The coupled physical and chemical dynamics model of ultraviolet matrix-assisted laser desorption/ionization (MALDI) has reproduced and explained a wide variety of MALDI phenomena. The rationale behind and elements of the model are reviewed, including the photophysics, kinetics, and thermodynamics of primary and secondary reaction steps. Experimental results are compared with model predictions to illustrate the foundations of the model, coupling of ablation and ionization, differences between and commonalities of matrices, secondary charge transfer reactions, ionization in both polarities, fluence and concentration dependencies, and suppression and enhancement effects.


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Literature Cited

  1. Karas M, Bachmann D, Hillenkamp F. 1.  1985. Influence of the wavelength in high-irradiance ultraviolet laser desorption mass spectrometry of organic molecules. Anal. Chem. 57:2935–39 [Google Scholar]
  2. Karas M, Bachmann D, Bahr U, Hillenkamp F. 2.  1987. Matrix-assisted ultraviolet laser desorption of non-volatile compounds. Int. J. Mass Spectrom. Ion Proc. 78:53–68 [Google Scholar]
  3. Dreisewerd K. 3.  2003. The desorption process in MALDI. Chem. Rev. 103:395–426 [Google Scholar]
  4. Knochenmuss R. 4.  2006. Ion formation mechanisms in UV-MALDI. Analyst 131:966–86 [Google Scholar]
  5. Knochenmuss R. 5.  2002. A quantitative model of ultraviolet matrix-assisted laser desorption and ionization. J. Mass Spectrom. 37:867–77 [Google Scholar]
  6. Knochenmuss R. 6.  2003. A quantitative model of UV-MALDI including analyte ion generation. Anal. Chem. 75:2199 [Google Scholar]
  7. Knochenmuss R. 7.  2009. A bipolar rate equation model of MALDI primary and secondary ionization processes, with application to positive/negative analyte ion rations and suppression effects. Int. J. Mass Spectrom. 285:105–13 [Google Scholar]
  8. Niu S, Zhang W, Chait BT. 8.  1998. Direct comparison of infrared and ultraviolet wavelength matrix-assisted laser desorption/ionization mass spectrometry of proteins. J. Am. Soc. Mass Spectrom. 9:1–7 [Google Scholar]
  9. Chen X, Carroll JA, Beavis RC. 9.  1998. Near-ultraviolet-induced matrix-assisted laser desorption/ionization as a function of wavelength. J. Am. Soc. Mass Spectrom. 9:885–91 [Google Scholar]
  10. Lu I-C, Lee CH, Lee Y-T, Ni C-K. 10.  2015. Ionization mechanism of matrix-assisted laser desorption/ionization. Annu. Rev. Anal. Chem. 8:21–39 [Google Scholar]
  11. Bae YJ, Kim MS. 11.  2015. A thermal mechanism of ion formation in MALDI. Annu. Rev. Anal. Chem. 8:41–60 [Google Scholar]
  12. Karas M, Glückmann M, Schäfer J. 12.  2000. Ionization in matrix-assisted laser desorption ionization: Singly charged molecular ions are the lucky survivors. J. Mass Spectrom. 35:1–12 [Google Scholar]
  13. Jaskolla TW, Karas M. 13.  2011. Compelling evidence for Lucky Survivor and gas phase protonation: the unified MALDI analyte protonation mechanism. J. Am. Soc. Mass Spectrom. 22:976–88 [Google Scholar]
  14. Karas M, Krueger R. 14.  2003. Ion formation in MALDI: the cluster ionization mechanism. Chem. Rev. 103:427–39 [Google Scholar]
  15. Ehring H, Sundqvist BUR. 15.  1995. Studies of the MALDI process by luminescence spectroscopy. J. Mass Spectrom. 30:1303–10 [Google Scholar]
  16. Ehring H, Sundqvist BUR. 16.  1996. Excited-state relaxation processes of MALDI-matrices studied by luminescence spectroscopy. Appl. Surf. Sci. 96:577–80 [Google Scholar]
  17. Lüdemann H-C, Redmond RW, Hillenkamp F. 17.  2002. Singlet-singlet annihilation in ultraviolet MALDI studied by fluorescence spectroscopy. Rapid Commun. Mass Spectrom. 16:1287–94 [Google Scholar]
  18. Setz P, Knochenmuss R. 18.  2005. Exciton mobility and trapping in a UV-MALDI matrix. J. Phys. Chem. A 109:4030–37 [Google Scholar]
  19. Ehring H, Karas M, Hillenkamp F. 19.  1992. Role of photoionization and photochemistry in ionization processes of organic molecules and relevance for matrix-assisted laser desorption/ionization mass spectrometry. Org. Mass Spectrom. 27:427–80 [Google Scholar]
  20. Liao P-C, Allison J. 20.  1995. Ionization processes in matrix-assisted laser desorption/ionization mass spectrometry: matrix-dependent formation of [M+H]+ versus [M+Na]+ ions of small peptides and some mechanistic comments. J. Mass Spectrom. 30:408–23 [Google Scholar]
  21. Karbach V, Knochenmuss R. 21.  1998. Do single matrix molecules generate primary ions in ultraviolet matrix-assisted laser desorption/ionization?. Rapid Commun. Mass Spectrom. 12:968–74 [Google Scholar]
  22. Lin Q, Knochenmuss R. 22.  2001. Two-photon ionization thresholds of matrix-assisted laser desorption/ionization matrix clusters. Rapid Comm. Mass Spectrom. 15:1422–26 [Google Scholar]
  23. Demirev P, Westman A, Reimann CT, Håkansson P, Barofsky D. 23.  et al. 1992. Matrix-assisted laser desorption with ultra-short laser pulses. Rapid Commun. Mass Spectrom. 6:187–91 [Google Scholar]
  24. Riahi K, Bolbach G, Brunot A, Breton F, Spiro M, Blais J-C. 24.  1994. Influence of laser focusing in matrix-assisted laser desorption/ionization. Rapid Commun. Mass Spectrom. 8:242–47 [Google Scholar]
  25. Beavis RC. 25.  1992. Phenomenological models for matrix-assisted laser desorption ion yields near the threshold fluence. Org. Mass Spectrom. 27:864–68 [Google Scholar]
  26. Soltwisch J, Jaskolla TW, Hillenkamp F, Karas M, Dreisewerd K. 26.  2012. Ion yields in UV-MALDI mass spectrometry as a function of excitation laser wavelength and optical and physico-chemical properties of classical and halogen-substituted MALDI matrixes. Anal. Chem. 84:6567–76 [Google Scholar]
  27. Asfandiarov NL, Pshenichnyuk SA, Fokin AI, Lukin VG, Fal'ko VS. 27.  2002. Electron capture negative ion mass spectra of some typical MALDI matrices. Rapid Commun. Mass Spectrom. 16:1760–65 [Google Scholar]
  28. Pshenichnyuk SA, Asfandiarov NL. 28.  2004. The role of free electrons in MALDI: electron capture by molecules of α-cyano-4-hydroxycinnamic acid. Eur. J. Mass Spectrom. 10:477–86 [Google Scholar]
  29. Zenobi R, Knochenmuss R. 29.  1998. Ion formation in MALDI mass spectrometry. Mass Spectrom. Rev. 17:337 [Google Scholar]
  30. Hoteling AJ, Nichols WF, Giesen DJ, Lenhard JR, Knochenmuss R. 30.  2006. Electron transfer reactions in LDI and MALDI: factors influencing matrix and analyte ion intensities. Eur. J. Mass Spectrom. 12:345–58 [Google Scholar]
  31. Liu B-L, Charkin OP, Klemenko N, Chen CW, Wang Y-S. 31.  2010. Initial ionization reaction in matrix-assisted laser desorption/ionization. J. Phys. Chem. B 114:10853–59 [Google Scholar]
  32. Knochenmuss R. 32.  2014. Energetics and kinetics of thermal ionization models of MALDI. J. Am. Soc. Mass Spectrom. 25:1521–27 [Google Scholar]
  33. Lippa TP, Eustis SN, Wang D, Bowen KH. 33.  2007. Electrophilic properties of common MALDI matrix molecules. Int. J. Mass Spectrom. 268:1–7 [Google Scholar]
  34. El-Sayed MA. 34.  1968. The triplet state: its radiative and nonradiative properties. Acc. Chem. Res. 1:8–16 [Google Scholar]
  35. Jacques P, Allonas X, Sarbach A, Haselbach E, Vauthey E. 35.  2003. Tuning the ion formation process from triplet-triplet annihilation to triplet-mediated photoionization. Chem. Phys. Lett. 378:185–91 [Google Scholar]
  36. Hoyer T, Tuszynski W, Lienau C. 36.  2007. Ultrafast photodimerization dynamics in α-cyano-4-hydroxycinnamic and sinapinic acid crystals. Chem. Phys. Lett. 443:107–12 [Google Scholar]
  37. Hoyer T. 37.  2009. Stationäre und zeitaufgelöste Photolumineszenz-Spektroskopie zur Analyse ultraschneller Photoreaktionen in MALDI- und Solarzellenproben PhD Thesis, Carl von Ossietzky Universität Oldenburg, Oldenburg, Ger.
  38. Hoyer T, Tuszynski W, Lienau C. 38.  2010. Competing ultrafast photoinduced quenching reactions in cinnamic acid peptide blends. Phys. Chem. Chem. Phys. 12:13052 [Google Scholar]
  39. Knochenmuss R. 39.  2014. MALDI mechanisms: wavelength and matrix dependence of the coupled photophysical and chemical dynamics model. Analyst 139:147–56 [Google Scholar]
  40. Miller DR. 40.  1988. Free jet sources. Atomic Mol. Beam Methods 1:14–43 [Google Scholar]
  41. Knochenmuss R, Zhigilei LV. 41.  2005. A molecular dynamics model of UV-MALDI including ionization processes. J. Phys. Chem. B 109:22947–57 [Google Scholar]
  42. Handschuh M, Nettesheim S, Zenobi R. 42.  1998. Laser-induced molecular desorption and particle ejection from organic films. Appl. Surf. Sci. 137:125–35 [Google Scholar]
  43. Zhigilei LV, Kodali PBS, Garrison BJ. 43.  1997. Molecular dynamics model for laser ablation and desorption of organic solids. J. Phys. Chem. B 101:2028–37 [Google Scholar]
  44. Kinsel G, Knochenmuss R, Setz P, Land CM, Goh S-K. 44.  et al. 2002. Ionization energy reductions in small 2,5-dihydroxybenzoic acid-proline clusters. J. Mass Spectrom. 37:1131–40 [Google Scholar]
  45. Yassin FH, Marynick DS. 45.  2006. Computational study of matrix-peptide interactions in MALDI mass spectrometry: interactions of 2,5- and 3,5-dihydroxybenzoic acid with the tripeptide valine-proline-leucine. J. Phys. Chem. A 110:3820–25 [Google Scholar]
  46. Knochenmuss R. 46.  2004. Photoionization pathways and free electrons in UV-MALDI. Anal. Chem. 76:3179–84 [Google Scholar]
  47. Agmon N. 47.  1981. From energy profiles to structure–reactivity correlations. Int. J. Chem. Kinet. 13:333–65 [Google Scholar]
  48. Knochenmuss R, Zhigilei LV. 48.  2012. What determines MALDI ion yields? A molecular dynamics study of ion loss mechanisms. Anal. Bioanal. Chem. 402:2511–19 [Google Scholar]
  49. Knochenmuss R. 49.  2013. MALDI and related methods: a solved problem or still a mystery?. Mass Spectrom. (Jpn. 2:S0006 [Google Scholar]
  50. Jaskolla TW, Karas M. 50.  2008. Using fluorescence dyes as a tool for analyzing the MALDI process. J. Am. Soc. Mass Spectrom. 19:1054–61 [Google Scholar]
  51. Kirmess KM, Knochenmuss R, Blanchard GJ, Kinsel GR. 51.  2016. MALDI ionization mechanisms investigated by comparison of isomers of dihydroxybenzoic acid. J. Mass Spectrom. 51:79–85 [Google Scholar]
  52. Knochenmuss R, Vertes A. 52.  2000. Time-delayed 2-pulse studies of MALDI matrix ionization mechanisms. J. Phys. Chem. B 104:5406–10 [Google Scholar]
  53. Bae YJ, Shin YS, Moon JH, Kim MS. 53.  2012. Degree of ionization in MALDI of peptides: thermal explanation for the gas-phase ion formation. J. Am. Soc. Mass Spectrom. 23:1326–35 [Google Scholar]
  54. Tsai M-T, Lee S, Lu I-C, Chu KY, Liang C-W. 54.  et al. 2013. Ion-to-neutral ratio of 2,5-dihydroxybenzoic acid in matrix-assisted laser desorption/ionization. Rapid Comm. Mass Spectrom. 27:955–63 [Google Scholar]
  55. Lu I-C, Chu KY, Lin C-Y, Wu S-Y, Dyakov YA. 55.  et al. 2015. Ion-to-neutral ratios and thermal proton transfer in matrix-assisted laser desorption/ionization. J. Am. Soc. Mass Spectrom. 26:1242–51 [Google Scholar]
  56. Knochenmuss R. 56.  2015. Ion yields in the coupled chemical and physical dynamics model of MALDI. J. Am. Soc. Mass Spectrom. 26:1645–48 [Google Scholar]
  57. Horneffer V, Forsmann A, Strupat K, Hillenkamp F, Kubitscheck U. 57.  2001. Localization of analyte molecules in MALDI preparations by confocal laser scanning microscopy. Anal. Chem. 73:1016–22 [Google Scholar]
  58. Salum ML, Itovich LM, Erra-Balsells R. 58.  2013. Z-sinapinic acid: the change of the stereochemistry of cinnamic acids as rational synthesis of a new matrix for carbohydrate MALDI-MS analysis. J. Mass Spectrom. 48:1160–69 [Google Scholar]
  59. Kirmess KM, Knochenmuss R, Blanchard GJ. 59.  2014. Excited state dynamics in the MALDI matrix 2,4,6-trihydroxyacetophenone: evidence for triplet pooling charge separation reactions. Rapid Commun. Mass Spectrom. 28:2134–40 [Google Scholar]
  60. Land CM, Kinsel GR. 60.  1998. Investigation of the mechanism of intracluster proton transfer from sinapinic acid to biomolecular analytes. J. Am. Soc. Mass Spectrom. 9:1060–67 [Google Scholar]
  61. Land CM, Kinsel GR. 61.  2001. The mechanism of matrix to analyte proton transfer in clusters of 2,5-dihydroxybenzoic acid and the tripeptide VPL. J. Am. Soc. Mass Spectrom. 12:726–31 [Google Scholar]
  62. Kinsel GR, Zhao Q, Narayanasamy J, Yassin F, Rasika Dias HV. 62.  et al. 2004. Arginine/2,5-dihydroxybenzoic acid clusters: an experimental and theoretical study of the gas-phase and solid-state systems. J. Phys. Chem. A 108:3153–61 [Google Scholar]
  63. McCombie G, Knochenmuss R. 63.  2006. Enhanced MALDI ionization efficiency at the metal-matrix interface: practical and mechanistic consequences of sample thickness and preparation method. J. Am. Soc. Mass Spectrom. 17:737–45 [Google Scholar]
  64. Knochenmuss R, McCombie G, Faderl M. 64.  2006. The dependence of MALDI ion yield on metal substrates: photoelectrons from the metal versus surface-enhanced matrix photoionization. J. Phys. Chem. A 110:12728–33 [Google Scholar]
  65. Knochenmuss R, Zhigilei LV. 65.  2010. Molecular dynamics simulations of MALDI: laser fluence and pulse width dependence of plume characteristics and consequences for matrix and analyte ionization. J. Mass Spectrom. 45:333–46 [Google Scholar]
  66. Fournier I, Brunot A, Tabet J-C, Bolbach G. 66.  2002. Delayed extraction experiments using a repulsive potential before ion extraction: evidence of clusters as ion precursors in UV-MALDI. Part I: dynamical effects with the matrix 2,5-dihydroxybenzoic acid. Int. J. Mass Spectrom. 213:203–15 [Google Scholar]
  67. Fournier I, Brunot A, Tabet J-C, Bolbach G. 67.  2005. Delayed extraction experiments using a repulsive potential before ion extraction: evidence of non-covalent clusters as ion precursors in UV MALDI. Part II: dynamic effects with alpha-cyano-4-hydroxycinnamic acid matrix. J. Mass Spectrom. 40:50–59 [Google Scholar]
  68. Alves S, Fournier I, Afonso C, Wind F, Tabet J-C. 68.  2006. Gas-phase ionization/desolvation processes and their effect on protein charge state distributions under MALDI conditions. Eur. J. Mass Spectrom. 12:369–83 [Google Scholar]
  69. Bökelmann V, Spengler B, Kaufmann R. 69.  1995. Dynamical parameters of ion ejection and ion formation in matrix-assisted laser desorption/ionization. Eur. Mass Spectrom. 1:81–93 [Google Scholar]
  70. Dreisewerd K, Schürenberg M, Karas M, Hillenkamp F. 70.  1995. Influence of the laser intensity and spot size on the desorption of molecules and ions in matrix-assisted laser-desorption/ionization with a uniform beam profile. Int. J. Mass Spectrom. Ion Proc. 141:127–48 [Google Scholar]
  71. Feldhaus D, Menzel C, Berkenkamp S, Hillenkamp F. 71.  2000. Influence of the laser fluence in infrared matrix-assisted laser desorption/ionization with a 2.94 μm Er:YAG laser and a flat-top beam profile. J. Mass Spectrom. 35:1320–28 [Google Scholar]
  72. Guenther S, Koestler M, Schulz O, Spengler B. 72.  2010. Laser spot size and laser power dependence of ion formation in high resolution MALDI imaging. Int. J. Mass Spectrom. 294:7–15 [Google Scholar]
  73. Qiao H, Spicer V, Ens W. 73.  2008. The effect of laser profile, fluence and spot size on sensitivity in orthogonal-injection MALDI mass spectrometry. Rapid Commun. Mass Spectrom. 22:2779–90 [Google Scholar]
  74. Schuerenberg M, Dreisewerd K, Kamanabrou S, Hillenkamp F. 74.  1998. Influence of the sample temperature on the desorption of matrix molecules and ions in MALDI. Int. J. Mass Spectrom. 172:89 [Google Scholar]
  75. Wallace WE, Arnould MA, Knochenmuss R. 75.  2005. 2,5-Dihydroxybenzoic acid: laser desorption/ionization as a function of elevated temperature. Int. J. Mass Spectrom. 242:13–22 [Google Scholar]
  76. Walker BN, Razunguzwa T, Powell M, Knochenmuss R, Vertes A. 76.  2009. Nanophotonic ion production from silicon microcolumn arrays. Angew. Chem. Int. Ed. 48:1669–72 [Google Scholar]
  77. Go EP, Apon JV, Luo G, Saghatelian A, Daniels RH. 77.  et al. 2005. Desorption/ionization on silicon nanowires. Anal. Chem. 77:1641–46 [Google Scholar]
  78. Luo GH, Chen Y, Daniels H, Dubrow R, Vertes A. 78.  2006. Internal energy transfer in laser desorption/ionization from silicon nanowires. J. Phys. Chem. B 110:13381–86 [Google Scholar]
  79. Knochenmuss R. 79.  2009. Laser desorption/ablation plumes from capillary-like restricted volumes. Eur. J. Mass Spectrom. 15:189–98 [Google Scholar]
  80. Knochenmuss R, Dubois F, Dale MJ, Zenobi R. 80.  1996. The matrix suppression effect and ionization mechanisms in matrix-assisted laser desorption/ionization. Rapid Commun. Mass Spectrom. 10:871–77 [Google Scholar]
  81. Knochenmuss R, Karbach V, Wiesli U, Breuker K, Zenobi R. 81.  1998. The matrix suppression effect in matrix-assisted laser desorption/ionization: application to negative ions and further characteristics. Rapid Commun. Mass Spectrom. 12:529–34 [Google Scholar]
  82. McCombie G, Knochenmuss R. 82.  2005. Small-molecule MALDI using the matrix suppression effect to reduce or eliminate background interferences. Anal. Chem. 76:4990–97 [Google Scholar]
  83. Knochenmuss R, Stortelder A, Breuker K, Zenobi R. 83.  2000. Secondary ion-molecule reactions in MALDI. J. Mass Spectrom. 35:1237–45 [Google Scholar]
  84. Dashtiev M, Wäfler E, Röhling U, Gorshkov M, Hillenkamp F, Zenobi R. 84.  2007. Positive and negative analyte ion yield in matrix-assisted laser desorption/ionization. Int. J. Mass Spectrom. 268:122–30 [Google Scholar]
  85. Hillenkamp F, Wäfler E, Jecklin MC, Zenobi R. 85.  2008. Positive and negative analyte ion yield in MALDI revisited. Int. J. Mass Spectrom. 285:114–19 [Google Scholar]
  86. Knochenmuss R. 86.  2008. Positive/negative ion ratios and in-plume reaction equilibria in MALDI. Int. J. Mass Spectrom. 273:84–86 [Google Scholar]
  87. Ahn SH, Park KM, Bae YJ, Kim MS. 87.  2013. Quantitative reproducibility of mass spectra in matrix-assisted laser desorption ionization and unraveling of the mechanism for gas-phase peptide ion formation. J. Mass Spectrom. 48:299–305 [Google Scholar]
  88. Knochenmuss R. 88.  2013. MALDI ionization mechanisms: The coupled photophysical and chemical dynamics model correctly predicts “temperature”-selected spectra. J. Mass Spectrom. 48:998–1004 [Google Scholar]
  89. Moon JH, Shin YS, Bae YJ, Kim MS. 89.  2011. Ion yields for some salts in MALDI: mechanism for the gas-phase ion formation from preformed ions. J. Am. Soc. Mass Spectrom. 23:162–70 [Google Scholar]

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