Proteomics: Opportunities and Challenges

DOI:

https://doi.org/10.37285/ijpsn.2010.3.4.1

Authors

  • Parag A Pathade
  • Vinod A Bairagi
  • Yogesh S. Ahire
  • Neela M Bhatia

Abstract

‘‘Proteomics’’, is the emerging technology leading to high-throughput identification and understanding of proteins. Proteomics is the protein equivalent of genomics and has captured the imagination of biomolecular scientists, worldwide. Because proteome reveals more accurately the dynamic state of a cell, tissue, or organism, much is expected from proteomics to indicate better disease markers for diagnosis and therapy monitoring.

Proteomics is expected to play a major role in biomedical research, and it will have a significant impact on the development of diagnostics and therapeutics for cancer, heart ailments and infectious diseases, in future. Proteomics research leads to the identification of new protein markers for diagnostic purposes and novel molecular targets for drug discovery. 

Though the potential is great, many challenges and issues remain to be solved, such as gene expression, peptides, generation of low abundant proteins, analytical tools, drug target discovery and cost. A systematic and efficient analysis of vast genomic and proteomic data sets is a major challenge for researchers, today. Nevertheless, proteomics is the groundwork for constructing and extracting useful comprehension to biomedical research. This review article covers some opportunities and challenges offered by proteomics.   

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Keywords:

Proteomics, genomics, protein markers, drug discovery

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Published

2011-02-28

How to Cite

1.
Pathade PA, Bairagi VA, Ahire YS, Bhatia NM. Proteomics: Opportunities and Challenges. Scopus Indexed [Internet]. 2011 Feb. 28 [cited 2024 May 10];3(4):1165-72. Available from: https://www.ijpsnonline.com/index.php/ijpsn/article/view/534

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Section

Review Articles

References

Alaiya AA, Franzen B, Auer G, and Linder S. Cancer proteomics: from identification of novel markers to creation of artificial learning models for tumor classification. Electrophoresis. 21:1210-1217 (2000).

Andersen P, Andersen AB, Sorensen AL, and Nagai S. Recall of long-lived immunity to Mycobacterium tuberculosis infection in mice. J. Immunol. 154:3359-72 (1995).

Andersen P. Effective vaccination of mice against Mycobacterium tuberculosis infection with a soluble mixture of secreted mycobacterial proteins. Infect. Immun. 62:2536-2544 (1994).

Anderson L, and Seilhamer Jd. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis. 18:533-537 (1997).

Anderson NL, and Anderson NG. Proteome and proteomics: New technologies, new concepts, and new words. Electrophoresis. 19:1853-1861 (1998).

Anderson NL, and Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics. 1:845-867 (2002).

Banks RE, Dunn MJ, Forbes MA et al., The potential use of laser capture microdissection to selectively obtain distinct populations of cells for proteomic analysis: preliminary findings. Electrophoresis. 20:689-700 (1999).

Blackstock WP, and Weir MP. Proteomics: quantitative and physical mapping of cellular proteins. Trends. Biotechnol. 17:121-27 (1999).

Cash P. Proteomics in medical microbiology. Electrophoresis. 21:1187-1201 (2000).

Celis JE, Celis P, Ostergaard M et al., Proteomics and immunohistochemistry define some of the steps involved in the squamous differentiation of the bladder transitional epithelium: a novel strategy for identifying metaplastic lesions. Cancer. Res. 59:3003-3009 (1999).

Chenau J, Michelland S, Sidibe J, and Seve M. Peptides OFFGEL electrophoresis: a suitable pre-analytical step for complex eukaryotic samples fractionation compatible with quantitative iTRAQ labeling. Proteome. Science. 6:9 (2008).

Cho WC. Contribution of oncoproteomics to cancer biomarker discovery. Mol. Cancer. 6:25 (2007).

Conrads KA et al., A combined proteome and microarray investigation or inorganic phosphate-induced pre-osteoblast cells. Mol. Cell. Proteomics. 4:1284-1296 (2005).

Conrads TP, Hood BL, and Veenstraet TD. Sampling and analytical strategies for biomarker discovery using mass spectrometry. Biotechniques. 40:799-805 (2006).

Corbett JM, Why HJ, Wheeler CH et al., Cardiac protein abnormalities in dilated cardiomyopathy detected by two-dimensional polyacrylamide gel electrophoresis. Electrophoresis. 19:2031-2042 (1998).

Dobson CM. Protein misfolding, evolution and disease. Trends. Biochem. Sci. 24:329-332 (1999).

Drews J. Genomic sciences and the medicine of tomorrow. Nat. Biotechnol. 14:1516-1518 (1996).

Druker BJ, and Lydon NB. Lessons learned from the development of an Abl tyrosine kinase inhibitor for chronic myelogenous leukemia. J. Clin. Invest. 105:3-7 (2000).

Emmert-Buck MR, Bonner RF, Smith PD et al., Laser capture microdissection. Science. 274:998-1001 (1996).

Gavin AC, Bosche M, Krause R et al., Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 415:141-147 (2002).

Gorg A, Obermaier C, Boguth G et al., The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis. 21:1037-1053 (2001).

Griffiths AD, Duncan AR. Strategies for selection of antibodies by phage display. Curr. Opin. Biotechnol. 9:102-108 (1998).

Gulmann C, Sheehan KM, Kay EW, Liotta LA, and Petricoin EF 3rd. Array-based proteomics: mapping of protein circuitries for diagnostics, prognostics, and therapy guidance in cancer. J. Pathol. 208:595-606 (2006).

Gygi SP, Corthals GL, Zhang Y, Rochon Y, and Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. USA 97:9390-9395 (2000).

Gygi SP, Rochon Y, Franza BR, and Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 19:1720-1730 (1999).

Ho Y, Gruhler A, Heilbut A et al., Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature. 415:180-183 (2002).

Hogenesch JB, Ching KA, Batalov S et al., A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell. 106:413-415 (2001).

Johnson GV, and Hartigan JA. Tau protein in normal and Alzheimer's disease brain: an update. J. Alzheimers Dis. 1:329-352 (1999).

Johnson GV, and Jenkins SM. Tau protein in normal and Alzheimer's disease brain. J. Alzheimers Dis. 1:307-328 (1999).

Karlin S, Bergman A, and Gentles AJ. Genomics. Annotation of the Drosophila genome. Nature. 411:259-260 (2001).

Klose J, and Kobalz U. Two-dimensional electrophoresis of proteins: An updated protocol and implications for a functional analysis of the genome. Electrophoresis. 16:1034-1059 (1995).

Knecht M, Regitz-Zagrosek V, Pleissner KP et al., Characterization of myocardial protein composition in dilated cardiomyopathy by two-dimensional gel electrophoresis. J. Eur. Heart. 15:37-44 (1994).

Kolch W, Mischak H, and Pitt AR. The molecular make-up of a tumour: proteomics in cancer research. Clin. Sci. (Lond.) 108:369-383 (2005).

Lamond AI, and Mann M. Cell biology and the genome projects: a concerted strategy for characterizing multiprotein complexes by using mass spectrometry. Trends. Cell. Biol. 7:139-142 (1998).

Latif N, Rose ML, Yacoub MH, and Dunn MJ. Association of pretransplantation antiheart antibodies with clinical course after heart transplantation. J. Heart. Lung. Transplant. 14:119-126 (1995).

Martzen MR, McCraith SM, Spinelli SL et al., Biochemical genomics approach for identifying genes by the activity of their products. Science. 286:1153-1155 (1999).

Neubauer G, King A, Rappsilber J et al., Mass spectrometry and ESTdatabase searching allows characterization of the multi-protein spliceosome complex. Nat. Genet. 20:46-50 (1998).

O’Farrell PH. High resolution two-dimensional electrophoresis of proteins J. Biol. Chem. 250:4007-4021 (1975).

Orme IM. New vaccines against tuberculosis: the status of current research. Infect. Dis. Clin. North. Am. 13:169-85 (1999).

Ostergaard M, Rasmussen HH, Nielsen HV et al., Proteome profiling of bladder squamous cell carcinomas: identification of markers that define their degree of differentiation. Cancer. Res. 57:4111-4117 (1997).

Pandey A, and Mann M. Proteomics to study genes and genomes. Nature. 405:837-846 (2000).

Perosa F, Luccarelli G, Neri M, De Pinto V, Ferrone S, and Dammacco F. Evaluation of biotinylated cells as a source of antigens for characterization of their molecular profile. Int. J. Clin. & Lab. Res. 28:246-251 (1998).

Pleissner KP, Soding P, Sander S et al., Dilated cardiomyopathy associated proteins and their presentation in a WWW-accessible twodimensional gel protein database. Electrophoresis. 18: 802-808 (1997).

Rogers S, Girolami M, Kolch W et al., Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models. Bioinformatics. 24:2894-2900 (2008).

Rout MP, Aitchison JD, Suprapto A et al., The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell. Biol. 148:635-51 (2000).

Samanich KM, Belisle JT, Sonnenberg MG et al., Delineation of human antibody responses to culture filtrate antigens of Mycobacterium tuberculosis. J. Infect. Dis. 178:1534-38 (1998).

Sanchez JC, Wirth P, Jaccoud S et al., Simultaneous analysis of cyclin and oncogene expression using multiple monoclonal antibody immunoblots. Electrophoresis. 18:638-41 (1997).

Scapin G. Structural biology and drug discovery. Curr. Pharm. Des. 12:2087-2097 (2006).

Schevchenko A, Wilm M, Vorm O, and Mann M. Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Anal. Chem. 68:850-858 (1996).

Sell S. Cancer markers of the 1990s: comparison of the new generation of markers defined by monoclonal antibodies and oncogene probes to prototypic markers. Clin. Lab. Med. 10:1-37 (1990).

Senior K. Fingerprinting disease with protein chip arrays. Mol. Med. Today. 5:326-327 (1999).

Tugarinov V, Hwang PM, and Kay LE. Nuclear magnetic resonance spectroscopy of high-molecular-weight proteins. Annu. Rev. Biochem. 73:107-146 (2004).

Uetz P, Giot L, Cagney G et al., A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 403:623-627 (2000).

Walter G, Bussow K, Cahill D, Lueking A, and Lehrach H. Protein arrays for gene xpression and molecular interaction screening. Curr. Opin. Microbiol. 3:298-302 (2000).

Weist S, Eravci M, Broedel O, Fuxius S, Eravci S, and Baumgartner A. Results and reliability of protein quantification for two-dimensional gel electrophoresis strongly depend on the type of protein sample and the method employed. Proteomics. 8:3389-3396 (2008).

Weldingh K, Rosenkrands I, Jacobsen S et al., Two-dimensional electrophoresis for analysis of Mycobacterium tuberculosis culture filtrate and purification and characterization of six novel proteins. Infect. Immun. 66:3492-500 (1998).

Wheeler CH, Collins A, Dunn MJ et al., Characterization of endothelial antigens associated with transplant-associated coronary artery disease. J. Heart. Lung. Transplant. 14:188-197 (1995).

Zhou Z, and Menard HA. Autoantigenic posttranslational modifications of proteins: does it apply to rheumatoid arthritis. Curr. Opin. Rheumatol. 14:250-253 (2002).