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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]

- Discovery of new molecular subtypes in oesophageal adenocarcinoma. Berg D, Wolff C, Langer R, Schuster T, Feith M, Slotta-Huspenina J, Malinowsky K, Becker KF. PLoS One. 2011;6(9):e23985. doi: 10.1371/journal.pone.0023985. PMID: #21966358# [Free]

- 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#