A quantitative proteomic workflow for characterization of frozen clinical biopsies: Laser capture microdissection coupled with label-free mass spectrometry

Journal of Proteomics

Volumn 77, Issue , 2012, Pages 433-440

  Shapiro, John P ^a   Biswas, Sabyasachi ^a   Merchant, Anand S ^a   Satoskar, Anjali ^a   Taslim, Cenny ^a   Lin, Shili ^b   Rovin, Brad H ^a   Sen, Chandan K ^a   Roy, Sashwati ^a   Freitas, Michael A ^a  

^a THE OHIO STATE UNIVERSITY COLLEGE OF MEDICINE   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

Biopsy; Label free; Laser capture microdissection; Mass spectrometry; Proteomics

Indexed keywords

ARTICLE; CELL ISOLATION; CLUSTER ANALYSIS; CONTROLLED STUDY; GLOMERULUS; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; KERATINOCYTE; KIDNEY DISEASE; LASER CAPTURE MICRODISSECTION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NEEDLE BIOPSY; PRIORITY JOURNAL; PROTEOMICS; PUNCH BIOPSY; TANDEM MASS SPECTROMETRY; WORKFLOW;

BIOLOGICAL MARKERS; BIOPSY; CRYOPRESERVATION; FEMALE; HUMANS; LASER CAPTURE MICRODISSECTION; MALE; MASS SPECTROMETRY; PROTEOMICS;

EID: 84870393344     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2012.09.019     Document Type: Article

References (34)

1. Anderson C.E., McLaren K.M., Rae F., Sanderson R.J., Cuschieri K.S. Human papilloma virus in squamous carcinoma of the head and neck: a study of cases in south east Scotland. J Clin Pathol 2007, 60:439-441.
2. Espina V., Heiby M., Pierobon M., Liotta L.A. Laser capture microdissection technology. Expert Rev Mol Diagn 2007, 7:647-657.
3. Gutstein H.B., Morris J.S. Laser capture sampling and analytical issues in proteomics. Expert Rev Proteomics 2007, 4:627-637.
4. Xu B.J. Combining laser capture microdissection and proteomics: methodologies and clinical applications. Proteomics Clin Appl 2010, 4:116-123.
5. Mustafa D., Kros J.M., Luider T. Combining laser capture microdissection and proteomics techniques. Methods Mol Biol 2008, 428:159-178.
6. Liu N.Q., Braakman R.B., Stingl C., Luider T.M., Martens J.W., Foekens J.A., et al. Proteomics pipeline for biomarker discovery of laser capture microdissected breast cancer tissue. J Mammary Gland Biol Neoplasia 2012.
7. Braakman R.B., Luider T.M., Martens J.W., Foekens J.A., Umar A. Laser capture microdissection applications in breast cancer proteomics. Methods Mol Biol 2011, 755:143-154.
8. Lawrie L.C., Curran S. Laser capture microdissection and colorectal cancer proteomics. Methods Mol Biol 2005, 293:245-253.
9. Cha S, Imielinski MB, Rejtar T, Richardson EA, Thakur D, Sgroi DC, et al. In situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection: annotation by protein set enrichment analysis and gene ontology. Mol Cell Proteomics;9:2529-44.
10. Greengauz-Roberts O., Stoppler H., Nomura S., Yamaguchi H., Goldenring J.R., Podolsky R.H., et al. Saturation labeling with cysteine-reactive cyanine fluorescent dyes provides increased sensitivity for protein expression profiling of laser-microdissected clinical specimens. Proteomics 2005, 5:1746-1757.
11. Umar A., Luider T.M., Foekens J.A., Pasa-Tolic L. NanoLC-FT-ICR MS improves proteome coverage attainable for approximately 3000 laser-microdissected breast carcinoma cells. Proteomics 2007, 7:323-329.
12. Waanders L.F., Chwalek K., Monetti M., Kumar C., Lammert E., Mann M. Quantitative proteomic analysis of single pancreatic islets. Proc Natl Acad Sci U S A 2009, 106:18902-18907.
13. Johann D.J., Rodriguez-Canales J., Mukherjee S., Prieto D.A., Hanson J.C., Emmert-Buck M., et al. Approaching solid tumor heterogeneity on a cellular basis by tissue proteomics using laser capture microdissection and biological mass spectrometry. J Proteome Res 2009, 8:2310-2318.
14. Johann D.J., Mukherjee S., Prieto D.A., Veenstra T.D., Blonder J. Profiling solid tumor heterogeneity by LCM and biological MS of fresh-frozen tissue sections. Methods Mol Biol 2011, 755:95-106.
15. Vrana J.A., Gamez J.D., Madden B.J., Theis J.D., Bergen H.R., Dogan A. Classification of amyloidosis by laser microdissection and mass spectrometry-based proteomic analysis in clinical biopsy specimens. Blood 2009, 114:4957-4959.
16. Patel V., Hood B.L., Molinolo A.A., Lee N.H., Conrads T.P., Braisted J.C., et al. Proteomic analysis of laser-captured paraffin-embedded tissues: a molecular portrait of head and neck cancer progression. Clin Cancer Res 2008, 14:1002-1014.
17. Robinson M.D., Smyth G.K. Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 2007, 23:2881-2887.
18. Robinson M.D., Smyth G.K. Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics 2008, 9:321-332.
19. Robinson M.D., McCarthy D.J., Smyth G.K. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:139-140.
20. Fei S.S., Wilmarth P.A., Hitzemann R.J., McWeeney S.K., Belknap J.K., David L.L. Protein database and quantitative analysis considerations when integrating genetics and proteomics to compare mouse strains. J Proteome Res 2011, 10:2905-2912.
21. Zhang B., Chambers M.C., Tabb D.L. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J Proteome Res 2007, 6:3549-3557.
22. Liu H., Sadygov R.G., Yates J.R. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 2004, 76:4193-4201.
23. Colinge J., Chiappe D., Lagache S., Moniatte M., Bougueleret L. Differential proteomics via probabilistic peptide identification scores. Anal Chem 2005, 77:596-606.
24. Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Stat Methodol 1995, 57:289-300.
25. Piedimonte G., Guetard D., Magnani M., Corsi D., Picerno I., Spataro P., et al. Oxidative protein damage and degradation in lymphocytes from patients infected with human immunodeficiency virus. J Infect Dis 1997, 176:655-664.
26. Dover R., Watt F.M. Measurement of the rate of epidermal terminal differentiation: expression of involucrin by S-phase keratinocytes in culture and in psoriatic plaques. J Invest Dermatol 1987, 89:349-352.
27. Mazzalupo S., Wong P., Martin P., Coulombe P.A. Role for keratins 6 and 17 during wound closure in embryonic mouse skin. Dev Dyn 2003, 226:356-365.
28. Sharma A., Singh A.K., Warren J., Thangapazham R.L., Maheshwari R.K. Differential regulation of angiogenic genes in diabetic wound healing. J Invest Dermatol 2006, 126:2323-2331.
29. Pollins A.C., Friedman D.B., Nanney L.B. Proteomic investigation of human burn wounds by 2D-difference gel electrophoresis and mass spectrometry. J Surg Res 2007, 142:143-152.
30. Moll I., Houdek P., Schafer S., Nuber U., Moll R. Diversity of desmosomal proteins in regenerating epidermis: immunohistochemical study using a human skin organ culture model. Arch Dermatol Res 1999, 291:437-446.
31. Castelletti F., Donadelli R., Banterla F., Hildebrandt F., Zipfel P.F., Bresin E., et al. Mutations in FN1 cause glomerulopathy with fibronectin deposits. Proc Natl Acad Sci U S A 2008, 105:2538-2543.
32. Alkhas A., Hood B.L., Oliver K., Teng P.N., Oliver J., Mitchell D., et al. Standardization of a sample preparation and analytical workflow for proteomics of archival endometrial cancer tissue. J Proteome Res 2011.
33. Brem H., Stojadinovic O., Diegelmann R.F., Entero H., Lee B., Pastar I., et al. Molecular markers in patients with chronic wounds to guide surgical debridement. Mol Med 2007, 13:30-39.
34. El-Okdi N., Smaili S., Raju V., Shidyak A., Gupta S., Fedorova L., et al. Effects of cardiotonic steroids on dermal collagen synthesis and wound healing. J Appl Physiol 2008, 105:30-36.