Enrichment of extracellular matrix proteins from tissues and digestion into peptides for mass spectrometry analysis

Journal of Visualized Experiments

Volumn 2015, Issue 101, 2015, Pages

  Naba, Alexandra ^a   Clauser, Karl R ^b   Hynes, Richard O ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

Biochemistry; Decellularization; Deglycosylation; Extracellular matrix; Mass spectrometry; Matrisome; Proteins; Proteomics; Sequential solubilization; Tryptic digestion

Indexed keywords

PEPTIDE; SCLEROPROTEIN;

ANIMAL; CELL PROLIFERATION; CHEMISTRY; EXTRACELLULAR MATRIX; FIBROSIS; HUMAN; ISOLATION AND PURIFICATION; MASS SPECTROMETRY; MOUSE; NEOPLASM; PROCEDURES;

ANIMALS; CELL PROLIFERATION; EXTRACELLULAR MATRIX; EXTRACELLULAR MATRIX PROTEINS; FIBROSIS; HUMANS; MASS SPECTROMETRY; MICE; NEOPLASMS; PEPTIDES;

EID: 84941254694     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/53057     Document Type: Article

References (19)

1. Hynes, R. O., & Naba, A. Overview of the matrisome--an inventory of extracellular matrix constituents and functions. Cold Spring Harb Perspect Biol. 4 (1), a004903, doi:10.1101/cshperspect.a004903 (2012).
2. Mouw, J. K., Ou, G., & Weaver, V. M. Extracellular matrix assembly: a multiscale deconstruction. Nat. Rev. Mol. Cell Biol.. 15 (12), 771–785, doi:10.1038/nrm3902 (2014).
3. Hynes, R. O. The extracellular matrix: not just pretty fibrils. Science. 326 (5957), 1216–9, doi:326/5957/1216 [pii] 10.1126/science.1176009 (2009).
4. Bonnans, C., Chou, J., & Werb, Z. Remodelling the extracellular matrix in development and disease. Nat. Rev. Mol. Cell Biol.. 15 (12), 786– 801, doi:10.1038/nrm3904 (2014).
5. Dvir, T., Timko, B. P., Kohane, D. S., & Langer, R. Nanotechnological strategies for engineering complex tissues. Nat Nanotechnol. 6 (1), 13– 22, doi:10.1038/nnano.2010.246 (2011).
6. Wilson, R. The extracellular matrix: an underexplored but important proteome. Expert Rev Proteomics. 7 (6), 803–806, doi:10.1586/epr.10.93 (2010).
7. Naba, A., Hoersch, S., & Hynes, R. O. Towards definition of an ECM parts list: an advance on GO categories. Matrix Biol.. 31 (7-8), 371–372, doi:10.1016/j.matbio.2012.11.008 (2012).
8. Naba, A., Clauser, K. R., Hoersch, S., Liu, H., Carr, S. A., & Hynes, R. O. The matrisome: in silico definition and in vivo. characterization by proteomics of normal and tumor extracellular matrices. Mol. Cell Proteomics. 11 (4), M111.014647, doi:10.1074/mcp.M111.014647 (2012).
9. Naba, A., Clauser, K. R., Whittaker, C. A., Carr, S. A., Tanabe, K. K., & Hynes, R. O. Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver. BMC Cancer. 14 (1), 518, doi:10.1186/1471-2407-14-518 (2014).
10. Naba, A., Clauser, K. R., Lamar, J. M., Carr, S. A., & Hynes, R. O. Extracellular matrix signatures of human mammary carcinoma identify novel metastasis promoters. eLife. 3:e01308, doi:http://dx.doi.org/10.7554/eLife.01308 (2014).
11. Naba, A., Ding, H., Whittaker, C. A., & Hynes, R. O. et al. Proteomic analysis of altered extracellular matrix turnover in bleomycin-induced pulmonary fibrosis. Mol. Cell Proteomics. 13 (7), 1741–1752, doi:10.1074/mcp.M113.037267 (2014).
12. Tsuchiya, T., Balestrini, J. L., Mendez, J. J., Calle, E. A., Zhao, L., & Niklason, L. Influence of pH on extracellular matrix preservation during lung decellularization. Tissue Eng Part C Methods. 20(12),1028-36, doi:10.1089/ten.TEC.2013.0492 (2014).
13. Byron, A., Humphries, J. D., & Humphries, M. J. Defining the extracellular matrix using proteomics. Int J Exp Pathol. 94 (2), 75–92, doi:10.1111/iep.12011 (2013).
14. Wilson, R., Diseberg, A. F., et al. Comprehensive profiling of cartilage extracellular matrix formation and maturation using sequential extraction and label-free quantitative proteomics. Mol. Cell Proteomics. 9 (6), 1296–1313, doi:10.1074/mcp.M000014-MCP201 (2010).
15. Belluoccio, D., Wilson, R., Thornton, D. J., Wallis, T. P., Gorman, J. J., & Bateman, J. F. Proteomic analysis of mouse growth plate cartilage. Proteomics. 6 (24), 6549–6553, doi:10.1002/pmic.200600191 (2006).
16. Barallobre-Barreiro, J., Didangelos, A., Yin, X., Doménech, N., & Mayr, M. A sequential extraction methodology for cardiac extracellular matrix prior to proteomics analysis. In: Heart Proteomics: Methods and Protocols. 1005, 215–223, doi: 10.1007/978-1-62703-386-2_17 (2013).
17. Hansen, K. C., Kiemele, L., et al. An in-solution ultrasonication-assisted digestion method for improved extracellular matrix proteome coverage. Mol. Cell Proteomics. 8 (7), 1648–57, doi:M900039-MCP200 [pii] 10.1074/mcp.M900039-MCP200 (2009).
18. Didangelos, A., Yin, X., Mandal, K., Baumert, M., Jahangiri, M., & Mayr, M. Proteomics characterization of extracellular space components in the human aorta. Mol. Cell Proteomics. 9 (9), 2048–2062, doi:10.1074/mcp.M110.001693 (2010).
19. Lennon, R., Byron, A., et al. Global analysis reveals the complexity of the human glomerular extracellular matrix. J. Am. Soc. Nephrol.. 25 (5), 939–951, doi:10.1681/ASN.2013030233 (2014).