Proteomic analysis of formalin-fixed paraffin-embedded tissue by MALDI imaging mass spectrometry

Nature Protocols

Volumn 6, Issue 11, 2011, Pages 1695-1709

  Casadonte, Rita ^a   Caprioli, Richard M ^a  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGEN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; DATA ANALYSIS; FORMALIN FIXED PARAFFIN EMBEDDED TISSUE; HIGH THROUGHPUT SEQUENCING; INFORMATION PROCESSING; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION IMAGING MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; REPRODUCIBILITY; TISSUE FIXATION; TISSUE MICROARRAY;

ANTIGENS; DATA INTERPRETATION, STATISTICAL; FORMALDEHYDE; HUMANS; NEOPLASMS; PARAFFIN EMBEDDING; PROTEOMICS; SOFTWARE; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TISSUE FIXATION;

EID: 80054825298     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2011.388     Document Type: Article

References (50)

1. Metz, B. et al. Identifcation of formaldehyde-induced modifcations in proteins: Reactions with insulin. Bioconjugate Chem. 17, 815-822 (2006). (Pubitemid 43794393)
2. Rahimi, F., Shepherd, C.E., Halliday, G.M., Geczy, C.L. & Raftery, M.J. Antigen-epitope retrieval to facilitate proteomic analysis of formalin-fxed archival brain tissue. Anal. Chem. 78, 7216-7221 (2006). (Pubitemid 44607566)
3. Werner, M., Chott, A., Fabiano, A. & Battifora, H. Effect of formalin tissue fxation and processing on immunohistochemistry. Am. J. Surg. Pathol. 24, 1016-1019 (2000). (Pubitemid 30430490)
4. Shi, S.R., Key, M.E. & Kalra, K.L. Antigen retrieval in formalin-fxed, paraffn-embedded tissues: an enhancement method for immunohistochemical staining based on microwave oven heating of tissue sections. J. Histochem. Cytochem. 39, 741-748 (1991).
5. Groseclose, M.R., Massion, P.P., Chaurand, P. & Caprioli, R.M. High-throughput proteomic analysis of formalin-fxed paraffn-embedded tissue microarrays using MALDI imaging mass spectrometry. Proteomics 8, 3715-3724 (2008).
6. Groseclose, M.R., Andersson, M., Hardesty, W.M. & Caprioli, R.M. Identifcation of proteins directly from tissue: in situ tryptic digestions coupled with imaging mass spectrometry. J. Mass Spectrom. 42, 254-262 (2007).
7. Schwartz, S.A., Reyzer, M.L. & Caprioli, R.M. Direct tissue analysis using matrix-assisted laser desorption/ionization mass spectrometry: practical aspects of sample preparation. J. Mass Spectrom. 38, 699-708 (2003). (Pubitemid 36950300)
8. Chaurand, P., Norris, J.L., Cornett, D.S., Mobley, J.A. & Caprioli, R.M. New developments in profling and imaging of proteins from tissue sections by MALDI mass spectrometry. J. Proteome Res. 5, 2889-2900 (2006). (Pubitemid 44749207)
9. Lemaire, R. et al. Direct analysis and MALDI imaging of formalin-fxed, paraffn-embedded tissue sections. J. Proteome Res. 6, 1295-1305 (2007). (Pubitemid 46724026)
10. Uhlen, M. & Ponten, F. Antibody-based proteomics for human tissue profling. Mol. Cell Proteomics 4, 384-393 (2005). (Pubitemid 40590558)
11. Wessels, J.T. et al. In vivo imaging in experimental preclinical tumor research-a review. Cytometry A 71, 542-549 (2007). (Pubitemid 47221716)
12. Ntziachristos, V. Going deeper than microscopy: the optical imaging frontier in biology. Nat. Methods 7, 603-614 (2010).
13. Pepperkok, R. & Ellenberg, J. High-throughput fuorescence microscopy for systems biology. Nat. Rev. Mol. Cell. Biol. 7, 690-696 (2006). (Pubitemid 44268214)
14. Becker, K.F. & Taylor, C.R. 'Liquid morphology': immunochemical analysis of proteins extracted from formalin-fxed paraffn-embedded tissues: combining proteomics with immunohistochemistry. Appl. Immunohistochem. Mol. Morphol. 19, 1-9 (2011).
15. Teruya-Feldstein, J. The immunohistochemistry laboratory: looking at molecules and preparing for tomorrow. Arch. Pathol. Lab. Med. 134, 1659-1665 (2010).
16. Leong, T.Y., Cooper, K. & Leong, A.S. Immunohistology-past, present, and future. Adv. Anat. Pathol. 17, 404-418 (2010).
17. Grey, A.C., Chaurand, P., Caprioli, R.M. & Schey, K.L. MALDI imaging mass spectrometry of integral membrane proteins from ocular lens and retinal tissue. J. Proteome Res. 8, 3278-3283 (2009).
18. Yang, Y.L. et al. Connecting chemotypes and phenotypes of cultured marine microbial assemblages by imaging mass spectrometry. Angew. Chem. Int. Ed. Engl. 50, 5839-5842 (2011).
19. Iijima, M. Visualization of lateral water transport pathways in soybean by a time of fight-secondary ion mass spectrometry cryo-system. J. Exp. Bot. 62, 2179-2188 (2011).
20. Reyzer, M.L. & Caprioli, R.M. MALDI-MS-based imaging of small molecules and proteins in tissues. Curr. Opin. Chem. Biol. 11, 29-35 (2007). (Pubitemid 46217921)
21. Cornett, D.S., Frappier, S.L. & Caprioli, R.M. MALDI-FTICR imaging mass spectrometry of drugs and metabolites in tissue. Anal. Chem. 80, 5648-5653 (2008).
22. Djidja, M.C. et al. Novel molecular tumour classifcation using MALDI-mass spectrometry imaging of tissue micro-array. Anal. Bioanal. Chem. 397, 587-601 (2010).
23. Caprioli, R.M. Deciphering protein molecular signatures in cancer tissues to aid in diagnosis, prognosis, and therapy. Cancer Res. 65, 10642-10645 (2005). (Pubitemid 41715226)
24. Shi, S.-R., Shi, Y. & Taylor, C.R. Antigen retrieval immunohistochemistry. J. Histochem. Cytochem. 59, 13-32 (2011).
25. Seeley, E.H. & Caprioli, R.M. Molecular imaging of proteins in tissues by mass spectrometry. Proc. Natl. Acad. Sci. USA 105, 18126-18131 (2008).
26. Westermark, P. & Nilsson, G.T. Demonstration of amyloid protein Aa in old museum specimens. Arch. Pathol. Lab. Med. 108, 217-219 (1984). (Pubitemid 14152875)
27. Schwamborn, K. & Caprioli, R.M. MALDI imaging mass spectrometry-painting molecular pictures. Mol. Oncol. 4, 529-538 (2010).
28. Kononen, J. et al. Tissue microarrays for high-throughput molecular profling of tumor specimens. Nat. Med. 4, 844-847 (1998). (Pubitemid 28331029)
29. Chaurand, P. et al. Integrating histology and imaging mass spectrometry. Anal. Chem. 76, 1145-1155 (2004). (Pubitemid 38235565)
30. Schwamborn, K. et al. Identifying prostate carcinoma by MALDI-Imaging. Int. J. Mol. Med. 20, 155-159 (2007).
31. Evers, P., Uylings, H.B.M. & Suurmeijer, A.J.H. Antigen retrieval in formaldehyde-fxed human brain tissue. Methods 15, 133-140 (1998). (Pubitemid 28380046)
32. Shi, S.R., Liu, C., Balgley, B.M., Lee, C. & Taylor, C.R. Protein extraction from formalin-fxed, paraffn-embedded tissue sections: quality evaluation by mass spectrometry. J. Histochem. Cytochem. 54, 739-743 (2006). (Pubitemid 43736896)
33. Sato, T.A., Aoki, Y., Toyama, A. & Shimada, T. A novel method for analyzing formalin-fxed paraffn-embedded (FFPE) tissue sections by mass spectrometry imaging. Neurosci. Res. 61, S19 (2008).
34. Shi, S.R., Cote, R.J. & Taylor, C.R. Antigen retrieval techniques: current perspectives. J. Histochem. Cytochem. 49, 931-937 (2001). (Pubitemid 32675000)
35. Taylor, C.R. et al. Comparative study of antigen retrieval heating methods: microwave, microwave and pressure cooker, autoclave, and steamer. Biotech. Histochem. 71, 263-270 (1996). (Pubitemid 26405844)
36. Yamashita, S. Heat-induced antigen retrieval: Mechanisms and application to histochemistry. Prog. Histochem. Cytochem. 41, 141-200 (2007). (Pubitemid 46013929)
37. Hoetelmans, R.W.M., van Slooten, H.J., Keijzer, R., van de Velde, C.J.H. & van Dierendonck, J.H. Comparison of the effects of microwave heating and high pressure cooking for antigen retrieval of human and rat Bcl-2 protein in formaldehyde-fxed, paraffn-embedded sections. Biotech. Histochem. 77, 137-144 (2002). (Pubitemid 34830961)
38. Aerni, H.R., Cornett, D.S. & Caprioli, R.M. High-throughput profling of formalin-fxed paraffn embedded tissue using parallel electrophoresis and matrix assisted laser desorption ionization mass spectrometry. Anal. Chem. 81, 7490-7495 (2009).
39. Nirmalan, N.J., Harnden, P., Selby, P.J. & Banks, R.E. Mining the archival formalin-fxed paraffn-embedded tissue proteome: opportunities and challenges. Mol. Biosyst. 4, 712-720 (2008). (Pubitemid 351871751)
40. Reyzer, M.L., Chaurand, P., Angel, P.M. & Caprioli, R.M. Direct molecular analysis of whole-body animal tissue sections by MALDI imaging mass spectrometry. Methods Mol. Biol. 656, 285-301 (2010).
41. Schuerenberg, M., Luebbert, C., Deininger, S.O., Ketterlinus, R. & Suckau, D. MALDI tissue imaging: mass spectrometric localization of biomarkers in tissue slices. Nat. Methods 4, iii-iv (2007).
42. Nilsson, A. et al. Fine mapping the spatial distribution and concentration of unlabeled drugs within tissue micro-compartments using imaging mass spectrometry. PLoS ONE 5, e11411 (2010).
43. Baluya, D.L., Garrett, T.J. & Yost, R.A. Automated MALDI matrix deposition method with inkjet printing for imaging mass spectrometry. Anal. Chem. 79, 6862-6867 (2007). (Pubitemid 47395079)
44. Wisztorski, M., Franck, J., Salzet, M. & Fournier, I. MALDI direct analysis and imaging of frozen versus FFPE tissues: what strategy for which sample? Methods Mol. Biol. 656, 303-322 (2010).
45. Aerni, H.R., Cornett, D.S. & Caprioli, R.M. Automated acoustic matrix deposition for MALDI sample preparation. Anal. Chem. 78, 827-834 (2006). (Pubitemid 43228590)
46. Hardesty, W.M. Proteomic Analysis and Classifcation of Metastatic Melanoma by MALDI Imaging Mass Spectrometry.Ph.D. Dissertation, Vanderbilt University. http://etd.library.vanderbilt.edu/available/etd-08252010-081820/ unrestricted/Hardesty.pdf. (2010).
47. Norris, J.L. et al. Processing MALDI mass spectra to improve mass spectral direct tissue analysis. Int. J. Mass Spectrom. 260, 212-221 (2007).
48. Mann, M., Hendrickson, R.C. & Pandey, A. Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 70, 437-473 (2001). (Pubitemid 32662217)
49. Tabb, D.L., Friedman, D.B. & Ham, A.J.L. Verifcation of automated peptide identifcations from proteomic tandem mass spectra. Nat. Protoc. 1, 2213-2222 (2006).
50. Holle, A., Haase, A., Kayser, M. & Hohndorf, J. Optimizing UV laser focus profles for improved MALDI performance. J. Mass Spectrom. 41, 705-716 (2006) (Pubitemid 44023098)