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proteomics from FFPE

Wednesday 23 December 2009

Open References

- Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma. Wiśniewski JR, Ostasiewicz P, Duś K, Zielińska DF, Gnad F, Mann M. Mol Syst Biol. 2012;8:611. doi : 10.1038/msb.2012.44 PMID: 22968445 [Free]

- Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues. Magdeldin S, Yamamoto T. Proteomics. 2012 Apr;12(7):1045-58. doi : 10.1002/pmic.201100550 PMID: 22318899 [Free]

- Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometry. Paulo JA, Lee LS, Banks PA, Steen H, Conwell DL. Pancreas. 2012 Mar;41(2):175-85. doi : 10.1097/MPA.0b013e318227a6b7 PMID: 22015969 [Free]

- Proteomic analysis of formalin-fixed paraffin-embedded tissue by MALDI imaging mass spectrometry. Casadonte R, Caprioli RM. Nat Protoc. 2011 Oct 13;6(11):1695-709. doi : 10.1038/nprot.2011.388 PMID: #22011652 [Free]

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- A quantitative proteomic analysis of FFPE melanoma. Byrum S, Avaritt NL, Mackintosh SG, Munkberg JM, Badgwell BD, Cheung WL, Tackett AJ. J Cutan Pathol. 2011 Nov;38(11):933-6. doi : 10.1111/j.1600-0560.2011.01761.x PMID: 21883366 [Free]

- A protein profile study to discriminate CIN lesions from normal cervical epithelium. Uleberg KE, Munk AC, Skaland I, Furlan C, van Diermen B, Gudlaugsson E, Janssen EA, Malpica A, Feng W, Hjelle A, Baak JP. Cell Oncol (Dordr). 2011 Oct;34(5):443-50. doi : 10.1007/s13402-011-0047-3 PMID: 21573931 [Free]

- Successful protein extraction from over-fixed and long-term stored formalin-fixed tissues. Wolff C, Schott C, Porschewski P, Reischauer B, Becker KF. PLoS One. 2011 Jan 31;6(1):e16353. doi : 10.1371/journal.pone.0016353 PMID: 21305021 [Free]

- Initial development and validation of a novel extraction method for quantitative mining of the formalin-fixed, paraffin-embedded tissue proteome for biomarker investigations. Nirmalan NJ, Hughes C, Peng J, McKenna T, Langridge J, Cairns DA, Harnden P, Selby PJ, Banks RE. J Proteome Res. 2011 Feb 4;10(2):896-906. doi : 10.1021/pr100812d PMID: 21117664 [Free]

- Quantitative proteomic analysis of formalin-fixed and paraffin-embedded nasopharyngeal carcinoma using iTRAQ labeling, two-dimensional liquid chromatography, and tandem mass spectrometry. Xiao Z, Li G, Chen Y, Li M, Peng F, Li C, Li F, Yu Y, Ouyang Y, Xiao Z, Chen Z. J Histochem Cytochem. 2010 Jun;58(6):517-27. doi : 10.1369/jhc.2010.955526 PMID: 20124091 [Free]

- Proteomics of uveal melanomas suggests HSP-27 as a possible surrogate marker of chromosome 3 loss. Coupland SE, Vorum H, Mandal N, Kalirai H, Honoré B, Urbak SF, Lake SL, Dopierala J, Damato B. Invest Ophthalmol Vis Sci. 2010 Jan;51(1):12-20. doi : 10.1167/iovs.09-3913 PMID: 19643972 [Free]

- Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Sprung RW Jr, Brock JW, Tanksley JP, Li M, Washington MK, Slebos RJ, Liebler DC. Mol Cell Proteomics. 2009 Aug;8(8):1988-98. doi : 10.1074/mcp.M800518-MCP200 PMID: 19467989 [Free]

- Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Sprung RW Jr, Brock JW, Tanksley JP, Li M, Washington MK, Slebos RJ, Liebler DC. Mol Cell Proteomics. 2009 Aug;8(8):1988-98. doi : 10.1074/mcp.M800518-MCP200 PMID: 19467989 [Free]

- Quantitative Proteomic Analysis of Formalin Fixed Paraffin Embedded Oral HPV Lesions from HIV Patients. Jain MR, Liu T, Hu J, Darfler M, Fitzhugh V, Rinaggio J, Li H. Open Proteomics J. 2008;1:40-45. PMID: 19081750 [Free]

- [A novel fixed paraffin-embedded tissue processing for proteomic analysis]. Bellet V, Rochaix P, Mange A, Solassol J. Ann Biol Clin (Paris). 2008 Jul-Aug;66(4):401-7. doi : 10.1684/abc.2008.0249. French PMID: 18725341 [Free]

- Proteomic analysis of laser-captured paraffin-embedded tissues: a molecular portrait of head and neck cancer progression. Patel V, Hood BL, Molinolo AA, Lee NH, Conrads TP, Braisted JC, Krizman DB, Veenstra TD, Gutkind JS. Clin Cancer Res. 2008 Feb 15;14(4):1002-14. doi : 10.1158/1078-0432.CCR-07-1497 PMID: 18281532 [Free]

References

- Proteomic workflow for analysis of archival formalin fixed and paraffin embedded clinical samples to a depth of 10,000 proteins. Wiśniewski JR, Duś K, Mann M. Proteomics Clin Appl. 2012 Oct 23. doi : 10.1002/prca.201200046 PMID: 23090905

- Universal sample preparation method for proteome analysis. Wiśniewski JR, Zougman A, Nagaraj N, Mann M. Nat Methods. 2009 May;6(5):359-62. doi : 10.1038/nmeth.1322 PMID: 19377485