• Larry Fowler
  • Wieslaw Furmaga
Part of the Molecular Pathology Library book series (MPLB, volume 1)


The establishment of a complete human genome sequence has opened a new era in biology referred to as omics. The term designates a complete analysis of biologic systems in which entire metabolic pathways are studied. This new methodologic approach becomes possible because of the dynamic development of advanced instrumentation unique for each of the omics subdisciplines. By increasing analytical sensitivity and through transformation into high-throughput analysis, such technologies as DNA and protein microarray or mass spectrometry have become a driving force for omics research. The amount of information derived from omics disciplines has in turn stimulated the development of bioinformatics. By improving the methods of storage and analysis of large amounts of data, an improved system of bioinformatics allows efficient exchange of information among researchers and contributes significantly to the development of omics disciplines. Despite its short history, this new methodology has proved its effectiveness by advancing our understanding of biologic processes, which brings hope for more accurate diagnosis and treatment of diseases.


Migration Inhibitory Factor Image Mass Spectrometry Bronchiolitis Obliterans Severe Acute Respiratory Syndrome Bronchiolitis Obliterans Syndrome 


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  1. 1.
    Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 1999;19:1720–1730.PubMedGoogle Scholar
  2. 2.
    Karin DR. Proteomics and cancer diagnosis: the potential of mass spectrometry. Clin Biochem 2004;37:579–583.CrossRefGoogle Scholar
  3. 3.
    Patterson DS. Proteomics: beginning to realize its promise? Arthritis Rheum 2004;12:3741–3744.CrossRefGoogle Scholar
  4. 4.
    Check E. Proteomics and cancer: running before we can walk? Nature 1004;429(6991):496–497.CrossRefGoogle Scholar
  5. 5.
    Petricoin III FE, Ardekani MA, Hitt AB, et al. Use of proteomics patterns in serum to identify ovarian cancer. Lancet 2002;359:572–577CrossRefPubMedGoogle Scholar
  6. 6.
    Henzel WJ, Stults JT, Wong SC, et al. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc Natl Acad Sci USA 1993;90:5011–5015.CrossRefPubMedGoogle Scholar
  7. 7.
    Moritz B, Meyer HE. Approaches for the quantification of protein concentration ratios. Proteomics 2003;3:2208–2220.CrossRefPubMedGoogle Scholar
  8. 8.
    Consoli L, Damerval C. Quantification of individual zein isoforms resolved by two-dimensional electrophoresis: genetic variability in 45 maize inbred lines. Electrophoresis 2001;22:2983–2989.CrossRefPubMedGoogle Scholar
  9. 9.
    Thiedea B, Höhenwarterb W, Kraha A, et al. Peptide mass fingerprinting. Methods 2005;35:237–247.CrossRefGoogle Scholar
  10. 10.
    Godovac-Zimmermann J, Kleiner O, Brown RL, Drukier KA. Perspectives in spicing up proteomics with splicing. Proteomics 2005;5:699–709.CrossRefPubMedGoogle Scholar
  11. 11.
    Karas M, Bachnann D, Bahr U, Hillenkamp F, Matrix. Assisted ultraviolet laser desorption of non-volatile compounds. Int J Mass Spectrom Ion Process 1987;78:53–68.CrossRefGoogle Scholar
  12. 12.
    Burtis AC, Ashwood RE, Burns D. Tietz Textbook of Clinical Chemistry and Molecular Diagnosis, 4th ed. Philadelphia: Elsevier; 2006:170.Google Scholar
  13. 13.
    Loboda AV, Krutchinsky AN, Bromirski M, et al. A tandem quadrupole/time-of-flight mass spectrometer with a matrixassisted laser desorption/ionization source: design and performance. Rapid Commun Mass Spectrom 2000;14:1047–1057.CrossRefPubMedGoogle Scholar
  14. 14.
    Chaurand P, Caprioli MR. Direct profiling and imaging of peptides and proteins from mammalian cells and tissue sections by mass spectrometry. Electrophoresis 2002;23:3125–3135.CrossRefPubMedGoogle Scholar
  15. 15.
    Stoeckli M, Farmer TB, Caprioli RM. Automated mass spectrometry imaging with a matrix-assisted laser desorption ionization time-of-flight instrument. J Am Soc Mass Spectrom 1999;10(1):67–71.CrossRefPubMedGoogle Scholar
  16. 16.
    Poetz O, Schwenk MJ, Kramer S, et al. Protein microarrays: catching the proteome. Mech Ageing Dev 2005;126:161–170.CrossRefPubMedGoogle Scholar
  17. 17.
    Petricoin E, Paweletz C, Liotta L. Clinical applications of proteomics: proteomic pattern diagnostics. J Mammary Gland Biol Neoplasia 2002;7:433–440.CrossRefPubMedGoogle Scholar
  18. 18.
    Petricoin EF, Ardekani AM, Hitt BA, et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002;359:572–577.CrossRefPubMedGoogle Scholar
  19. 19.
    Petricoin EI, Ornstein D, Paweletz C, et al. Serum proteomic patterns for detection of prostate cancer. J Natl Cancer Inst 2002;94:1576–1578.PubMedGoogle Scholar
  20. 20.
    Zhang L, Rosenzweig J, Wang Y, Chan D. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 2002;48:1296–1304.PubMedGoogle Scholar
  21. 21.
    Rodland DK. Proteomics and cancer diagnosis: the potential of mass spectrometry. Clin Bioch 2004;37:579–583.CrossRefGoogle Scholar
  22. 22.
    Reinders J, Lewandrowski U, Moebius J, et al. Challenges in mass spectrometry-based proteomics. Proteomics 2004;4:3686–3703.CrossRefPubMedGoogle Scholar
  23. 23.
    Schrader W, Klein WH. Liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR MS): an early overview. Anal Bioanal Chem 2004;379:1013–1024.CrossRefPubMedGoogle Scholar
  24. 24.
    Johnsona RS, Davisa MT, Taylorb JA, Pattersona SD. Informatics for protein identification by mass spectrometry. Methods 2005;35:223–236.CrossRefGoogle Scholar
  25. 25.
    Papayannopoulos IA. The analysis of progressive spectra yields information about the amino acid sequence for the chosen peptide. Mass Spectrom Rev 1995;14:49–73.CrossRefGoogle Scholar
  26. 26.
    Thiedea B, Höhenwarterb W, Kraha A, et al. Peptide mass fingerprinting. Methods 2005;35:237–247.CrossRefGoogle Scholar
  27. 27.
    Schmidt F, Schmid M, Jungblut PR, et al. Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis J Am Soc Mass Spectrom 2004;14:943–956.CrossRefGoogle Scholar
  28. 28.
    Tabb LD, Smith LL, Breci AL, et al. Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal Chem 2003;75:1155–1163.CrossRefPubMedGoogle Scholar
  29. 29.
    Shadforth I, Crowther D, Bessant C. Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines. Proteomics 2005;5:4082–4095.CrossRefPubMedGoogle Scholar
  30. 30.
    Gygi SP, Corthals GL, Zhang Y, et al. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci USA 2000;97:9390–9395.CrossRefPubMedGoogle Scholar
  31. 31.
    Kleiner O, Price DA, Ossetrova N, et al. Ultra-high sensitivity multi-photon detection imaging in proteomics analyses. Proteomics 2005;5(9):2322–2330.CrossRefPubMedGoogle Scholar
  32. 32.
    Mann M. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol 2002;20:261–268.CrossRefPubMedGoogle Scholar
  33. 33.
    MacCoss M J. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc Natl Acad Sci USA 2002;99:7900–7905.CrossRefPubMedGoogle Scholar
  34. 34.
    Galvani M, Hamdan M, Herbert B, Righetti GP. Alkylation kinetics of proteins in preparation for two-dimensional maps: a matrix assisted laser desorption/ionization-mass spectrometry investigation. Electrophoresis 2001;22:2058–2065.CrossRefPubMedGoogle Scholar
  35. 35.
    Rotheneder H, Geymayer S, Haidweger E. Transcription factors of the Sp1 family: interaction with E2F and regulation of the murine thymidine kinase promoter. J Mol Biol 1999;293:1005–1015.CrossRefPubMedGoogle Scholar
  36. 36.
    Granville CA, Dennis PA. An overview of lung cancer genomics and proteomics. Am J Respir Cell Mol Biol 2005;32:169–176.CrossRefPubMedGoogle Scholar
  37. 37.
    Chanin TD, Merrick DT, Franklin WA, Hirsch FR. Recent developments in biomarkers for the early detection of lung cancer: perspectives based on publications 2003 to present. Curr Opin Pulm Med 2004;10(4):242–247.CrossRefPubMedGoogle Scholar
  38. 38.
    Noël-Georis I, Bernard A, Falmagne P, Wattiez R. Proteomics as the tool to search for lung disease markers in bronchoalveolar lavage. Dis Markers 2001;17(4):271–284.PubMedGoogle Scholar
  39. 39.
    Houtman R, van den Worm E. Asthma, the ugly duckling of lung disease proteomics? J Chromatograph B 2005;815(1–2):285–294.CrossRefGoogle Scholar
  40. 40.
    Hirsch J, Hansen KC, Burlingame AL, Matthay MA. Proteomics: current techniques and potential applications to lung disease. Am J Physiol Lung Cell Mol Physiol 2004;287:1–23.CrossRefGoogle Scholar
  41. 41.
    Malmström J, Larsen K, Malmström L, et al. Proteome annotations and identifications of the human pulmonary fibroblast. J Proteome Res 2004;3(3):525–537.CrossRefPubMedGoogle Scholar
  42. 42.
    Sepper R, Prikk K. Proteomics: is it an approach to understand the progression of chronic lung disorders? J Proteome Res 2004;3(2):277–281.CrossRefPubMedGoogle Scholar
  43. 43.
    Merkel D, Rist W, Seither P, et al. Proteomic study of human bronchoalveolar lavage fluids from smokers with chronic obstructive pulmonary disease by combining surfaceenhanced laser desorption/ionization—mass spectrometry profiling with mass spectrometric protein identification. Proteomics 2005;5(11):2972–2980.CrossRefPubMedGoogle Scholar
  44. 44.
    Pollard HB, Ji X-D, Jozwik C, Jacobowitz DM. High abundance protein profiling of cystic fibrosis lung epithelial cells. Proteomics 2005;8:2210–2226.CrossRefGoogle Scholar
  45. 45.
    Kriegova E, Melle C, Kolek V, et al. Protein profiles of bronchoalveolar lavage fluid from patients with pulmonary sarcoidosis. Am J Respir Crit Care Med 2006;173:1145–1154.CrossRefPubMedGoogle Scholar
  46. 46.
    Drake RR, Deng Y, Schwegler EE, Gravenstein S. Proteomics for biodefense applications: progress and opportunities. Expert Rev Proteomics 2005;2(2):203–213.CrossRefPubMedGoogle Scholar
  47. 47.
    Kang X, Xu Y, Wu X. Proteomic fingerprints for potential application to early diagnosis of severe acute respiratory syndrome. Clin Chem 2005;51(1):56–64.CrossRefPubMedGoogle Scholar
  48. 48.
    Srivastava S, Verma M, Gopal-Srivastava R. Proteomic maps of the cancer-associated infectious agents. J Proteome Res 2005;4:1171–1180.CrossRefPubMedGoogle Scholar
  49. 49.
    Gimino VJ, Lande JD, Berryman TR, et al. Gene expression profiling of bronchoalveolar lavage cells in acute lung rejection. Am J Respir Crit Care Med 2003;168:1237–1242.CrossRefPubMedGoogle Scholar
  50. 50.
    Nelsestuen GL, Michael B, Martinez MB, et al. Proteomic identification of human neutrophil alpha-defensins in chronic lung allograft rejection. Proteomics 2005;5(6):1705–1713.CrossRefPubMedGoogle Scholar
  51. 51.
    Xiao X, Liu D, Tang Y, Guo et al. Development of proteomic patterns for detecting lung cancer. Dis Markers 2003–2004;19(1):33–39.PubMedGoogle Scholar
  52. 52.
    Robinson BWS, Creaney J, Lake R, et al. Mesothelin-family proteins and diagnosis of mesothelioma. Lancet 2003;362(9396):1612–1616.CrossRefPubMedGoogle Scholar
  53. 53.
    Zhukov TA, Johanson RA, Cantor AB. Discovery of distinct protein profiles specific for lung tumors and pre-malignant lung lesions by SELDI mass spectrometry. Lung Cancer 2003;40:267–279.PubMedGoogle Scholar
  54. 54.
    Yanagisawa K, Shyr Y, Xu BJ. Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet 2003;362:433–439.CrossRefPubMedGoogle Scholar
  55. 55.
    Campa MJ, Wang MZ, Howard B, et al, Protein expression profiling identifies macrophage migration inhibitory factor and cyclophilin as potential molecular targets in non-small cell lung cancer. Cancer Res 2003, 63:1652–1656.PubMedGoogle Scholar
  56. 56.
    Fowler LJ, Lovell MO, Izbicka E. Fine-needle aspiration in PreservCyt®: a novel and reproducible method for ancillary proteomic pattern evaluation of breast neoplasms by SELDI-TOF. Mod Pathol 2004;17:1012–1020.CrossRefPubMedGoogle Scholar
  57. 57.
    Tyan YC, Wu HY, Su WC, et al. Proteomic analysis of human pleural effusion. Proteomics 2001;5(4):1062–1074.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC. 2008

Authors and Affiliations

  • Larry Fowler
    • 1
  • Wieslaw Furmaga
    • 1
  1. 1.Department of PathologyUniversity of Texas Health Science Center at San AntonioSan AntonioUSA

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