Evaluation of archival time on shotgun proteomics of formalin-fixed and paraffin-embedded tissues

Journal of Proteome Research

Volumn 8, Issue 2, 2009, Pages 917-925

  Balgley, Brian M ^a   Guo, Tong ^b   Zhao, Kejia ^b   Fang, Xueping ^b   Tavassoli, Fattaneh A ^c   Lee, Cheng S ^b  

^a Calibrant Biosystems Inc   (United States)

^b Bldg 142   (United States)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Archival time; Capillary isotachophoresis; Electrospray ionization mass spectrometry; Formalin fixed and paraffin embedded tissues; Shotgun proteomics

Indexed keywords

ANTIBODY; FORMALDEHYDE; PARAFFIN; PROTEIN SUBUNIT; PROTEOME; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE;

ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; EXTRACTION; FEMALE; HUMAN; HUMAN TISSUE; MASS SPECTROMETRY; MESENCHYME; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; QUANTITATIVE ANALYSIS; SARCOMA; UTERUS MYOMA;

BIOLOGICAL SPECIMEN BANKS; CLUSTER ANALYSIS; FEMALE; FORMALDEHYDE; GENITAL NEOPLASMS, FEMALE; HUMANS; PARAFFIN EMBEDDING; PEPTIDES; PROTEOMICS; TUMOR MARKERS, BIOLOGICAL;

EID: 61849114172     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr800503u     Document Type: Article

References (36)

1. Lewis, F.; Maughan, N. J.; Smith, V.; Hillan, K.; Quirke, P. J. Pathol. 2001, 195, 66-71.
2. Hong, H.-H. L.; Dunnick, J.; Herbert, R.; Devereux, T. R.; Kim, Y.; Sills, R. C. Environ. Mol. Mutagen 2007, 48, 299-306.
3. Shi, S. R.; Cote, R. J.; Taylor, C. R. J. Histochem. Cytochem. 2001, 49, 931-937.
4. Shi, S. R.; Key, M. E.; Kalra, K. L. J. Histochem. Cytochem. 1991, 39, 741-748.
5. Shi, S. R.; Cote, R. J.; Taylor, C. R. J. Histochem. Cytochem. 1997, 45, 327-343.
6. Gown, A. M. Am. J. Clin. Pathol. 2004, 121, 172-174.
7. Ikeda, K.; Monden, T.; Kanoh, T.; Tsujie, M.; Izawa, H.; Haba, A.; Ohnishi, T.; Sekimoto, M.; Tomita, N.; Shiozaki, H.; Monden, M. J. Histochem. Cytochem. 1998, 46, 397-403.
8. Yamashita, S.; Okada, Y. J. Histochem. Cytochem. 2005, 53, 1421-1432.
9. Prieto, D. A.; Hood, B. L.; Darfler, M. M.; Guiel, T. G.; Lucas, D. A.; Conrads, T. P.; Veenstra, T. D.; Krizman, D. B. Biotechniques 2005, 32-35.
10. Jiang, X.; Jiang, X.; Feng, S.; Tian, R.; Ye, M.; Zou, H. J. Proteome Res. 2007, 6, 1038-1047.
11. Hwang, S. I.; Thumar, J.; Lundgren, D. H.; Rezaul, K.; Mayya, V.; Wu, L.; Eng, J.; Wright, M. E.; Han, D. K. Oncogene 2007, 26, 65-76.
12. Shi, S.-R.; Liu, C.; Balgley, B. M.; Lee, C.; Taylor, C. R. J. Histochem. Cytochem. 2006, 54, 739-743.
13. Guo, T.; Wang, W.; Rudnick, P. A.; Song, T.; Li, J.; Zhuang, Z.; Weil, R. J.; DeVoe, D. L.; Lee, C. S.; Balgley, B. M. J. Histochem. Cytochem. 2007, 55, 763-772.
14. Xu, H.; Yang, L.; Wang, W.; Shi, S.-R.; Liu, C.; Liu, Y.; Fang, X.; Taylor, C. R.; Lee, C. S.; Balgley, B. M. J. Proteome Res. 2008, 7, 1098-1108.
15. Fang, X.; Yang, L.; Wang, W.; Song, T.; Lee, C.; Devoe, D.; Balgley, B. Anal. Chem. 2007, 79, 5785-5792.
16. Fang, X.; Wang, W.; Yang, L.; Chandrasekaran, K.; Kristian, T.; Balgley, B. M.; Lee, C. S. Electrophoresis 2008, 29, 2215-2223.
17. Liu, H.; Sadygov, R. G.; Yates, J. R. Anal. Chem. 2004, 76, 4193-4201.
18. Rappsilber, J.; Ryder, U.; Lamond, A. I.; Mann, M. Genome Res. 2002, 12, 1231-1245.
19. Ishihama, Y.; Oda, Y.; Tabata, T.; Sato, T.; Nagasu, T.; Rappsilber, J.; Mann, M. Mol Cell. Proteomics 2005, 4, 1265-1272.
20. Shen, Y.; Berger, S. J.; Anderson, G. A.; Smith, R. D. Anal. Chem. 2000, 72, 2154-2159.
21. Chen, J.; Balgley, B. M.; DeVoe, D. L.; Lee, C. S. Anal. Chem. 2003, 75, 3145-3152.
22. Yang, L.; Lee, C. S.; Hofstadler, S. A.; Smith, R. D. Anal. Chem. 1998, 70, 4945-4950.
23. Geer, L. Y.; Markey, S. P.; Kowalak, J. A.; Wagner, L.; Xu, M.; Maynard, D. M.; Yang, X.; Shi, W.; Bryant, S. H. J. Proteome Res. 2004, 3, 958-964.
24. Elias, J. E.; Haas, W.; Faherty, B. K.; Gygi, S. P. Nat. Methods 2005, 2, 667-675.
25. Balgley, B. M.; Laudeman, T.; Yang, L.; Song, T.; Lee, C. S. Mol. Cell. Proteomics 2007, 6, 1599-1608.
26. Elias, J. E.; Gygi, S. P. Nat. Methods 2007, 4, 207-214.
27. Eisen, M. B.; Spellman, P. T.; Brown, P. O.; Botstein, D. Proc. Natl. Acad. Sci. U.SA. 1998, 95, 14863-14868.
28. Taylor, C. R. J. Histochem. Cytochem. 1979, 27, 1189-1191.
29. Taylor, C. R. J. Histochem. Cytochem. 1980, 28, 777-787.
30. Shi, S. R.; Cote, C.; Kalra, K. L.; Taylor, C. R.; Tandon, A. K. J. Histochem. Cytochem. 1992, 40, 787-792.
31. Fowler, C. B.; Cunningham, R. E.; O'Leary, T. J.; Mason, J. T. Lab. Invest. 2007, 87, 836-846.
32. Balgley, B. M.; Wang, W.; Song, T.; Fang, X.; Yang, L.; Lee, C. S. Electrophoresis 2008, 29, 3047-3054.
33. Zhang, B.; VerBerkmoes, N. C.; Langston, M. A.; Uberbacher, E.; Hettich, R. L.; Samatova, N. F. J. Proteome Res. 2006,5, 2909-2918.
34. Turck, C. W.; Falick, A. M.; Kowalak, I. A.; Lane, W. S.; Lilley, K. S.; Phinney, B. S.; Weintraub, S. T.; Witkowska, H. E.; Yates, N. A. Mol. Cell. Proteomics 2007, 6, 1291-1298.
35. Lu, P.; Vogel, C.; Wang, R.; Yao, X.; Marcotte, E. M. Nat. Biotechnol. 2007, 25, 117-124.
36. Nirmalan, N. J.; Harnden, P.; Selby, P. J.; Banks, R. E. Mol. Biosyst. 2008, 4, 712-720.