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MALDI-Imaging Mass Spectrometry on Tissues

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Clinical Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1243))

Abstract

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)—profiling and imaging mass spectrometry (MSI) are promising technologies for measuring hundreds of different molecules directly on tissues. For instance, small molecules, drugs and their metabolites, endogenous lipids, carbohydrates and complex peptides/proteins can be measured at the same time. In the most advanced instruments, it is achieved without significant disruption of sample integrity. MSI is a unique approach for assessing the spatial distribution of molecules using graphical multidimensional maps of their constituent analytes, which may for instance be correlated with histopathological alterations in patient tissues. MALDI-TOF-MSI technology has been implemented in hospitals of several countries, where it is routinely used for quick pathogen(s) identification, a task formerly accomplished by laborious and expensive DNA/RNA-based PCR (polymerase chain reaction) screening.

In this chapter, we describe how MSI is performed, what is required from the researcher, the instrument vendors and finally what can be achieved with MSI. We restrict our descriptions only to MALDI-MSI although several other MS techniques of ionization can easily be linked to MSI.

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References

  1. Caldwell RL, Caprioli RM (2005) Tissue profiling by mass spectrometry: a review of methodology and applications. Mol Cell Proteomics 4:394–401

    Article  CAS  PubMed  Google Scholar 

  2. Chaurand P, Norris JL, Cornett DS et al (2006) New developments in profiling and imaging of proteins from tissue sections by MALDI mass spectrometry. J Proteome Res 5:2889–2900

    Article  CAS  PubMed  Google Scholar 

  3. Lalowski M, Magni F, Mainini V et al (2013) Imaging mass spectrometry: a new tool for kidney disease investigations. Nephrol Dial Transplant 28:1648–1656. doi:10.1093/ndt/gft008

    Article  PubMed  Google Scholar 

  4. Cornett DS, Reyzer ML, Chaurand P et al (2007) MALDI imaging mass spectrometry: molecular snapshots of biochemical systems. Nat Methods 4:828–833

    Article  CAS  PubMed  Google Scholar 

  5. Rompp A, Schafer KC, Guenther S et al (2013) High-resolution atmospheric pressure infrared laser desorption/ionization mass spectrometry imaging of biological tissue. Anal Bioanal Chem 405:6959–6968

    Article  PubMed  Google Scholar 

  6. Altelaar AF, Klinkert I, Jalink K et al (2006) Gold-enhanced biomolecular surface imaging of cells and tissue by SIMS and MALDI mass spectrometry. Anal Chem 78:734–742

    Article  CAS  PubMed  Google Scholar 

  7. Mainini V, Bovo G, Chinello C et al (2013) Detection of high molecular weight proteins by MALDI imaging mass spectrometry. Mol Biosyst 9:1101–1107

    Article  CAS  PubMed  Google Scholar 

  8. Lemaire R, Desmons A, Tabet JC et al (2007) Direct analysis and MALDI imaging of formalin-fixed, paraffin-embedded tissue sections. J Proteome Res 6:1295–1305

    Article  CAS  PubMed  Google Scholar 

  9. Schwamborn K (2012) Imaging mass spectrometry in biomarker discovery and validation. J Proteomics 75:4990–4998

    Article  CAS  PubMed  Google Scholar 

  10. Goudy S, Angel P, Jacobs B et al (2013) Cell-autonomous and non-cell-autonomous roles for IRF6 during development of the tongue. PLoS One 8:e56270

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  11. McDonnell LA, Corthals GL, Willems SM et al (2010) Peptide and protein imaging mass spectrometry in cancer research. J Proteomics 73:1921–1944

    Article  CAS  PubMed  Google Scholar 

  12. Rubakhin SS, Sweedler JV (2008) Quantitative measurements of cell-cell signaling peptides with single-cell MALDI MS. Anal Chem 80:7128–7136

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  13. Trede D, Schiffler S, Becker M et al (2012) Exploring three-dimensional matrix-assisted laser desorption/ionization imaging mass spectrometry data: three-dimensional spatial segmentation of mouse kidney. Anal Chem 84:6079–6087

    Article  CAS  PubMed  Google Scholar 

  14. Svensson M, Boren M, Skold K et al (2009) Heat stabilization of the tissue proteome: a new technology for improved proteomics. J Proteome Res 8:974–981

    Article  CAS  PubMed  Google Scholar 

  15. Schwartz SA, Reyzer ML, Caprioli RM (2003) Direct tissue analysis using matrix-assisted laser desorption/ionization mass spectrometry: practical aspects of sample preparation. J Mass Spectrom 38:699–708

    Article  CAS  PubMed  Google Scholar 

  16. Chughtai K, Heeren RM (2010) Mass spectrometric imaging for biomedical tissue analysis. Chem Rev 110:3237–3277

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  17. Hopfgartner G, Varesio E, Stoeckli M (2009) Matrix-assisted laser desorption/ionization mass spectrometric imaging of complete rat sections using a triple quadrupole linear ion trap. Rapid Commun Mass Spectrom 23:733–736

    Article  CAS  PubMed  Google Scholar 

  18. Strohalm M, Strohalm J, Kaftan F et al (2011) Poly[N-(2-hydroxypropyl)methacrylamide]-based tissue-embedding medium compatible with MALDI mass spectrometry imaging experiments. Anal Chem 83:5458–5462

    Article  CAS  PubMed  Google Scholar 

  19. Goodwin RJ, Pennington SR, Pitt AR (2008) Protein and peptides in pictures: imaging with MALDI mass spectrometry. Proteomics 8:3785–3800

    Article  CAS  PubMed  Google Scholar 

  20. Seeley EH, Oppenheimer SR, Mi D et al (2008) Enhancement of protein sensitivity for MALDI imaging mass spectrometry after chemical treatment of tissue sections. J Am Soc Mass Spectrom 19:1069–1077

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Lemaire R, Wisztorski M, Desmons A et al (2006) MALDI-MS direct tissue analysis of proteins: improving signal sensitivity using organic treatments. Anal Chem 78:7145–7153

    Article  CAS  PubMed  Google Scholar 

  22. Lemaire R, Tabet JC, Ducoroy P et al (2006) Solid ionic matrixes for direct tissue analysis and MALDI imaging. Anal Chem 78:809–819

    Article  CAS  PubMed  Google Scholar 

  23. Mainini V, Angel PM, Magni F et al (2011) Detergent enhancement of on-tissue protein analysis by matrix-assisted laser desorption/ionization imaging mass spectrometry. Rapid Commun Mass Spectrom 25:199–204

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  24. Yang J, Caprioli RM (2011) Matrix sublimation/recrystallization for imaging proteins by mass spectrometry at high spatial resolution. Anal Chem 83:5728–5734

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  25. Yang C, He Z, Yu W (2009) Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis. BMC Bioinformatics 10:4

    Article  PubMed Central  PubMed  Google Scholar 

  26. Deininger SO, Cornett DS, Paape R et al (2011) Normalization in MALDI-TOF imaging datasets of proteins: practical considerations. Anal Bioanal Chem 401:167–181

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  27. Du P, Kibbe WA, Lin SM (2006) Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. Bioinformatics 22:2059–2065

    Article  CAS  PubMed  Google Scholar 

  28. Antoniadis A, Bigot J, Lambert-Lacroix S (2010) Peaks detection and alignment for mass spectrometry data. J de la SFdS 151:17–37

    Google Scholar 

  29. Morris JS, Coombes KR, Koomen J et al (2005) Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. Bioinformatics 21:1764–1775

    Article  CAS  PubMed  Google Scholar 

  30. Deininger SO, Ebert MP, Futterer A et al (2008) MALDI imaging combined with hierarchical clustering as a new tool for the interpretation of complex human cancers. J Proteome Res 7:5230–5236

    Article  CAS  PubMed  Google Scholar 

  31. Stone G, Clifford D, Gustafsson JO et al (2012) Visualisation in imaging mass spectrometry using the minimum noise fraction transform. BMC Res Notes 5:419

    Article  PubMed Central  PubMed  Google Scholar 

  32. Siy P, Moffitt R, Parry R et al. (2008) Matrix factorization techniques for analysis of imaging mass spectrometry data. In: BioInformatics and Bioengineering. BIBE 2008. 8th IEEE international conference on 2008. pp 1–6.

    Google Scholar 

  33. Hanselmann M, Kirchner M, Renard BY et al (2008) Concise representation of mass spectrometry images by probabilistic latent semantic analysis. Anal Chem 80:9649–9658

    Article  CAS  PubMed  Google Scholar 

  34. Jones EA, van Remoortere A, van Zeijl RJ et al (2011) Multiple statistical analysis techniques corroborate intratumor heterogeneity in imaging mass spectrometry datasets of myxofibrosarcoma. PLoS One 6:e24913

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  35. Lin SM, Zhu L, Winter AQ et al (2005) What is mzXML good for? Expert Rev Proteomics 2:839–845

    Article  CAS  PubMed  Google Scholar 

  36. Martens L, Chambers M, Sturm M, et al. (2011) mzML–a community standard for mass spectrometry data. Mol Cell Proteomics 10, R110 000133

    Google Scholar 

  37. Schramm T, Hester A, Klinkert I et al (2012) imzML–a common data format for the flexible exchange and processing of mass spectrometry imaging data. J Proteomics 75:5106–5110

    Article  CAS  PubMed  Google Scholar 

  38. Alexandrov T (2012) MALDI imaging mass spectrometry: statistical data analysis and current computational challenges. BMC Bioinformatics 13(Suppl 16):S11

    CAS  PubMed Central  PubMed  Google Scholar 

  39. Philipson O, Lord A, Lalowski M et al (2011) The Arctic amyloid-beta precursor protein (AbetaPP) mutation results in distinct plaques and accumulation of N- and C-truncated Abeta. Neurobiol Aging 33(1010):e1–e13

    PubMed  Google Scholar 

  40. Minerva L, Clerens S, Baggerman G et al (2008) Direct profiling and identification of peptide expression differences in the pancreas of control and ob/ob mice by imaging mass spectrometry. Proteomics 8:3763–3774

    Article  CAS  PubMed  Google Scholar 

  41. Cornett DS, Mobley JA, Dias EC et al (2006) A novel histology-directed strategy for MALDI-MS tissue profiling that improves throughput and cellular specificity in human breast cancer. Mol Cell Proteomics 5:1975–1983

    Article  CAS  PubMed  Google Scholar 

  42. Chaurand P, Schwartz SA, Billheimer D et al (2004) Integrating histology and imaging mass spectrometry. Anal Chem 76:1145–1155

    Article  CAS  PubMed  Google Scholar 

  43. Agar NY, Yang HW, Carroll RS et al (2007) Matrix solution fixation: histology-compatible tissue preparation for MALDI mass spectrometry imaging. Anal Chem 79:7416–7423

    Article  CAS  PubMed  Google Scholar 

  44. Walch A, Rauser S, Deininger SO et al (2008) MALDI imaging mass spectrometry for direct tissue analysis: a new frontier for molecular histology. Histochem Cell Biol 130:421–434

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  45. Rompp A, Guenther S, Schober Y et al (2010) Histology by mass spectrometry: label-free tissue characterization obtained from high-accuracy bioanalytical imaging. Angew Chem Int Ed Engl 49:3834–3838

    Article  PubMed  Google Scholar 

  46. Schwartz SA, Weil RJ, Thompson RC et al (2005) Proteomic-based prognosis of brain tumor patients using direct-tissue matrix-assisted laser desorption ionization mass spectrometry. Cancer Res 65:7674–7681

    CAS  PubMed  Google Scholar 

  47. Deutskens F, Yang J, Caprioli RM (2011) High spatial resolution imaging mass spectrometry and classical histology on a single tissue section. J Mass Spectrom 46:568–571

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  48. Jungmann JH, Heeren RM (2013) Detection systems for mass spectrometry imaging: a perspective on novel developments with a focus on active pixel detectors. Rapid Commun Mass Spectrom 27:1–23

    Article  CAS  PubMed  Google Scholar 

  49. Elsner M, Rauser S, Maier S et al (2012) MALDI imaging mass spectrometry reveals COX7A2, TAGLN2 and S100-A10 as novel prognostic markers in Barrett’s adenocarcinoma. J Proteomics 75:4693–4704

    Article  CAS  PubMed  Google Scholar 

  50. Yanagisawa K, Shyr Y, Xu BJ et al (2003) Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet 362:433–439

    Article  CAS  PubMed  Google Scholar 

  51. Lemaire R, Menguellet SA, Stauber J et al (2007) Specific MALDI imaging and profiling for biomarker hunting and validation: fragment of the 11S proteasome activator complex, Reg alpha fragment, is a new potential ovary cancer biomarker. J Proteome Res 6:4127–4134

    Article  CAS  PubMed  Google Scholar 

  52. Schwamborn K, Krieg RC, Reska M et al (2007) Identifying prostate carcinoma by MALDI-Imaging. Int J Mol Med 20:155–159

    CAS  PubMed  Google Scholar 

  53. Schwartz SA, Weil RJ, Johnson MD et al (2004) Protein profiling in brain tumors using mass spectrometry: feasibility of a new technique for the analysis of protein expression. Clin Cancer Res 10:981–987

    Article  CAS  PubMed  Google Scholar 

  54. Oppenheimer SR, Mi D, Sanders ME et al (2010) Molecular analysis of tumor margins by MALDI mass spectrometry in renal carcinoma. J Proteome Res 9:2182–2190

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  55. Meding S, Balluff B, Elsner M et al (2012) Tissue-based proteomics reveals FXYD3, S100A11 and GSTM3 as novel markers for regional lymph node metastasis in colon cancer. J Pathol. doi:10.1002/path.4021

    PubMed  Google Scholar 

  56. Pierson J, Norris JL, Aerni HR et al (2004) Molecular profiling of experimental Parkinson’s disease: direct analysis of peptides and proteins on brain tissue sections by MALDI mass spectrometry. J Proteome Res 3:289–295

    Article  CAS  PubMed  Google Scholar 

  57. Skold K, Svensson M, Nilsson A et al (2006) Decreased striatal levels of PEP-19 following MPTP lesion in the mouse. J Proteome Res 5:262–269

    Article  PubMed  Google Scholar 

  58. Stauber J, Lemaire R, Franck J et al (2008) MALDI imaging of formalin-fixed paraffin-embedded tissues: application to model animals of Parkinson disease for biomarker hunting. J Proteome Res 7:969–978

    Article  CAS  PubMed  Google Scholar 

  59. Rohner TC, Staab D, Stoeckli M (2005) MALDI mass spectrometric imaging of biological tissue sections. Mech Ageing Dev 126:177–185

    Article  CAS  PubMed  Google Scholar 

  60. Stoeckli M, Staab D, Staufenbiel M et al (2002) Molecular imaging of amyloid beta peptides in mouse brain sections using mass spectrometry. Anal Biochem 311:33–39

    Article  CAS  PubMed  Google Scholar 

  61. Magni F, Lalowski M, Mainini V et al (2013) Proteomics imaging and the kidney. J Nephrol 26:430–436

    Article  CAS  PubMed  Google Scholar 

  62. Ait-Belkacem R, Sellami L, Villard C et al (2012) Mass spectrometry imaging is moving toward drug protein co-localization. Trends Biotechnol 30:466–474

    Article  CAS  PubMed  Google Scholar 

  63. Seeley EH, Schwamborn K, Caprioli RM (2011) Imaging of intact tissue sections: moving beyond the microscope. J Biol Chem 286:25459–25466

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  64. Cillero Pastor B, Heeren RM (2013) Matrix assisted laser desorption ionization mass spectrometry imaging for peptide and protein analyses: a critical review of on-tissue digestion. J Proteome Res (Epub ahead of print)

    Google Scholar 

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Acknowledgements

V.M. acknowledges Dr. Michael Becker and Bruker Daltonik GmbH, Bremen, Germany for technical assistance and Dr. Daniela Pillo for critical review of the FFPE protocols. This work was supported by grants from the Italian Ministry of University and Research: PRIN 2006 (no. 69373), FIRB 2007 (Rete nazionale per lo studio del proteoma umano, no.RBRN07BMCT_11), FAR 2006-2011 (ex 60 %), from Italian Institute of Technology (IIT), Project SEED: “IPG-CHIP”, by “FONDO PER LA PRO-MOZIONE DI ACCORDI ISTITUZIONALI” Regione Lombardia DGR N. 5200/2007, project no. 14546: “Network Enabled Drug Design (NEDD)” and in part by the EuroKUP COST Action (BM0702) and Mass Spectrometry Imaging: New Tools for Healthcare Research COST Action (BM1104). A.G. work was sponsored by the joint grant for junior researchers from Biomedicum Helsinki, University of Helsinki and Aalto University (award for 2013). The authors also wish to thank MSc Enzo Scifo for critical review of the manuscript.

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    Authors and Affiliations

    1. Department of Health Sciences, University Milano-Bicocca, Via Cadore 48, Monza, 20900, Italy

      Veronica Mainini & Fulvio Magni

    2. Meilahti Clinical Proteomics Core Unit, Department of Biochemistry and Developmental Biology, Institute of Biomedicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland

      Maciej Lalowski & Marc Baumann

    3. Folkhälsan Institute of Genetics, Helsinki, Finland

      Maciej Lalowski

    4. Brain and Mind Laboratory, Department of Biomedical Engineering and Computational Science (BECS), Aalto University School of Science, Helsinki, Finland

      Athanasios Gotsopoulos

    5. Biotechnology Division, Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece

      Vasiliki Bitsika

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    1. Veronica Mainini
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    2. Maciej Lalowski
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    3. Athanasios Gotsopoulos
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    4. Vasiliki Bitsika
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    5. Marc Baumann
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    6. Fulvio Magni
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    Correspondence to Fulvio Magni .

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    1. Biomedical Research Foundation, Academy of Athens, Athens, Greece

      Antonia Vlahou

    2. Biomedical Research Foundation, Academy of Athens, Athens, Greece

      Manousos Makridakis

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    Mainini, V., Lalowski, M., Gotsopoulos, A., Bitsika, V., Baumann, M., Magni, F. (2015). MALDI-Imaging Mass Spectrometry on Tissues. In: Vlahou, A., Makridakis, M. (eds) Clinical Proteomics. Methods in Molecular Biology, vol 1243. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1872-0_8

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    • DOI: https://doi.org/10.1007/978-1-4939-1872-0_8

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