Critical comparison of sample preparation strategies for shotgun proteomic analysis of formalin-fixed, paraffin-embedded samples: Insights from liver tissue

Clinical Proteomics

Volumn 11, Issue 1, 2014, Pages

  Tanca, Alessandro ^a   Abbondio, Marcello ^a   Pisanu, Salvatore ^a   Pagnozzi, Daniela ^a   Uzzau, Sergio ^a,b   Addis, Maria Filippa ^a  

^a Porto Conte Ricerche Srl   (Italy)

^b UNIVERSITY OF SASSARI   (Italy)

Author keywords

Archival tissues; FASP; FFPE; LC MS MS; Protein extraction

Indexed keywords

KERATIN; MEMBRANE PROTEIN; PLECTIN; PROTEIN DISULFIDE ISOMERASE; SPECTRIN;

ARTICLE; CLINICAL PROTEOMICS; COLLISIONALLY ACTIVATED DISSOCIATION; COMPARATIVE STUDY; CONTROLLED STUDY; CYTOSKELETON; FORMALIN FIXED PARAFFIN EMBEDDED TISSUE; HUMAN; HUMAN TISSUE; HYDROPHOBICITY; LIVER; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEOMICS; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; TISSUE SECTION; TWO DIMENSIONAL ELECTROPHORESIS; TWO DIMENSIONAL GEL ELECTROPHORESIS;

EID: 84961291890     PISSN: 15426416     EISSN: 15590275     Source Type: Journal    
DOI: 10.1186/1559-0275-11-28     Document Type: Article

References (51)

1. Nirmalan N, Banks R, Van Eyk JE: Proteomic analysis of formalin fixed tissue. Proteomics Clin Appl 2013, 7:215-216.
2. Blonder J, Veenstra TD: Clinical proteomic applications of formalin-fixed paraffin-embedded tissues. Clin Lab Med 2009, 29:101-113.
3. Tanca A, Pagnozzi D, Addis MF: Setting proteins free: Progresses and achievements in proteomics of formalin-fixed, paraffin-embedded tissues. Proteomics Clin Appl 2012, 6:7-21.
4. Addis MF, Tanca A, Pagnozzi D, Rocca S, Uzzau S: 2-D PAGE and MS analysis of proteins from formalin-fixed, paraffin-embedded tissues. Proteomics 2009, 9:4329-4339.
5. Tanca A, Pagnozzi D, Burrai GP, Polinas M, Uzzau S, Antuofermo E, Addis MF: Comparability of differential proteomics data generated from paired archival fresh-frozen and formalin-fixed samples by GeLC-MS/MS and spectral counting. J Proteomics 2012, 77:561-576.
6. Tanca A, Pagnozzi D, Falchi G, Tonelli R, Rocca S, Roggio T, Uzzau S, Addis MF: Application of 2-D DIGE to formalin-fixed, paraffin-embedded tissues. Proteomics 2011, 11:1005-1011.
7. Tanca A, Pisanu S, Biosa G, Pagnozzi D, Antuofermo E, Burrai GP, Canzonieri V, Cossu-Rocca P, De Re V, Eccher A, Fanciulli G, Rocca S, Uzzau S, Addis MF: Application of 2D-DIGE to formalin-fixed diseased tissue samples from hospital repositories: results from four case studies. Proteomics Clin Appl 2013, 7:252-263.
8. Magdeldin S, Yamamoto T: Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues. Proteomics 2012, 12:1045-1058.
9. Maes E, Broeckx V, Mertens I, Sagaert X, Prenen H, Landuyt B, Schoofs L: Analysis of the formalin-fixed paraffin-embedded tissue proteome: pitfalls, challenges, and future prospectives. Amino Acids 2013, 45:205-218.
10. Giusti L, Lucacchini A: Proteomic studies of formalin-fixed paraffin-embedded tissues. Expert Rev Proteomics 2013, 10:165-177.
11. Shi SR, Taylor CR, Fowler CB, Mason JT: Complete solubilization of formalin-fixed, paraffin-embedded tissue may improve proteomic studies. Proteomics Clin Appl 2013, 7:264-272.
12. Vincenti DC, Murray GI: The proteomics of formalin-fixed wax-embedded tissue. Clin Biochem 2013, 46:546-551.
13. Fowler CB, O'Leary TJ, Mason JT: Toward improving the proteomic analysis of formalin-fixed, paraffin-embedded tissue. Expert Rev Proteomics 2013, 10:389-400.
14. Steiner C, Ducret A, Tille JC, Thomas M, McKee TA, Rubbia-Brandt L, Scherl A, Lescuyer P, Cutler P: Applications of mass spectrometry for quantitative protein analysis in formalin-fixed paraffin-embedded tissues. Proteomics 2013, 14:441-451.
15. Wisztorski M, Franck J, Salzet M, Fournier I: MALDI direct analysis and imaging of frozen versus FFPE tissues: what strategy for which sample? Methods Mol Biol 2010, 656:303-322.
16. Prieto DA, Hood BL, Darfler MM, Guiel TG, Lucas DA, Conrads TP, Veenstra TD, Krizman DB: Liquid Tissue: proteomic profiling of formalin-fixed tissues. Biotechniques 2005, 38:S32-S35.
17. Nazarian J, Santi M, Hathout Y, Macdonald TJ: Protein profiling of formalin fixed paraffin embedded tissue: Identification of potential biomarkers for pediatric brainstem glioma. Proteomics Clin Appl 2008, 2:915-924.
18. Alkhas A, Hood BL, Oliver K, Teng PN, Oliver J, Mitchell D, Hamilton CA, Maxwell GL, Conrads TP: Standardization of a sample preparation and analytical workflow for proteomics of archival endometrial cancer tissue. J Proteome Res 2011, 10:5264-5271.
19. Tian Y, Gurley K, Meany DL, Kemp CJ, Zhang H: N-linked glycoproteomic analysis of formalin-fixed and paraffin-embedded tissues. J Proteome Res 2009, 8:1657-1662.
20. Sprung RW Jr, Brock JW, Tanksley JP, Li M, Washington MK, Slebos RJ, Liebler DC: 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.
21. Ly L, Barnett MH, Zheng YZ, Gulati T, Prineas JW, Crossett B: Comprehensive tissue processing strategy for quantitative proteomics of formalin-fixed multiple sclerosis lesions. J Proteome Res 2011, 10:4855-4868.
22. Wakabayashi M, Yoshihara H, Masuda T, Tsukahara M, Sugiyama N, Ishihama Y: Phosphoproteome analysis of formalin-fixed and paraffin-embedded tissue sections mounted on microscope slides. J Proteome Res 2014, 13:915-924.
23. Shi SR, Liu C, Balgley BM, Lee C, Taylor CR: Protein extraction from formalin-fixed, paraffin-embedded tissue sections: quality evaluation by mass spectrometry. J Histochem Cytochem 2006, 54:739-743.
24. Gamez-Pozo A, Ferrer NI, Ciruelos E, Lopez-Vacas R, Martinez FG, Espinosa E, Vara JA: Shotgun proteomics of archival triple-negative breast cancer samples. Proteomics Clin Appl 2013, 7:283-291.
25. Xiao Z, Li G, Chen Y, Li M, Peng F, Li C, Li F, Yu Y, Ouyang Y, Chen Z: 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.
26. Donadio E, Giusti L, Cetani F, Da Valle Y, Ciregia F, Giannaccini G, Pardi E, Saponaro F, Torregrossa L, Basolo F, Marcocci C, Lucacchini A: Evaluation of formalin-fixed paraffin-embedded tissues in the proteomic analysis of parathyroid glands. Proteome Sci 2011, 9:29.
27. Jin GZ, Li Y, Cong WM, Yu H, Dong H, Shu H, Liu XH, Yan GQ, Zhang L, Zhang Y, Kang XN, Guo K, Wang ZD, Yang PY, Liu YK: iTRAQ-2DLC-ESI-MS/MS based identification of a new set of immunohistochemical biomarkers for classification of dysplastic nodules and small hepatocellular carcinoma. J Proteome Res 2011, 10:3418-3428.
28. Fu Z, Yan K, Rosenberg A, Jin Z, Crain B, Athas G, Heide RS, Howard T, Everett AD, Herrington D, Van Eyk JE: Improved protein extraction and protein identification from archival formalin-fixed paraffin-embedded human aortas. Proteomics Clin Appl 2013, 7:217-224.
29. 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.
30. 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.
31. Wisniewski JR, Ostasiewicz P, Dus K, Zielinska DF, Gnad F, Mann M: Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma. Mol Syst Biol 2012, 8:611.
32. Wisniewski JR, Dus K, Mann M: Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10 000 proteins. Proteomics Clin Appl 2013, 7:225-233.
33. Craven RA, Cairns DA, Zougman A, Harnden P, Selby PJ, Banks RE: Proteomic analysis of formalin-fixed paraffin-embedded renal tissue samples by label-free MS: assessment of overall technical variability and the impact of block age. Proteomics Clin Appl 2013, 7:273-282.
34. Donnarumma F, Vegvari A, Rezeli M, Welinder C, Jansson B, Marko-Varga G: Accessing microenvironment compartments in formalin-fixed paraffin-embedded tissues by protein expression analysis. Bioanalysis 2013, 5:2647-2659.
35. Manza LL, Stamer SL, Ham AJ, Codreanu SG, Liebler DC: Sample preparation and digestion for proteomic analyses using spin filters. Proteomics 2005, 5:1742-1745.
36. Wisniewski JR, Zougman A, Nagaraj N, Mann M: Universal sample preparation method for proteome analysis. Nat Methods 2009, 6:359-362.
37. Eichacker LA, Granvogl B, Mirus O, Muller BC, Miess C, Schleiff E: Hiding behind hydrophobicity. Transmembrane segments in mass spectrometry. J Biol Chem 2004, 279:50915-50922.
38. Tanca A, Pagnozzi D, Falchi G, Biosa G, Rocca S, Foddai G, Uzzau S, Addis MF: Impact of fixation time on GeLC-MS/MS proteomic profiling of formalin-fixed, paraffin-embedded tissues. J Proteomics 2011, 74:1015-1021.
39. Fox C, Johnson F, Whiting J, Roller P: Formaldehyde fixation. J Histochem Cytochem 1985, 33:845-853.
40. Dapson RW: Macromolecular changes caused by formalin fixation and antigen retrieval. Biotech Histochem 2007, 82:133-140.
41. Shi SR, Shi Y, Taylor CR: Antigen Retrieval Immunohistochemistry: Review and Future Prospects in Research and Diagnosis over Two Decades. J Histochem Cytochem 2011, 59:13-32.
42. Metz B, Kersten GFA, Hoogerhout P, Brugghe HF, Timmermans HAM, de Jong A, Meiring H: Hove Jt, Hennink WE, Crommelin DJA, Jiskoot W: Identification of Formaldehyde-induced Modifications in Proteins. J Biol Chem 2004, 279:6235-6243.
43. Hood BL, Conrads TP, Veenstra TD: Mass spectrometric analysis of formalin-fixed paraffin-embedded tissue: Unlocking the proteome within. Proteomics 2006, 6:4106-4114.
44. Toews J, Rogalski J, Clark T, Kast J: Mass spectrometric identification of formaldehyde-induced peptide modifications under in vivo protein cross-linking conditions. Anal Chim Acta 2008, 618:168-183.
45. Coutard B, Danchin EG, Oubelaid R, Canard B, Bignon C: Single pH buffer refolding screen for protein from inclusion bodies. Protein Expr Purif 2012, 82:352-359.
46. Bereman MS, Egertson JD, MacCoss MJ: Comparison between procedures using SDS for shotgun proteomic analyses of complex samples. Proteomics 2011, 11:2931-2935.
47. Antharavally BS, Mallia KA, Rosenblatt MM, Salunkhe AM, Rogers JC, Haney P, Haghdoost N: Efficient removal of detergents from proteins and peptides in a spin column format. Anal Biochem 2011, 416:39-44.
48. Tanca A, Biosa G, Pagnozzi D, Addis MF, Uzzau S: Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of the Escherichia coli proteome. Proteomics 2013, 13:2597-2607.
49. Wang CI, Alekseyenko AA, LeRoy G, Elia AE, Gorchakov AA, Britton LM, Elledge SJ, Kharchenko PV, Garcia BA, Kuroda MI: Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila. Nat Struct Mol Biol 2013, 20:202-209.
50. Addis MF, Tanca A, Pagnozzi D, Crobu S, Fanciulli G, Cossu-Rocca P, Uzzau S: Generation of high-quality protein extracts from formalin-fixed, paraffin-embedded tissues. Proteomics 2009, 9:3815-3823.
51. Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP: Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res 2006, 5:2339-2347.