Development of efficient protein extraction methods for shotgun proteome analysis of formalin-fixed tissues

Journal of Proteome Research

Volumn 6, Issue 3, 2007, Pages 1038-1047

  Jiang, Xiaogang ^a,b   Jiang, Xinning ^a   Feng, Shun ^a   Tian, Ruijun ^a   Ye, Mingliang ^a   Zou, Hanfa ^a  

^a DALIAN INSTITUTE OF CHEMICAL PHYSICS   (China)

^b SOOCHOW UNIVERSITY   (China)

Author keywords

Formalin fixed tissue; Protein extraction; Shotgun proteome; Tandem mass spectrometry

Indexed keywords

BIOLOGICAL MARKER; FORMALDEHYDE; GUANIDINE;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; FROZEN SECTION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HIGH TEMPERATURE; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEOMICS; TANDEM MASS SPECTROMETRY;

ANIMALS; FORMALDEHYDE; GUANIDINE; HEAT; LIVER; METHODS; MICE; PROTEINS; PROTEOMICS; TANDEM MASS SPECTROMETRY; TISSUE FIXATION;

EID: 33947572920     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr0605318     Document Type: Article

References (35)

1. Edgar, P. F.; Schonberger, S. J.; Dean, B.; Faull, R. L.; Kydd, R.; Cooper, G. J. A comparative proteome analysis of hippocampal tissue from schizophrenic and Alzheimer's disease individuals. Mol. Psychiatry 1999, 4, 173-178.
2. Kim, J.; Kim, S. H.; Lee, S. U.; Ha, G. H.; Kang, D. G.; Ha, N. Y.; Ahn, J. S.; Cho, H. Y.; Kang, S. J.; Lee, Y. J.; Hong, S. C.; Ha, W. S.; Bae, J. M.; Lee, C. W.; Kim, J. W. Proteome analysis of human liver tumor tissue by two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization-mass spectrometry for identification of disease-related proteins. Electrophoresis 2002, 23, 4142-4156.
3. Chen, J.; Kahne, T.; Rocken, C.; Gotze, T.; Yu, J.; Sung, J. J.; Chen, M.; Hu, P.; Malfertheiner, P.; Ebert, M. P. Proteome analysis of gastric cancer metastasis by two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization-mass spectrometry for identification of metastasis-related proteins. J. Proteome Res. 2004, 3, 1009-1016.
4. Friedman, D. B.; Hill, S.; Keller, J. W.; Merchant, N. B.; Levy, S. E.; Coffey, R. J.; Caprioli, R. M. Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 2004, 4, 793-811.
5. Lee, I. N.; Chen, C. H.; Sheu, J. C.; Lee, H. S.; Huang, G. T.; Yu, C. Y.; Lu, F. J.; Chow, L. P. Identification of human hepatocellular carcinoma-related biomarkers by two-dimensional difference gel electrophoresis and mass spectrometry. J. Proteome Res. 2005, 4, 2062-2069.
6. Davidsson, P.; Paulson, L.; Hesse, C.; Blennow, K.; Nilsson, C. L. Proteome studies of human cerebrospinal fluid and brain tissue using a preparative two-dimensional electrophoresis approach prior to mass spectrometry. Proteomics 2001, 1, 444-452.
7. Ha, G. H.; Lee, S. U.; Kang, D. G.; Ha, N. Y.; Kim, S. H.; Kim, J.; Bae, J. M.; Kim, J. W.; Lee, C. W. Proteome analysis of human stomach tissue: separation of soluble proteins by two-dimensional polyacrylamide gel electrophoresis and identification by mass spectrometry. Electrophoresis 2002, 23, 2513-2524.
8. Wang, H.; Kachman, M. T.; Schwartz, D. R.; Cho, K. R.; Lubman, D. M. Comprehensive proteome analysis of ovarian cancers using liquid phase separation, mass mapping and tandem mass spectrometry: a strategy for identification of candidate cancer biomarkers. Proteomics 2004, 4, 2476-2495.
9. Liang, C. R.; Leow, C. K.; Neo, J. C.; Tan, G. S.; Lo, S. L.; Lim, J. W.; Seow, T. K.; Lai, P. B.; Chung, M. C. Proteome analysis of human hepatocellular carcinoma tissues by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 2005, 5, 2258-2271.
10. Hood, B. L.; Conrads, T. P.; Veenstra, T. D. Mass spectrometric analysis of formalin-fixed paraffin-embedded tissue: unlocking the proteome within. Proteomics 2006, 6, 4106-4114.
11. Nesvizhskii, A. I.; Aebersold, R. Interpretation of shotgun proteomics data: the protein inference problem. Mol. Cell. Proteomics 2005, 4, 1419-1440.
12. Feng, S.; Ye, M.; Jiang, X.; Jin, W.; Zou, H. Coupling the immobilized trypsin microreactor of monolithic capillary with μRPLC-MS/MS for shotgun proteome analysis. J. Proteome Res. 2006, 5, 422-428.
13. Xie, C.; Ye, M.; Jiang, X.; Jin, W.; Zou, H. Octadecylated silica monolith capillary column with integrated nanoelectrospray ionization emitter for highly efficient proteome analysis. Mol. Cell. Proteomics 2006, 5, 454-461.
14. Prieto, D. A.; Hood, B. L.; Darfler, M. M.; Guiel, T. G.; Lucas, D. A.; Conrads, T. P.; Veenstra, T. D.; Krizman, D. B. Liquid Tissue: proteomic profiling of formalin-fixed tissues. BioTechniques 2005, Suppl., 32-35.
15. Hood, B. L.; Darfler, M. M.; Guiel, T. G.; Furusato, B.; Lucas, D. A.; Ringeisen, B. R.; Sesterhenn, I. A.; Conrads, T. P.; Veenstra, T. D.; Krizman, D. B. Proteomic analysis of formalin-fixed prostate cancer tissue. Mol. Cell. Proteomics 2005, 4, 1741-1753.
16. Crockett, D. K.; Lin, Z.; Vaughn, C. P.; Lim, M. S.; Elenitoba-Johnson, K. S. Identification of proteins from formalin-fixed paraffin-embedded cells by LC-MS/MS. Lab. Invest. 2005, 85, 1405-1415.
17. Shi, S. R.; Liu, C.; Balgley, B. M.; Lee, C.; Taylor, C. R. Protein extraction from formalin-fixed, paraffin-embedded tissue sections: quality evaluation by mass spectrometry. J. Histochem. Cytochem. 2006, 54, 739-743.
18. Hwang, S. I.; Thumar, J.; Lundgren, D. H.; Rezaul, K.; Mayya, V.; Wu, L.; Eng, J.; Wright, M. E.; Han, D. K. Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. Oncogene 2007, 26, 65-76.
19. Peng, J. M.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2003, 2, 43-50.
20. Zheng, X.; Baker, H.; Hancock, W. S. Analysis of the low molecular weight serum peptidome using ultrafiltration and a hybrid ion trap-Fourier transform mass spectrometer. J. Chromatogr., A. 2006, 1120, 173-184.
21. Costa, P. P.; Jacobsson, B.; Collins, V. P.; Biberfeld, P. Unmasking antigen determinants in amyloid. J. Histochem. Cytochem. 1986, 34, 1683-1685.
22. Kiernan, J. Formaldehyde, formalin, paraformaldehyde and glutaraldehyde: What they are and what they do. Microsc. Today 2000, 00-1, 8-12.
23. Pileri, S. A.; Roncador, G.; Ceccarelli, C.; Piccioli, M.; Briskomatis, A.; Sabattini, E.; Ascani, S.; Santini, D.; Piccaluga, P. P.; Leone, O.; Damiani, S.; Ercolessi, C.; Sandri, F.; Pieri, P.; Leoncini, L.; Falini, B. Antigen retrieval techniques in immunohistochemistry: comparison of different methods. J. Pathol. 1997, 183, 116-123.
24. Washburn, M. P.; Wolters, D.; Yates, J. R., III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19, 242-247.
25. Yi, E. C.; Lee, H.; Aebersold, R.; Goodlett, D. R. A microcapillary trap cartridge-microcapillary high-performance liquid chromatography electrospray ionization emitter device capable of peptide tandem mass spectrometry at the attomole level on an ion trap mass spectrometer with automated routine operation. Rapid Commun. Mass Spectrom. 2003, 17, 2093-2098.
26. Xie, H.; Bandhakavi, S.; Griffin, T. J. Evaluating preparative isoelectric focusing of complex peptide mixtures for tandem mass spectrometry-based proteomics: a case study in profiling chromatin-enriched subcellular fractions in Saccharomyces cerevisiae. Anal. Chem. 2005, 77, 3198-3207.
27. Zeeberg, B. R.; Feng, W.; Wang, G.; Wang, M. D.; Fojo, A. T.; Sunshine, M.; Narasimhan, S.; Kane, D. W.; Reinhold, W. C.; Lababidi, S.; Bussey, K. J.; Riss, J.; Barrett, J. C.; Weinstein, J. N. GoMiner: a resource for biological interpretation of genomic and proteomic data. GenomeBiology 2003, 4, R28.
28. Kyte, J.; Doolittle, R. F. A simple method for displaying the hydropathic charater of a protein. J. Mol. Biol. 1982, 157, 105-132.
29. Saravanan, R. S.; Rose, J. K. A critical evaluation of sample extraction techniques for enhanced proteomic analysis of recalcitrant plant tissues. Proteomics 2004, 4, 2522-2532.
30. Palmer-Toy, D. E.; Krastins, B.; Sarracino, D. A.; Nadol, J. B., Jr.; Merchant, S. N. Efficient method for the proteomic analysis of fixed and embedded tissues. J. Proteome Res. 2005, 4, 2404-2411.
31. Shi, S. R.; Cote, R. J.; Taylor, C. R. Antigen retrieval immunohistochemistry: past, present, and future. J. Histochem. Cytochem. 1997, 45, 327-343.
32. Liu, H.; Sadygov, R. G.; Yates, J. R., III. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
33. Ahram, M.; Flaig, M. J.; Gillespie, J. W.; Duray, P. H.; Linehan, W. M.; Ornstein, D. K.; Niu, S.; Zhao, Y.; Petricoin, E. F., III; Emmert-Buck, M. R. Evaluation of ethanol-fixed, paraffin-embedded tissues for proteomic applications. Proteomics 2003, 3, 413- 421.
34. Chen, R.; Pan, S.; Brentnall, T. A.; Aebersold, R. Proteomic profiling of pancreatic cancer for biomarker discovery. Mol. Cell. Proteomics 2005, 4, 523-533.
35. Elias, J. E.; Haas, W.; Faherty, B. K.; Gygi, S. P. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2005, 2, 667-675.