Optimization of human dendritic cell sample preparation for mass spectrometry-based proteomic studies

Analytical Biochemistry

Volumn 484, Issue , 2015, Pages 40-50

  Zhang, Ying ^a   Bottinelli, Dario ^a   Lisacek, Frédérique ^a,b   Luban, Jeremy ^c   Strambio De Castillia, Caterina ^c   Varesio, Emmanuel ^a   Hopfgartner, Gérard ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

LC MS MS; Monocyte derived dendritic cells; Protein precipitation; Protein solubilization; Proteomics; Sample preparation

Indexed keywords

ACETONE; CELLS; CYTOLOGY; MASS SPECTROMETRY; PELLETIZING; PROTEOMICS; SOLUBILITY; TRICHLOROACETIC ACID;

ADAPTIVE IMMUNE RESPONSE; DENDRITIC CELLS; HUMAN DENDRITIC CELLS; LC-MS/MS; MECHANICAL DISRUPTION; PROTEIN IDENTIFICATION; PROTEIN PRECIPITATION; SAMPLE PREPARATION;

PROTEINS;

ACETONE; BICARBONATE; CELL EXTRACT; DEOXYCHOLATE SODIUM; DETERGENT; DODECYL SULFATE SODIUM; NUCLEAR PROTEIN; QUATERNARY AMMONIUM DERIVATIVE; TRICHLOROACETIC ACID; TRIETHYLAMMONIUM BICARBONATE; TRITON X 100; UNCLASSIFIED DRUG; BUFFER; OCTOXINOL;

ARTICLE; CELL DISRUPTION; CONTROLLED STUDY; CYTOLYSIS; DENDRITIC CELL; DISSOLUTION; HUMAN; HUMAN CELL; HYDROPHOBICITY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MONOCYTE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DENATURATION; PROTEOMICS; RADIOIMMUNOPRECIPITATION; SOLUBILITY; SOLUBILIZATION; TANDEM MASS SPECTROMETRY; ANALYSIS; CHEMISTRY; CYTOLOGY; METABOLISM; PRECIPITATION; PROCEDURES; PROTEIN TRANSPORT;

ACETONE; ANALYTIC SAMPLE PREPARATION METHODS; BUFFERS; CHEMICAL PRECIPITATION; DENDRITIC CELLS; HUMANS; MONOCYTES; OCTOXYNOL; PROTEIN DENATURATION; PROTEIN TRANSPORT; PROTEOMICS; RADIOIMMUNOPRECIPITATION ASSAY; SOLUBILITY; TANDEM MASS SPECTROMETRY; TRICHLOROACETIC ACID;

EID: 84935899784     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2015.05.007     Document Type: Article

References (40)

1. J. Banchereau, and R.M. Steinman Dendritic cells and the control of immunity Nature 392 1998 245 252
2. G. Vassalli Dendritic cell-based approaches for therapeutic immune regulation in solid-organ transplantation J. Transplant. 2013 2013 761429
3. C.C. Gross, and H. Wiendl Dendritic cell vaccination in autoimmune disease Curr. Opin. Rheumatol. 25 2013 268 274
4. K. Palucka, and J. Banchereau Dendritic-cell-based therapeutic cancer vaccines Immunity 39 2013 38 48
5. J. Luban Innate immune sensing of HIV-1 by dendritic cells Cell Host Microbe 12 2012 408 418
6. L. Wu, and V.N. KewalRamani Dendritic-cell interactions with HIV: Infection and viral dissemination Nat. Rev. Immunol. 6 2006 859 868
7. S. Rahman, Z.K. Khan, and P. Jain The tug-of-war between dendritic cells and human chronic viruses Int. Rev. Immunol. 30 2011 341 365
8. M. Sehgal, Z.K. Khan, A.H. Talal, and P. Jain Dendritic cells in HIV-1 and HCV infection: can they help win the battle? Virology 4 2013 1 25
9. G.B. Ferreira, C. Mathieu, and L. Overbergh Understanding dendritic cell biology and its role in immunological disorders through proteomic profiling Proteomics 4 2010 190 203
10. G.B. Ferreira, L. Overbergh, E. van Etten, K. Lage, W. D'Hertog, D.A. Hansen, M. Maris, Y. Moreau, C.T. Workman, E. Waelkens, and C. Mathieu Protein-induced changes during the maturation process of human dendritic cells: a 2-D DIGE approach Proteomics 2 2008 1349 1360
11. F. Le Naour, L. Hohenkirk, A. Grolleau, D.E. Misek, P. Lescure, J.D. Geiger, S. Hanash, and L. Beretta Profiling changes in gene expression during differentiation and maturation of monocyte-derived dendritic cells using both oligonucleotide microarrays and proteomics J. Biol. Chem. 276 2001 17920 17931
12. S.R. Pereira, V.M. Faca, G.G. Gomes, R. Chammas, A.M. Fontes, D.T. Covas, and L.J. Greene Changes in the proteomic profile during differentiation and maturation of human monocyte-derived dendritic cells stimulated with granulocyte macrophage colony stimulating factor/interleukin-4 and lipopolysaccharide Proteomics 5 2005 1186 1198
13. A. Rivollier, L. Perrin-Cocon, S. Luche, H. Diemer, J.M. Strub, D. Hanau, A. van Dorsselaer, V. Lotteau, C. Rabourdin-Combe, T. Rabilloud, and C. Servet-Delprat High expression of antioxidant proteins in dendritic cells: possible implications in atherosclerosis Mol. Cell. Proteomics 5 2006 726 736
14. C. Horlock, F. Shakib, J. Mahdavi, N.S. Jones, H.F. Sewell, and A.M. Ghaemmaghami Analysis of proteomic profiles and functional properties of human peripheral blood myeloid dendritic cells, monocyte-derived dendritic cells, and the dendritic cell-like KG-1 cells reveals distinct characteristics Genome Biol. 8 2007 R30
15. N. Sanarico, A. Colone, M. Grassi, V. Speranza, D. Giovannini, A. Ciaramella, V. Colizzi, and F. Mariani Different transcriptional profiles of human monocyte-derived dendritic cells infected with distinct strains of Mycobacterium tuberculosis and Mycobacterium bovis Bacillus Calmette-Guérin Clin. Dev. Immunol. 2011 2011 14
16. N.M. Boukli, Z.M. Saiyed, M. Ricaurte, J.W. Rodriguez, E. Rios Olivares, L.A. Cubano, and M.P. Nair Implications of ER stress, the unfolded protein response, and pro- and anti-apoptotic protein fingerprints in human monocyte-derived dendritic cells treated with alcohol Alcoholism 34 2010 2081 2088
17. J.L. Reynolds, S.D. Mahajan, R. Aalinkeel, B. Nair, D.E. Sykes, and S.A. Schwartz Proteomic analyses of the effects of drugs of abuse on monocyte-derived mature dendritic cells Immunol. Invest. 38 2009 526 550
18. J.L. Reynolds, S.D. Mahajan, D.E. Sykes, S.A. Schwartz, and M.P. Nair Proteomic analyses of methamphetamine (METH)-induced differential protein expression by immature dendritic cells (IDC) Biochim. Biophys. Acta 1774 2007 433 442
19. C.Y. Wang, V. Staniforth, M.T. Chiao, C.C. Hou, H.M. Wu, K.C. Yeh, C.H. Chen, P.I. Hwang, T.N. Wen, L.F. Shyur, and N.S. Yang Genomics and proteomics of immune modulatory effects of a butanol fraction of Echinacea purpurea in human dendritic cells BMC Genomics 9 2008 479
20. D.B. Fearnley, L.F. Whyte, S.A. Carnoutsos, A.H. Cook, and D.N.J. Hart Monitoring human blood dendritic cell numbers in normal individuals and in stem cell transplantation Blood 93 1999 728 736
21. + dendritic cells Proc. Natl. Acad. Sci. U.S.A. 93 1996 2588 2592
22. S. Duclos, G. Clavarino, G. Rousserie, G. Goyette, J. Boulais, V. Camossetto, E. Gatti, S. LaBoissiere, P. Pierre, and M. Desjardins The endosomal proteome of macrophage and dendritic cells Proteomics 11 2011 854 864
23. N.C. Gundacker, V.J. Haudek, H. Wimmer, A. Slany, J. Griss, V. Bochkov, C. Zielinski, O. Wagner, J. Stockl, and C. Gerner Cytoplasmic proteome and secretome profiles of differently stimulated human dendritic cells J. Proteome Res. 8 2009 2799 2811
24. J. Ge, H. Yan, S. Li, W. Nie, K. Dong, L. Zhang, W. Zhu, F. Fan, and J. Zhu Changes in proteomics profile during maturation of marrow-derived dendritic cells treated with oxidized low-density lipoprotein Proteomics 11 2011 1893 1902
25. D. Nicholas, H. Tang, Q. Zhang, J. Rudra, F. Xu, W. Langridge, and K. Zhang Quantitative proteomics reveals a role for epigenetic reprogramming during human monocyte differentiation Mol. Cell. Proteomics 14 2015 15 29
26. D.M. Schlatzer, J. Sugalski, J.E. Dazard, M.R. Chance, and D.D. Anthony A quantitative proteomic approach for detecting protein profiles of activated human myeloid dendritic cells J. Immunol. Methods 375 2012 39 45
27. C. Abdallah, E. Dumas-Gaudot, J. Renaut, and K. Sergeant Gel-based and gel-free quantitative proteomics approaches at a glance Int. J. Plant Genomics 2012 2012 17
28. K.L. Rundlett, and D.W. Armstrong Mechanism of signal suppression by anionic surfactants in capillary electrophoresis-electrospray ionization mass spectrometry Anal. Chem. 68 1996 3493 3497
29. N. Zhang, and L. Li Effects of common surfactants on protein digestion and matrix-assisted laser desorption/ionization mass spectrometric analysis of the digested peptides using two-layer sample preparation Rapid Commun. Mass Spectrom. 18 2004 889 896
30. D. Botelho, M.J. Wall, D.B. Vieira, S. Fitzsimmons, F. Liu, and A. Doucette Top-down and bottom-up proteomics of SDS-containing solutions following mass-based separation J. Proteome Res. 9 2010 2863 2870
31. Y. Lin, H. Liu, Z. Liu, Y. Liu, Q. He, P. Chen, X. Wang, and S. Liang Development and evaluation of an entirely solution-based combinative sample preparation method for membrane proteomics Anal. Biochem. 432 2013 41 48
32. E.I. Chen, D. Cociorva, J.L. Norris, and J.R. Yates 3rd Optimization of mass spectrometry-compatible surfactants for shotgun proteomics J. Proteome Res. 6 2007 2529 2538
33. Y. Lin, J. Zhou, D. Bi, P. Chen, X. Wang, and S. Liang Sodium-deoxycholate-assisted tryptic digestion and identification of proteolytically resistant proteins Anal. Biochem. 377 2008 259 266
34. J.L. Proc, M.A. Kuzyk, D.B. Hardie, J. Yang, D.S. Smith, A.M. Jackson, C.E. Parker, and C.H. Borchers A quantitative study of the effects of chaotropic agents, surfactants, and solvents on the digestion efficiency of human plasma proteins by trypsin J. Proteome Res. 9 2010 5422 5437
35. Y. Lin, H. Liu, Z. Liu, X. Wang, and S. Liang Shotgun analysis of membrane proteomes using a novel combinative strategy of solution-based sample preparation coupled with liquid chromatography-tandem mass spectrometry J. Chromatogr. B 901 2012 18 24
36. I.R. Leon, V. Schwammle, O.N. Jensen, and R.R. Sprenger Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis Mol. Cell. Proteomics 12 2013 2992 3005
37. C. Reinhard, D. Bottinelli, B. Kim, and J. Luban Vpx rescue of HIV-1 from the antiviral state in mature dendritic cells is independent of the intracellular deoxynucleotide concentration Retrovirology 11 2014 12
38. I.V. Shilov, S.L. Seymour, A.A. Patel, A. Loboda, W.H. Tang, S.P. Keating, C.L. Hunter, L.M. Nuwaysir, and D.A. Schaeffer The paragon algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra Mol. Cell. Proteomics 6 2007 1638 1655
39. J. Kyte, and R.F. Doolittle A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 157 1982 105 132
40. E.I. Boyle, S. Weng, J. Gollub, H. Jin, D. Botstein, J.M. Cherry, and G. Sherlock GO::TermFinder - Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes Bioinformatics 20 2004 3710 3715