Study of cellular oncometabolism via multidimensional protein identification technology

Methods in Enzymology

Volumn 543, Issue , 2014, Pages 217-234

  Aukim Hastie, Claire ^a,b   Garbis, Spiros D ^b  

^a UNIVERSITY OF SURREY   (United Kingdom)

^b UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

Liquid chromatography; Mass spectrometry; Metabolomics; MuDPIT; Protein biochemistry; Proteomics

Indexed keywords

PROTEOME; TUMOR PROTEIN;

ACCURACY; ANALYTIC METHOD; ARTICLE; CANCER CELL; CARCINOGENESIS; CELL METABOLISM; MULTIDIMENSIONAL PROTEIN IDENTIFICATION TECHNOLOGY; ONCOMETABOLISM; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; TUMOR GROWTH; FEMALE; HUMAN; ION EXCHANGE CHROMATOGRAPHY; MALE; METABOLISM; NEOPLASM; PATHOLOGY; TANDEM MASS SPECTROMETRY;

CHROMATOGRAPHY, ION EXCHANGE; FEMALE; HUMANS; MALE; NEOPLASM PROTEINS; NEOPLASMS; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 84902151678     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-801329-8.00011-8     Document Type: Chapter

References (26)

1. V.G. Antico Arciuch, M.E. Elguero, J.J. Poderoso, and M.C. Carreras Mitochondrial regulation of cell cycle and proliferation Antioxid Redox Signal 16 10 2012 1150 1180 10.1089/ars.2011.4085
2. R.E. Banks, M.J. Dunn, D.F. Hochstrasser, J.C. Sanchez, W. Blackstock, and D.J. Pappin et al. Proteomics: New perspectives, new biomedical opportunities Lancet 356 9243 2000 1749 1756 10.1016/S0140-6736(00)03214-1
3. W. Blackstock, and A. Rowley Probing cellular complexity with proteomics Current Opinion in Molecular Therapeutics 1 6 1999 702 711
4. Z. Cai, J.F. Chiu, and Q.Y. He Application of proteomics in the study of tumor metastasis Genomics, Proteomics & Bioinformatics 2 3 2004 152 166
5. J.E. Celis, H. Wolf, and M. Ostergaard Proteomic strategies in bladder cancer IUBMB Life 48 1 1999 19 23 10.1080/713803472
6. A.F. Chambers, G.N. Naumov, S.A. Vantyghem, and A.B. Tuck Molecular biology of breast cancer metastasis. Clinical implications of experimental studies on metastatic inefficiency Breast Cancer Research 2 6 2000 400 407
7. A.Q. Emili, and G. Cagney Large-scale functional analysis using peptide or protein arrays Nature Biotechnology 18 4 2000 393 397 10.1038/74442
8. E. Emmanouilidou, K. Melachroinou, T. Roumeliotis, S.D. Garbis, M. Ntzouni, and L.H. Margaritis et al. Cell-produced alpha-synuclein is secreted in a calcium-dependent manner by exosomes and impacts neuronal survival Journal of Neuroscience 30 20 2010 6838 6851 10.1523/JNEUROSCI.5699-09.2010
9. S.D. Garbis, T.I. Roumeliotis, S.I. Tyritzis, K.M. Zorpas, K. Pavlakis, and C.A. Constantinides A novel multidimensional protein identification technology approach combining protein size exclusion prefractionation, peptide zwitterion-ion hydrophilic interaction chromatography, and nano-ultraperformance RP chromatography/nESI-MS2 for the in-depth analysis of the serum proteome and phosphoproteome: Application to clinical sera derived from humans with benign prostate hyperplasia Analytical Chemistry 83 3 2011 708 718 10.1021/ac102075d
10. S.D. Garbis, S.I. Tyritzis, T. Roumeliotis, P. Zerefos, E.G. Giannopoulou, and A. Vlahou et al. Search for potential markers for prostate cancer diagnosis, prognosis and treatment in clinical tissue specimens using amine-specific isobaric tagging (iTRAQ) with two-dimensional liquid chromatography and tandem mass spectrometry Journal of Proteome Research 7 8 2008 3146 3158 10.1021/pr800060r
11. J. Granger, J. Siddiqui, S. Copeland, and D. Remick Albumin depletion of human plasma also removes low abundance proteins including the cytokines Proteomics 5 18 2005 4713 4718 10.1002/pmic.200401331
12. R.L. Gundry, Q. Fu, C.A. Jelinek, J.E. Van Eyk, and R.J. Cotter Investigation of an albumin-enriched fraction of human serum and its albuminome Proteomics Clinical Applications 1 1 2007 73 88 10.1002/prca.200600276
13. A. Kaushik, S. Vareed, S. Basu, V. Putluri, N. Putluri, and K. Panzitt et al. Metabolomic profiling identifies biochemical pathways associated with castration-resistant prostate cancer Journal of Proteome Research, (Dec 20) 13 2 2013 1088 1100 10.1021/pr401106h
14. A. Kelly, S. Breitkopf, M. Yuan, J. Goldsmith, D. Spentzos, and J. Asara Metabolomic profiling from formalin-fixed, paraffin-embedded tumor tissue using targeted LC/MS/MS: Application in sarcoma PLoS One 6 10 2011
15. V. Kulasingam, and E.P. Diamandis Strategies for discovering novel cancer biomarkers through utilization of emerging technologies Nature Clinical Practice Oncology 5 10 2008 588 599 10.1038/ncponc1187
16. M.R. Larsen, G.L. Sørensen, S.J. Fey, P.M. Larsen, and P. Roepstorff Phospho-proteomics: Evaluation of the use of enzymatic de-phosphorylation and differential mass spectrometric peptide mass mapping for site specific phosphorylation assignment in proteins separated by gel electrophoresis Proteomics 1 2 2001 223 238 10.1002/1615-9861(200102)1:2<223: :AID-PROT223>3.0.CO;2-B
17. S. Naaby-Hansen, K. Nagano, P. Gaffney, J.R. Masters, and R. Cramer Proteomics in the analysis of prostate cancer Methods in Molecular Medicine 81 2003 277 297 10.1385/1-59259-372-0:277
18. E.K. Papachristou, T.I. Roumeliotis, A. Chrysagi, C. Trigoni, E. Charvalos, and P.A. Townsend et al. The shotgun proteomic study of the human ThinPrep cervical smear using iTRAQ mass-tagging and 2D LC-FT-Orbitrap-MS: The detection of the human papillomavirus at the protein level Journal of Proteome Research 12 5 2013 2078 2089 10.1021/pr301067r
19. L.J. Pike, and J.E. Sadler Proteomics, genomics and the future of medical education Missouri Medicine 101 5 2004 496 499
20. A. Prabhu, B. Sarcar, S. Kahali, Z. Yuan, J.J. Johnson, and K.P. Adam et al. Cysteine catabolism: A novel metabolic pathway contributing to glioblastoma growth Cancer Research Vol. 74 2013 787 796
21. K. Simons, and D. Toomre Lipid rafts and signal transduction Nature Reviews Molecular Cell Biology 1 1 2000 31 39 10.1038/35036052
22. B. Yan, C. Pan, V.N. Olman, R.L. Hettich, and Y. Xu Separation of ion types in tandem mass spectrometry data interpretation - A graph-theoretic approach Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference 2004 236 244
23. A.K. Yocum, K. Yu, T. Oe, and I.A. Blair Effect of immunoaffinity depletion of human serum during proteomic investigations Journal of Proteome Research 4 5 2005 1722 1731 10.1021/pr0501721
24. L. Zolla Proteomics studies reveal important information on small molecule therapeutics: A case study on plasma proteins Drug Discovery Today 13 23-24 2008 1042 1051 10.1016/j.drudis.2008.09.013
25. N. Zolotarjova, J. Martosella, G. Nicol, J. Bailey, B.E. Boyes, and W.C. Barrett Differences among techniques for high-abundant protein depletion Proteomics 5 13 2005 3304 3313 10.1002/pmic.200402021
26. X. Zuo, and D.W. Speicher A method for global analysis of complex proteomes using sample prefractionation by solution isoelectrofocusing prior to two-dimensional electrophoresis Analytical Biochemistry 284 2 2000 266 278 10.1006/abio.2000.4714