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Toward deciphering proteomes of formalin‐fixed paraffin‐embedded ( FFPE ) tissues
Sameh Magdeldin, Tadashi Yamamoto
PROTEOMICS · 2012 · Review
Abstract
Formalin‐fixed paraffin‐embedded ( FFPE ) tissue specimens comprise a potentially valuable resource for both prospective and retrospective biomarker discovery. Unlocking the proteomic profile of clinicopathological FFPE tissues is a critically essential step for annotating clinical findings and predicting biomarkers for ultimate disease prognosis and therapeutic follow‐up.
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References 71
- 1.
Fox CH, Johnson FB, Whiting J, Roller PP. Formaldehyde fixation. J. Histochem. Cytochem. 1985;33:845-853.
Not in our library10.1177/33.8.3894502
- 2.
Puchtler H, Meloan SN. On the chemistry of formaldehyde fixation and its effects on immunohistochemical reactions. Histochemistry. 1985;82:201-204.
Not in our library10.1007/bf00501395
- 3.
Ahram M, Flaig MJ, Gillespie JW, Duray PH, et al. Evaluation of ethanol-fixed, paraffin-embedded tissues for proteomic applications. Proteomics. 2003;3:413-421.
Not in our library10.1002/pmic.200390056
- 4.
Nirmalan NJ, Harnden P, Selby PJ, Banks RE. Mining the archival formalin-fixed paraffin-embedded tissue proteome: opportunities and challenges. Mol. BioSyst. 2008;4:712-720.
Not in our library10.1039/b800098k
- 5.
Zhang H, Lin Q, Ponnusamy S, Kothandaraman N, et al. Differential recovery of membrane proteins after extraction by aqueous methanol and trifluoroethanol. Proteomics. 2007;7:1654-1663.
Not in our library10.1002/pmic.200600579
- 6.
Ishibe N, Schully S, Freedman A, Ramsey SD. Use of oncotype DX in women with node-positive breast cancer. Plos Curr. 2011;21:PMC3145540.
Not in our library10.1371/currents.rrn1249
- 7.
Flanagan MB, Dabbs DJ, Brufsky AM, Beriwal S, et al. Histopathologic variables predict oncotype DX recurrence score. Mod. Pathol. 2008;21:1255-1261.
Not in our library10.1038/modpathol.2008.54
- 8.
Solassol J, Ramos J, Crapez E, Saifi M, et al. KRAS mutation detection in paired frozen and formalin-fixed paraffin-embedded (FFPE) colorectal cancer tissues. Int. J. Mol. Sci. 2011;12:3191-3204.
Not in our library10.3390/ijms12053191
- 9.
Chung JY, Lee SJ, Kris Y, Braunschweig T, et al. A well-based reverse-phase protein array applicable to extracts from formalin-fixed paraffin-embedded tissue. Proteomics Clin. Appl. 2008;2:1539-1547.
Not in our library10.1002/prca.200800005
- 10.
Hood BL, Conrads TP, Veenstra TD. Mass spectrometric analysis of formalin-fixed paraffin-embedded tissue: unlocking the proteome within. Proteomics. 2006;6:4106-4114.
Not in our library10.1002/pmic.200600016
- 11.
Crockett DK, Lin Z, Vaughn CP, Lim MS, et al. Identification of proteins from formalin-fixed paraffin-embedded cells by LCMSMS. Lab. Invest. 2005;85:1405-1415.
Not in our library10.1038/labinvest.3700343
- 12.
Yamashita S. Heat-induced antigen retrieval: mechanisms and application to histochemistry. Prog. Histochem. Cytochem. 2007;41:141-200.
Not in our library10.1016/j.proghi.2006.09.001
- 13.
Sprung RW, Brock JW, Tanksley JP, Li M, et al. Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol. Cell. Proteomics. 2009;8:1988-1998.
Not in our library10.1074/mcp.m800518-mcp200
- 14.
Matsuda KM, Chung JY, Hewitt SM. Histo-proteomic profiling of formalin-fixed, paraffin-embedded tissue. Expert Rev. Proteomics. 2010;7:227-237.
Not in our library10.1586/epr.09.106
- 15.
Xiao Z, Li G, Chen Y, Li M, et al. Quantitative proteomic analysis of formalin-fixed and paraffin-embedded nasopharyngeal carcinoma using iTRAQ labeling, two-dimensional liquid chromatography, and tandem mass spectrometry. J. Histochem. Cytochem. 2010;58:517-527.
Not in our library10.1369/jhc.2010.955526
- 16.
Toews J, Rogalski JC, Clark TJ, Kast J. Mass spectrometric identification of formaldehyde-induced peptide modifications under in vivo protein cross-linking conditions. Anal. Chim. Acta. 2008;618:168-183.
Not in our library10.1016/j.aca.2008.04.049
- 17.
Azimzadeh O, Barjaktarovic Z, Aubele M, Calzada-Wack J, et al. Formalin-fixed paraffin-embedded (FFPE) proteome analysis using gel-free and gel-based proteomics. J. Proteome. Res. 2010;9:4710-4720.
Not in our library10.1021/pr1004168
- 18.
Wisniewski JR, Ostasiewicz P, Mann M. High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. J. Proteome. Res. 2011;10:3040-3049.
Not in our library10.1021/pr200019m
- 19.
Jiang X, Feng S, Tian R, Ye M, et al. Development of efficient protein extraction methods for shotgun proteome analysis of formalin-fixed tissues. J. Proteome. Res. 2007;6:1038-1047.
Not in our library10.1021/pr0605318
- 20.
Mason JT, O'Leary TJ. Effects of formaldehyde fixation on protein secondary structure: a calorimetric and infrared spectroscopic investigation. J. Histochem. Cytochem. 1991;39:225-229.
Not in our library10.1177/39.2.1987266
- 21.
Ronci M, Bonanno E, Colantoni A, Pieroni L, et al. Protein unlocking procedures of formalin-fixed paraffin-embedded tissues: application to MALDITOF imaging MS investigations. Proteomics. 2008;8:3702-3714.
Not in our library10.1002/pmic.200701143
- 22.
Sompuram SR, Vani K, Messana E, Bogen SA. A molecular mechanism of formalin fixation and antigen retrieval. Am. J. Clin. Pathol. 2004;121:190-199.
Not in our library10.1309/brn7-ctx1-e84n-wwpl
- 23.
Addis MF, Tanca A, Pagnozzi D, Crobu S, et al. Generation of high-quality protein extracts from formalin-fixed, paraffin-embedded tissues. Proteomics. 2009;9:3815-3823.
Not in our library10.1002/pmic.200800971
- 24.
Tian Y, Gurley K, Meany DL, Kemp CJ, et al. N-linked glycoproteomic analysis of formalin-fixed and paraffin-embedded tissues. J. Proteome. Res. 2009;8:1657-1662.
Not in our library10.1021/pr800952h
- 25.
Berg D, Hipp S, Malinowsky K, Bollner C, et al. Molecular profiling of signalling pathways in formalin-fixed and paraffin-embedded cancer tissues. Eur. J. Cancer. 2010;46:47-55.
Not in our library10.1016/j.ejca.2009.10.016
- 26.
Ostasiewicz P, Zielinska DF, Mann M, Wisniewski JR. Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. J. Proteome. Res. 2010;9:3688-3700.
Not in our library10.1021/pr100234w
- 27.
Cohen P. The role of protein phosphorylation in human health and disease. The Sir Hans Krebs Medal Lecture. Eur. J. Biochem. 2001;268:5001-5010.
Not in our library10.1046/j.0014-2956.2001.02473.x
- 28.
Kornfeld S. Diseases of abnormal protein glycosylation: an emerging area. J. Clin. Invest. 1998;101:1293-1295.
Not in our library10.1172/jci3140
- 29.
Durand G, Seta N. Protein glycosylation and diseases: blood and urinary oligosaccharides as markers for diagnosis and therapeutic monitoring. Clin. Chem. 2000;46(6 Pt 1):795-805.
Not in our library
- 30.
Fowler CB, Cunningham RE, O'Leary TJ, Mason JT. ‘Tissue surrogates’ as a model for archival formalin-fixed paraffin-embedded tissues. Lab. Invest. 2007;87:836-846.
Not in our library10.1038/labinvest.3700596
- 31.
Fowler CB, Chesnick IE, Moore CD, O'Leary TJ, et al. Elevated pressure improves the extraction and identification of proteins recovered from formalin-fixed, paraffin-embedded tissue surrogates. PLoS One. 2010;5:e14253.
Not in our library10.1371/journal.pone.0014253
- 32.
Yamashita S, Okada Y. Mechanisms of heat-induced antigen retrieval: analyses in vitro employing SDSPAGE and immunohistochemistry. J. Histochem. Cytochem. 2005;53:13-21.
Not in our library10.1177/002215540505300103
- 33.
Tanca A, Pagnozzi D, Falchi G, Biosa G, et al. Impact of fixation time on GeLCMSMS proteomic profiling of formalin-fixed, paraffin-embedded tissues. J. Proteomics. 2011;74:1015-1021.
Not in our library10.1016/j.jprot.2011.03.015
- 34.
Godfrey TE, Kim SH, Chavira M, Ruff DW, et al. Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5’ nuclease quantitative reverse transcription-polymerase chain reaction. J. Mol. Diagn. 2000;2:84-91.
Not in our library10.1016/s1525-1578(10)60621-6
- 35.
Klopfleisch R, Weiss AT, Gruber AD. Excavation of a buried treasure-DNA, mRNA, miRNA and protein analysis in formalin fixed, paraffin embedded tissues. Histol. Histopathol. 2011;26:797-810.
Not in our library10.14670/hh-26.797
- 36.
Dani C, Blanchard JM, Piechaczyk M, El Sabouty S, et al. Extreme instability of myc mRNA in normal and transformed human cells. Proc. Natl. Acad. Sci. U.S.A. 1984;81:7046-7050.
Not in our library10.1073/pnas.81.22.7046
- 37.
Balgley BM, Guo T, Zhao K, Fang X, et al. Evaluation of archival time on shotgun proteomics of formalin-fixed and paraffin-embedded tissues. J. Proteome. Res. 2009;8:917-925.
Not in our library10.1021/pr800503u
- 38.
Ikeda K, Monden T, Kanoh T, Tsujie M, et al. Extraction and analysis of diagnostically useful proteins from formalin-fixed, paraffin-embedded tissue sections. J. Histochem. Cytochem. 1998;46:397-403.
Not in our library10.1177/002215549804600314
- 39.
Ha GH, Lee SU, Kang DG, Ha NY, et al. 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.
Not in our library10.1002/1522-2683(200208)23:15<2513::aid-elps2513>3.0.co;2-w
- 40.
Xie H, Bandhakavi S, Griffin TJ. 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.
Not in our library10.1021/ac0482256
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