Direct comparison of MS-based label-free and SILAC quantitative proteome profiling strategies in primary retinal Müller cells

Proteomics

Volumn 12, Issue 12, 2012, Pages 1902-1911

  Merl, Juliane ^a,b   Ueffing, Marius ^a,c   Hauck, Stefanie M ^a   von Toerne, Christine ^a  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c UNIVERSITY HOSPITAL TÜBINGEN   (Germany)

Author keywords

Label free; MaxQuant; Progenesis LC MS; Retinal M ller glial cells; SILAC; Technology

Indexed keywords

AMINO ACID; PROTEIN; STABLE ISOTOPE;

ANIMAL CELL; ANTIBODY LABELING; ARTICLE; CELL CULTURE; GLIA CELL; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; RETINA CELL; RETINA MULLER GLIAL CELL; SWINE;

ANIMALS; CELLS, CULTURED; IMMUNOBLOTTING; ISOTOPE LABELING; LINEAR MODELS; MASS SPECTROMETRY; NEUROGLIA; PROTEOME; PROTEOMICS; RETINA; SWINE;

SUS;

EID: 84862996761     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201100549     Document Type: Article

References (30)

1. Bringmann, A., Pannicke, T., Grosche, J., Francke, M. et al., Muller cells in the healthy and diseased retina. Prog. Retin. Eye Res. 2006, 25, 397-424.
2. Willbold, E., Berger, J., Reinicke, M., Wolburg, H., On the role of Muller glia cells in histogenesis: only retinal spheroids, but not tectal, telencephalic and cerebellar spheroids develop histotypical patterns. J. Hirnforsch 1997, 38, 383-396.
3. Poitry-Yamate, C. L., Poitry, S., Tsacopoulos, M., Lactate released by Muller glial cells is metabolized by photoreceptors from mammalian retina. J. Neurosci. 1995, 15, 5179-5191.
4. Barnett, N. L., Pow, D. V., Antisense knockdown of GLAST, a glial glutamate transporter, compromises retinal function. Invest. Ophthalmol. Vis. Sci. 2000, 41, 585-591.
5. Winter, M., Eberhardt, W., Scholz, C., Reichenbach, A., Failure of potassium siphoning by Muller cells: a new hypothesis of perfluorocarbon liquid-induced retinopathy. Invest. Ophthalmol. Vis. Sci. 2000, 41, 256-261.
6. Hauck, S. M., Gloeckner, C. J., Harley, M. E., Schoeffmann, S. et al., Identification of paracrine neuroprotective candidate proteins by a functional assay-driven proteomics approach. Mol. Cell Proteomics 2008, 7, 1349-1361.
7. Del Rio, P., Irmler, M., Arango-Gonzalez, B., Favor, J. et al., GDNF-induced osteopontin from Muller glial cells promotes photoreceptor survival in the Pde6brd1 mouse model of retinal degeneration. Glia 2011, 59, 821-832.
8. Hauck, S. M., Kinkl, N., Deeg, C. A., Swiatek-de Lange, M. et al., GDNF family ligands trigger indirect neuroprotective signaling in retinal glial cells. Mol. Cell Biol. 2006, 26, 2746-2757.
9. Bringmann, A., Iandiev, I., Pannicke, T., Wurm, A. et al., Cellular signaling and factors involved in Muller cell gliosis: neuroprotective and detrimental effects. Prog. Retin. Eye Res. 2009, 28, 423-451.
10. Hauck, S. M., Suppmann, S., Ueffing, M., Proteomic profiling of primary retinal Muller glia cells reveals a shift in expression patterns upon adaptation to in vitro conditions. Glia 2003, 44, 251-263.
11. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B. et al., Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics 2002, 1, 376-386.
12. Ong, S. E., Mann, M., A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat. Protoc. 2006, 1, 2650-2660.
13. Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26, 1367-1372.
14. Cox, J., Matic, I., Hilger, M., Nagaraj, N. et al., A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat. Protoc. 2009, 4, 698-705.
15. Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A. et al., Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 2011, 10, 1794-1805.
16. Colaert, N., Gevaert, K., Martens, L., RIBAR and xRIBAR: methods for reproducible relative MS/MS-based label-free protein quantification. J. Proteome Res. 2011, 10, 3183-3189.
17. Turck, C. W., Falick, A. M., Kowalak, J. A., Lane, W. S. et al., The Association of Biomolecular Resource Facilities Proteomics Research Group 2006 study: relative protein quantitation. Mol. Cell Proteomics 2007, 6, 1291-1298.
18. Asara, J. M., Christofk, H. R., Freimark, L. M., Cantley, L. C., A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen. Proteomics 2008, 8, 994-999.
19. Hauck, S. M., Dietter, J., Kramer, R. L., Hofmaier, F. et al., Deciphering membrane-associated molecular processes in target tissue of autoimmune uveitis by label-free quantitative mass spectrometry. Mol. Cell Proteomics 2010, 9, 2292-2305.
20. Hubner, N. C., Mann, M., Extracting gene function from protein-protein interactions using Quantitative BAC InteraCtomics (QUBIC). Methods 2011, 53, 453-459.
21. Geiger, T., Cox, J., Mann, M., Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation. Mol. Cell Proteomics 2010, 9, 2252-2261.
22. Bantscheff, M., Schirle, M., Sweetman, G., Rick, J. et al., Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 2007, 389, 1017-1031.
23. Collier, T. S., Sarkar, P., Franck, W. L., Rao, B. M. et al., Direct comparison of stable isotope labeling by amino acids in cell culture and spectral counting for quantitative proteomics. Anal. Chem. 82, 8696-8702.
24. Wu, W. W., Wang, G., Yu, M.-J., Knepper, M. A. et al., Identification and quantification of basic and acidic proteins using solution-based two-dimensional protein fractionation and label-free or 18O-labeling mass spectrometry. J. Proteome Res. 2007, 6, 2447-2459.
25. Spellman, D. S., Deinhardt, K., Darie, C. C., Chao, M. V. et al., Stable isotopic labeling by amino acids in cultured primary neurons: application to brain-derived neurotrophic factor-dependent phosphotyrosine-associated signaling. Mol. Cell Proteomics 2008, 7, 1067-1076.
26. Liao, L., Park, S. K., Xu, T., Vanderklish, P. et al., Quantitative proteomic analysis of primary neurons reveals diverse changes in synaptic protein content in fmr1 knockout mice. Proc. Natl. Acad. Sci. USA 2008, 105, 15281-15286.
27. Tyler, J. R., Robertson, H., Booth, T. A., Burt, A. D. et al., Chronic allograft nephropathy: intraepithelial signals generated by transforming growth factor-beta and bone morphogenetic protein-7. Am. J. Transplant 2006, 6, 1367-1376.
28. Assinder, S. J., Stanton, J. A., Prasad, P. D., Transgelin: an actin-binding protein and tumour suppressor. Int. J. Biochem. Cell Biol. 2009, 41, 482-486.
29. Guidry, C., Isolation and characterization of porcine Muller cells. Myofibroblastic dedifferentiation in culture. Invest. Ophthalmol. Vis. Sci. 1996, 37, 740-752.
30. Shi, X., Qu, H., Kretzler, M., Wu, C., Roles of PINCH-2 in regulation of glomerular cell shape change and fibronectin matrix deposition. Am. J. Physiol. Renal Physiol. 2008, 295, F253-F263.