickerman JC. Enhancing secondary ion yields in time of flight-secondary ion mass spectrometry using water cluster primary beams. Anal Chem. 2013;85(12):5654–8.

  20. 20.

    Winograd N. The magic of cluster SIMS. Anal Chem. 2005;77:142A–9A.

  21. 21.

    Mahoney CM. Cluster secondary ion mass spectrometry of polymers and related materials. Mass Spectrom Rev. 2010;29(2):247–93.

  22. 22.

    Jones EA, Fletcher JS, Thompson CE, Jackson DA, Lockyer NP, Vickerman JC. ToF-SIMS analysis of bio-systems: are polyatomic primary ions the solution? Appl Surf Sci. 2006;252(19):6844–54.

  23. 23.

    Wucher A. Molecular secondary ion formation under cluster bombardment: A fundamental review. Appl Surf Sci. 2006;252(19):6482–289.

  24. 24.

    Monroe EB, Annangudi SP, Hatcher NG, Gutstein HB, Rubakhin SS, Sweedler JV. SIMS and MALDI MS imaging of the spinal cord. Proteomics. 2008;8(18):3746–54.

  25. 25.

    Solon EG, Schweitzer A, Stoeckli M, Prideaux B. Autoradiography, MALDI-MS, and SIMS-MS imaging in pharmaceutical discovery and development. AAPS J. 2010;12(1):11–26.

  26. 26.

    Hanton SD, Clark PAC, Owens KG. Investigations of matrix-assisted laser desorption/ionization sample preparation by time-of-flight secondary ion mass spectrometry. J Am Soc Mass Spectrom. 1998;10:104–11.

  27. 27.

    Lanni EJ, Rubakhin SS, Sweedler JV. Mass spectrometry imaging and profiling of single cells. J Proteomics. 2012;75(16):5036–51.

  28. 28.

    Wu KJ, Odom RW. Matrix-enhanced secondary ion mass spectrometry: a method for molecular analysis of solid surfaces. Anal Chem. 1996;68:873–82.

  29. 29.

    Delcorte A. Matrix-enhanced secondary ion mass spectrometry: the alchemist's solution? Appl Surf Sci. 2006;252(19):6582–7.

  30. 30.

    Fitzgerald JD, Kunnath P, Walker AV. Matrix-enhanced secondary ion mass spectrometry (ME SIMS) using room temperature ionic liquid matrices. Anal Chem. 2010;82:4413–9.

  31. 31.

    Hanton SD, Owens KG. Using MESIMS to analyze polymer MALDI matrix solubility. J Am Soc Mass Spectrom. 2005;16(7):1172–80.

  32. 32.

    Lerach JO, Keskin S, Winograd N. Investigations into the interactions of a MALDI Matrix with organic thin films using C60+SIMS depth profiling. Surf Interface Anal. 2014;46(S1):67–9.

  33. 33.

    Nicola AJ, Muddiman DC, Hercules DM. Enhancement of ion intensity in time-of-flight secondary-ionization mass spectrometry. J Am Soc Mass Spectrom. 1996;7(5):467–72.

  34. 34.

    Heeren RMA, Kukrer-Kaletas B, Taban IM, MacAleese L, McDonnell LA. Quality of surface: the influence of sample preparation on MS-based biomolecular tissue imaging with MALDI-MS and (ME-)SIMS. Appl Surf Sci. 2008;255(4):1289–97.

  35. 35.

    Altelaar AF, Luxembourg SL, McDonnell LA, Piersma SR, Heeren RM. Imaging mass spectrometry at cellular length scales. Nat Protoc. 2007;2(5):1185–96.

  36. 36.

    Hankin JA, Barkley RM, Murphy RC. Sublimation as a method of matrix application for mass spectrometric imaging. J Am Soc Mass Spectrom. 2007;18(9):1646–52.

  37. 37.

    Kaletas BK, van der Wiel IM, Stauber J, Lennard JD, Guzel C, Kros JM, et al. Sample preparation issues for tissue imaging by imaging MS. Proteomics. 2009;9(10):2622–33.

  38. 38.

    Sodhi RN. Time-of-flight secondary ion mass spectrometry (TOF-SIMS):--versatility in chemical and imaging surface analysis. Analyst (Cambridge, U K). 2004;129(6):483–7.

  39. 39.

    Angerer TB, Dowlatshahi Pour M, Malmberg P, Fletcher JS. Improved molecular imaging in rodent brain with time-of-flight-secondary ion mass spectrometry using gas cluster ion beams and reactive vapor exposure. Anal Chem. 2015;87(8):4305–13.

  40. 40.

    Sjovall P, Johansson B, Lausmaa J. Localization of lipids in freeze-dried mouse brain sections by imaging TOF-SIMS. Appl Surf Sci. 2006;252(19):6966–674.

  41. 41.

    Debois D, Brunelle A, Laprevote O. Attempts for molecular depth profiling directly on a rat brain tissue section using fullerene and bismuth cluster ion beams. Int J Mass Spectrom. 2007;260(2-3):115–20.

  42. 42.

    Bich C, Havelund R, Moellers R, Touboul D, Kollmer F, Niehuis E, et al. Argon cluster ion source evaluation on lipid standards and rat brain tissue samples. Anal Chem. 2013;85(16):7745–52.

Download references

Author information

Correspondence to Per Malmberg or Andrew Ewing.

Ethics declarations

Conflicts of interest

The authors hereby declare that there are no conflicts of interest.

All instrumental and national guidelines for the use of animals were followed.

Electronic supplementary material

Below is the link to the electronic supplementary material.


(PDF 1017 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Dowlatshahi Pour, M., Malmberg, P. & Ewing, A. An investigation on the mechanism of sublimed DHB matrix on molecular ion yields in SIMS imaging of brain tissue. Anal Bioanal Chem 408, 3071–3081 (2016).

Download citation


  • ME-SIMS mechanism
  • Cholesterol migration
  • MS imaging