Proteomics

Preclinical Development Handbook: Toxicology

Volumn , Issue , 2007, Pages 839-865

  Casado, Juan ^a   Casal, J Ignacio ^a  

^a Centro Nacional de Investigaciones Oncológicas   (Spain)

Author keywords

Abundance based microarrays and Function Based Protein Microarrays; Protein extraction and purification; Two dimensional polyacrylamide gel electrophoresis (2D PAGE)

Indexed keywords

EID: 70349930557     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470249055.ch23     Document Type: Chapter

References (70)

1. Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery SI, Hochstrasser DF, Williams KL. Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 1996; 13: 19-50.
2. Wu CC, MacCoss MJ, Howell KE, Yates JR. A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol 2003; 21: 532-538.
3. Alfonso P, Dolado I, Swat A, Núñez A, Cuadrado A, Nebreda A, Casal JI. Membrane protein alterations induced by oncogenic H-ras transformation of p38 MAPK-deficient fibroblasts. Proteomics 2006; 6 (Supp 1): S262-S271.
4. Bordier C. Phase separation of integral membrane proteins in Triton X-114 solution. J Biol Chem 1981; 256: 1604-1607.
5. States DJ, Omenn GS, Blackwell TW, Fermin D, Eng J, Speicher DW, Hanash SM. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol 2006; 24: 333-338.
6. Foster LJ, de Hoog CL, Zhang YL, Zhang Y, Xie XH, Mootha VK, Mann M. A mammalian organelle map by protein correlation profiling. Cell 2006; 125: 187-199.
7. Bensadoun A, Weinstein D. Assay of proteins in the presence of interfering materials. Anal Biochem 1975; 70: 241-250.
8. Bradford M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. A nal Biochem 1976; 72: 248-254.
9. Laemmli UK. Cleavage of structural proteins during assembly of head of bacteriophage-T4. Nature 1970; 227: 680-685.
10. Neuhoff V, Arold N, Taube D, Ehrhardt W. Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie Brilliant Blue G-250 and R-250. Electrophoresis 1988; 9: 255-262.
11. Blum H, Beier H, Gross HJ. Improved silver staining of plant proteins, RNA and DNA in polyacrylamide gels. Electrophoresis 1987; 8: 93-99.
12. Lanne B, Panfilov O. Protein staining influences the quality of mass spectra obtained by peptide mass fingerprinting after separation on 2-D gels. A comparison of staining with Coomassie brilliant blue and SYPRO Ruby. J Proteome Res 2005; 4: 175-179.
13. Chevalier F, Rofidal V, Vanova P, Bergoin A, Rossignol M. Proteomic capacity of recent fluorescent dyes for protein staining. Phytochemistry 2004; 65: 1499-1506.
14. White IR, Pickford R, Wood J, Skehel JM, Gangadharan B, Cutler P. A statistical comparison of silver and SYPRO Ruby staining for proteomic analysis. Electrophoresis 2007; 25: 3048-3054.
15. Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, Davison M. Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 2001; 1: 377-396.
16. Alban A, David SO, Bjorkesten L, Andersson C, Sloge E, Lewis S, Currie I. A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 2003; 3: 527-533.
17. Gharbi S, Gaffney P, Yang A, Zvelebil MJ, Cramer R, Waterfield MD, Timms JF. Evaluation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system. Mol Cell Proteomics 2002; 1: 91-98.
18. Friedman DB, Hill S, Keller JW, Merchant NB, Levy SE, Coffey RJ, Caprioli RM. Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 2004; 4: 793-811.
19. Alfonso P, Núñez A, Madoz-Gurpide J, Lombardia L, Sánchez L, Casal JI. Proteomic expression analysis of colorectal cancer by two dimensional gel electrophoresis. Proteomics 2005; 5: 2602-2611.
20. González-Santiago L, Alfonso P, S u á rez Y, N ú ñ ez A, Garc í a-Fern á ndez LF, Alvarez E, Mu ñ oz A, Casal JI. Proteomic analysis of the resistance to Aplidin in human cancer cells. J Proteome Res 2007; 6: 1286-1294.
21. Rauman B, Cheung A, Marten M. Quantitative comparison and evaluation of two commercially available, two-dimensional electrophoresis image analysis software packges, Z3 and Melanie. Electrophoresis 2002; 23: 2194-2202.
22. Shevchenko A, Wilm M, Vorm O, Mann M. Mass spectrometric sequencing of proteins from silver stained polyacrylamide gels. Anal Chem 1996; 68: 850-858.
23. Domon B, Aebersold R. Mass spectrometry and protein analysis. Science 2006; 212-217.
24. Karas M, Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 1988; 60: 2299-2301.
25. Mann M, Hojrup P, Roepstorff P. Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol Mass Spectrom 1993; 22: 338-345.
26. Chamrad DC, Korting G, Stuhler K, Meyer HE, Klose J, Bluggel M. Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data. Proteomics 2004; 4: 619-668.
27. Baldwin MA. Protein identification by mass spectrometry: issues to be considered. Mol Cell Proteomics 2004; 3: 1-9.
28. Fenn JB, Mann M, Meng CK, et al. Electrospray ionisation for mass spectrometry of large biomolecules. Science 1989; 246: 64-71.
29. Han XM, Jin M, Breuker K, McLafferty FW. Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons. Science 2006; 314: 109-112.
30. Hayter JR, Robertson DHL, Gaskell SJ, Beynon RJ. Proteome analysis of intact proteins in complex mixtures. Mol Cell Proteomics 2003; 2: 85-95.
31. Biemann K. Contributions of mass spectrometry to peptide and protein structure. Biomed Environ Mass Spectrom 1988; 16: 99-111.
32. Syka JEP, Coon JJ, Schroeder MJ, Shabanowitz J, H unt DF. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci USA 2004; 101: 9528-9533.
33. Coon JJ, Ueberheide B, Syka JEP, Dryhurst DD, Ausio J, Shabanowitz J, Hunt DF. Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc Natl Acad Sci USA 2005; 102: 9463-9468.
34. Washburn MP, Wolters D, Yates JR. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001; 19: 242-247.
35. Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TKB, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao ZX, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang LL, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JGN, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003; 13: 2363-2371.
36. Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006; 127: 635-648.
37. Mann M, Jensen ON. Proteomic analysis of post-translational modifications. Nat Biotechnol 2003; 21: 255-261.
38. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science 2002; 298: 1912-1934.
39. Cohen P. The role of protein phosphorylation in human health and disease. Eur J Biochem 2001; 268: 5001-5010.
40. Hunter T, Sefton BM. Transforming gene product of Rous sarcoma virus phosphorylates tyrosine. Proc Natl Acad Sci USA Biol Sci 1980; 77: 1311-1315.
41. Mann M, Hendrickson RC, Pandey A. Analysis of proteins and proteomes by mass spectrometry. Annu Rev Biochem 2001; 70: 437-473.
42. Meng FY, Forbes AJ, Miller LM, Kelleher NL. Detection and localization of protein modifications by high resolution tandem mass spectrometry. Mass Spectrom Rev 2005; 24: 126-134.
43. Villar M, Ortega-Perez I, Were F, Cano E, Redondo JM, Vazquez J. Systematic characterization of phosphorylation sites in NFATc2 by linear ion trap mass spectrometry. Proteomics 2006; 6 (Suppl 1): S16-S27.
44. Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li JX, Cohn MA, Cantley LC, Gygi SP. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci USA 2004; 101: 12130-12135.
45. Larsen MR, Thingholm TE, Jensen ON, Roepstorff P, Jorgensen TJD. Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol Cell Proteomics 2005; 4: 873-886.
46. Steen H, Jebanathirajah JA, Rush J, Morrice N, Kirschner MW. Phosphorylation analysis by mass spectrometry-myths, facts, and the consequences for qualitative and quantitative measurements. Mol Cell Proteomics 2006; 5: 172-181.
47. Kweon HK, Hakansson K. Selective zirconium dioxide-based enrichment of phosphorylated peptides for mass spectrometric analysis. Anal Chem 2006; 78: 1743-1749.
48. Pinkse MWH, Uitto PM, Hilhorst MJ, Ooms B, Heck AJR. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-nanoLC-ESI-MS/MS and titanium oxide precolumns. Anal Chem 2004; 76: 3935-3943.
49. Fraga MF, Ballestar E, Villar-Garea A, Boix-Chornet M, Espada J, Schotta G, Bonaldi T, Haydon C, Ropero S, Petrie K, Iyer NG, Perez-Rosado A, Calvo E, Lopez JA, Cano A, Calasanz MJ, Colomer D, Piris MA, Ahn N, Imhof A, Caldas C, Jenuwein T, Esteller M. Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nat Genet 2005; 37: 391-400.
50. Boix-Chornet M, Fraga MF, Villar-Garea A, Caballero R, Espada J, Nunez A, Casado J, Largo C, Casal JI, Cigudosa JC, Franco L, Esteller M, Ballestar E. Release of hypoacetylated and trimethylated histone H4 is an epigenetic marker of early apoptosis. J Biol Chem 2006; 281: 13540-13547.
51. Shiio Y, Aebersold R. Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Nat Protocols 2006; 1: 139-145.
52. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. 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.
53. Gruhler A, Olsen JV, Mohammed S, Mortensen P, Faergeman NJ, Mann M, Jensen ON. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics 2005; 4; 310-327.
54. Mann M. Functional and quantitative proteomics using SILAC. N at Rev Mol Cell Biol 2006; 7: 952-958.
55. Yao X, Freas A, Ramirez J, Demirev PA, Fenselau C. Proteolytic 18 O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem 2001; 73: 2836-2842.
56. Yao X, Afonso C, Fenselau C. Dissection of proteolytic 18 O labeling: endoprotease-catalyzed 16 O-to-18 O exchange of truncated peptide substrates. J Proteome Res 2003; 2: 147-152.
57. Miller JC, Zhou H, Kwekel J, Cavallo R, Burke J, Butler EB, Teh BS, Haab BB. Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers. Proteomics 2003; 3: 56-63.
58. Celis JE, Moreira JM, Cabezon T, Gromov P, Friis E, Rank F, Gromova I. Identification of extracellular and intracellular signaling components of the mammary adipose tissue and its interstitial fluid in high risk breast cancer patients: toward dissecting the molecular circuitry of epithelial-adipocyte stromal cell interactions. Mol Cell Proteomics 2005; 4: 492-522.
59. Speer R, Wulfkuhle JD, Liotta LA, Petricoin EF3. Reverse-phase protein microarrays for tissue-based analysis. Curr Opin Mol Ther 2005; 7: 240-245.
60. Nishizuka S, Charboneau L, Young L, Major S, Reinhold WC, Waltham M, Kouros-Mehr H, Bussey KJ, Lee JK, Espina V, Munson PJ, Petricoin E3, Liotta LA, Weinstein JN. Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc Natl Acad Sci USA 2003; 100: 14229-14234.
61. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M. Global analysis of protein activities using proteome chips. Science 2001; 293: 2101-2105.
62. MacBeath G, Schreiber SL. Printing proteins as microarrays for high-throughput function determination. Science 2000; 289: 1760-1763.
63. Ramachandran N, Hainsworth E, Bhullar B, Eisenstein S, Rosen B, Lau AY, Walter JC, LaBaer J. Self-assembling protein microarrays. Science 2004; 305: 86-90.
64. LaBaer J, Ramachandran N. Protein microarrays as tools for functional proteomics. Curr Opin Chem Biol 2005; 9: 14-19.
65. Espejo A, Cote J, Bednarek A, Richard S, Bedford MT. A protein-domain microarray identifies novel protein-protein interactions. Biochem J 2002; 367: 697-702.
66. Varambally S, Yu JJ, Laxman B, Rhodes DR, Mehra R, Tomlins SA, Shah RB, Chandran U, Monzon FA, Becich MJ, Wei JT, Pienta KJ, Ghosh D, Rubin MA, Chinnaiyan AM. Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell 2005; 8: 393-406.
67. Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics 2002; 1: 323-333.
68. Washburn MP, Koller A, Oshiro G, Ulaszek RR, Plouffe D, Deciu C, Winzeler E, Yates JR. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2003; 100: 3107-3112.
69. Baliga NS, Pan M, Goo YA, Yi EC, Goodlett DR, Dimitrov K, Shannon P, Aebersold R, Ng WV, Hood L. Coordinate regulation of energy transduction modules in Halobacterium sp analyzed by a global systems approach. Proc Natl Acad Sci USA 2002; 99: 14913-14918.
70. Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai HY, Thorsson V, Eng J, Goodlett D, Berger JP, Gunter B, Linseley PS, Stoughton RB, Aebersold R, Collins SJ, Hanlon WA, Hood LE. Integrated genomic and proteomic analyses of gene expression in mammalian cells. Mol Cell Proteomics 2004; 3: 960-969.