Enrichment of plasma membrane proteins using nanoparticle pellicles: Comparison between silica and higher density nanoparticles

Journal of Proteome Research

Volumn 12, Issue 3, 2013, Pages 1134-1141

  Choksawangkarn, Waeowalee ^a   Kim, Sung Kyoung ^a   Cannon, Joe R ^a   Edwards, Nathan J ^b   Lee, Sang Bok ^a,c   Fenselau, Catherine ^a  

^a Bldg 142   (United States)

^b GEORGETOWN UNIVERSITY   (United States)

^c Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

nanoparticles; pellicle enrichment; plasma membrane; proteomics; spectral counting

Indexed keywords

MEMBRANE PROTEIN; NANOPARTICLE; SILICON DIOXIDE;

ARTICLE; CELL GROWTH; CELL MEMBRANE; CONTROLLED STUDY; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MYELOMA CELL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS;

EID: 84874601536     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr301107x     Document Type: Article

References (33)

1. Stevens, T. J.; Arkin, I. T. Do more complex organisms have a greater proportion of membrane proteins in their genomes? Proteins: Struct., Funct., Genet. 2000, 39, 417-420
2. Overington, J. P.; Al-Lazikzni, B.; Hopkins, A. L. How many drug targets are there? Nat. Rev. Drug Discovery 2006, 5, 993-996
3. Zhang, W.; Zhao, C.; Wang, S.; Fang, C.; Xu, Y.; Lu, H.; Yang, P. Coating cells with cationic silica-magnetite nanocomposites for rapid purification of integral plasma membrane proteins Proteomics 2011, 11, 3482-3490
4. Speers, A. E.; Wu, C. C. Proteomics of integral membrane proteins: theory and application Chem. Rev. 2007, 107, 3687-3714
5. Shin, B. K.; Wang, H.; Yim, A. M.; LeNaour, F.; Brichory, F.; Jang, J. H.; Zhao, R.; Puravs, E.; Tra, J.; Michael, C. W.; Misek, D. E.; Hanash, S. M. Global profiling of the cell surface proteome of cancer cells uncovers an abundance of proteins with chaperone function J. Biol. Chem 2003, 278, 7607-7616
6. Zhang, H.; Li, X. J.; Martin, D. B.; Aebersold, R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry Nat. Biotechnol. 2003, 21, 660-666
7. Zhao, Y.; Zhang, W.; Kho, Y.; Zhao, Y. Proteomic analysis of integral plasma membrane proteins Anal. Chem. 2004, 76, 1817-1823
8. Choksawangkarn, W.; Edwards, N.; Wang, Y.; Gutierrez, P.; Fenselau, C. Comparative study of workflows optimized for in-gel, in-solution, and on-filter proteolysis in the analysis of plasma membrane proteins J. Proteome Res. 2012, 11, 3030-3034
9. Chaney, L. K.; Jacobson, B. S. Coating cells with colloidal silica for high yield isolation of plasma membrane sheets and identification of transmembrane proteins J. Biol. Chem. 1983, 258, 10062-10072
10. Stolz, D. B.; Jacobson, B. S. Examination of transcellular membrane protein polarity of bovine aortic endothelial cells in vitro using the cationic colloidal silica microbead membrane-isolation procedure J. Cell Sci. 1992, 103 ((Pt 1)) 39-51
11. Stolz, D. B.; Ross, M. A.; Salem, H. M.; Mars, W. M.; Michalopoulos, G. K.; Enomoto, K. Cationic colloidal silica membrane perturbation as a means of examining changes at the sinusoidal surface during liver regeneration Am. J. Pathol. 1999, 155, 1487-1498
12. Robinson, J. M.; Ackerman, W. E. T.; Tewari, A. K.; Kniss, D. A.; Vandre, D. D. Isolation of highly enriched apical plasma membranes of the placental syncytiotrophoblast Anal. Biochem. 2009, 387, 87-94
13. Harvey, S.; Zhang, Y.; Landry, F.; Miller, C.; Smith, J. W. Insights into a plasma membrane signature Physiol. Genomics 2001, 5, 129-136
14. Rahbar, A. M.; Fenselau, C. Integration of Jacobson's pellicle method into proteomic strategies for plasma membrane proteins J. Proteome Res. 2004, 3, 1267-1277
15. Rahbar, A. M.; Fenselau, C. Unbiased examination of changes in plasma membrane proteins in drug resistant cancer cells J. Proteome Res. 2005, 4, 2148-2153
16. Li, X.; Xie, C.; Cao, J.; He, Q.; Cao, R.; Lin, Y.; Jin, Q.; Chen, P.; Wang, X.; Liang, S. An in vivo membrane density perturbation strategy for identification of liver sinusoidal surface proteome accessible from the vasculature J. Proteome Res. 2009, 8, 123-132
17. Li, X.; Jin, Q.; Cao, J.; Xie, C.; Cao, R.; Liu, Z.; Xiong, J.; Li, J.; Yang, X.; Chen, P.; Liang, S. Evaluation of two cell surface modification methods for proteomic analysis of plasma membrane from isolated mouse hepatocytes Biochim. Biophys. Acta 2009, 1794, 32-41
18. Leduc-Nadeau, A.; Lahjouji, K.; Bissonnette, P.; Lapointe, J. Y.; Bichet, D. G. Elaboration of a novel technique for purification of plasma membranes from Xenopus laevis oocyte s Am. J. Physiol. Cell Physiol. 2007, 292, C1132-C1136
19. Jacobson, B. S.; Stolz, D. B.; Schnitzer, J. E. Identification of endothelial cell-surface proteins as targets for diagnosis and treatment of disease Nat. Med. 1996, 2, 482-484
20. Li, X.; Jia, X.; Xie, C.; Lin, Y.; Cao, R.; He, Q.; Chen, P.; Wang, X.; Liang, S. Development of cationic colloidal silica-coated magnetic nanospheres for highly selective and rapid enrichment of plasma membrane fractions for proteomics analysis Biotechnol. Appl. Biochem. 2009, 54, 213-220
21. Durr, E.; Yu, J.; Krasinska, K. M.; Carver, L. A.; Yates, J. R.; Testa, J. E.; Oh, P.; Schnitzer, J. E. Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture Nat. Biotechnol. 2004, 22, 985-992
22. Prior, M. J.; Larance, M.; Lawrence, R. T.; Soul, J.; Humphrey, S.; Burchfield, J.; Kistler, C.; Davey, J. R.; La-Borde, P. J.; Buckley, M.; Kanazawa, H.; Parton, R. G.; Guilhaus, M.; James, D. E. Quantitative proteomic analysis of the adipocyte plasma membrane J. Proteome Res. 2011, 10, 4970-4982
23. Mathias, R. A.; Chen, Y. S.; Goode, R. J.; Kapp, E. A.; Mathivanan, S.; Moritz, R. L.; Zhu, H. J.; Simpson, R. J. Tandem application of cationic colloidal silica and Triton X-114 for plasma membrane protein isolation and purification: towards developing an MDCK protein database Proteomics 2011, 11, 1238-1253
24. Vandre, D. D.; Ackerman, W. D.; Tewari, A.; Kniss, D. A.; Robinson, J. M. A placental sub-proteome: the apical plasma membrane of the syncytiotrophoblast Placenta 2012, 33, 207-213
25. Arjunan, S.; Reinartz, M.; Emde, B.; Zanger, K.; Schrader, J. Limitations of the colloidal silica method in mapping the endothelial plasma membrane proteome of the mouse heart Cell. Biochem. Biophys. 2009, 53, 135-143
26. Jang, J. H.; Hanash, S. Profiling the cell surface proteome Proteomics 2003, 3, 1947-1954
27. Bai, X.; Son, S. J.; Zhang, S.; Liu, W.; Frank, J. A.; Venkatesan, T.; Lee, S. B. Synthesis of superparamagnetic nanotubes as MRI contrast agents and for cell labeling Nanomedicine 2008, 3, 163-166
28. Wessel, D.; Flugge, U. I. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids Anal. Biochem. 1984, 138 (1) 141-143
29. Kessner, D.; Chambers, M.; Burke, R.; Agus, D.; Mallick, P. ProteoWizard: Open source software for rapid proteomics tools development Bioinformatics 2008, 24 (21) 2534-2536
30. Edwards, N.; Wu, X.; Tseng, T. W. An unsupervised, model-free, machine-learning combiner for peptide identifications from tandem mass spectra Clin. Proteomics 2009, 5, 23-36
31. Krogh, A.; Larsson, B.; von Heijne, G.; Sonnhammer, E. L. L. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes J. Mol. Biol. 2001, 305 (3) 567-580
32. Huang, W.; Sherman, B. T.; Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Nat. Protoc. 2009, 4, 44-57
33. 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