Skip to main content
SpringerLink
Log in

Overview and Introduction to Clinical Proteomics

  • Protocol
Clinical Proteomics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 428))

Summary

As the field of clinical proteomics progresses, discovery of disease biomarkers becomes paramount. However, the immediate challenges are to establish standard operating procedures for both clinical specimen handling and reduction of sample complexity and to increase the ability to detect proteins and peptides present in low amounts. The traditional concept of a disease biomarker is shifting toward a new paradigm, namely, that an ensemble of proteins or peptides would be more efficient than a single protein/peptide in the diagnosis of disease. Because clinical proteomics usually requires easy access to well-defined fresh clinical specimens (including morphologically consistent tissue and properly pretreated body fluids of sufficient quantity), biorepository systems need to be established. Here, we address these questions and emphasize the necessity of developing various microdissection techniques for tissue specimens, multidimensional fractionation for body fluids, and other related techniques (including bioinformatics), tools which could become integral parts of clinical proteomics for disease biomarker discovery.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Abbreviations

CSF:

Cerebrospinal Fluid

SILAC:

Stable Isotope Labeling with Amino acids in Cell culture

FFE:

Free Flow Electrophoresis

IMAC:

Immobilized Metal Affinity Chromatography

2DE:

2-dimensional Gel electrophoresis

CBB:

Coomassie Brilliant Blue

SELDI:

Surface-Enhanced Laser Desorption/Ionization

MALDI:

Matrix-Assisted laser desorption/ionization

MDLC:

Multi-dimensional Liquid Chromatography

LC:

Liquid Chromatography

TOF:

Time-of-Flight

CID:

Collision-induced dissociation

ETD:

Electron Transfer Dissociation

LIT:

Linear Ion-Trap

FT:

Fourier-Transform

Q:

Quadrupole

ELISA:

Enzyme-Linked Immunosorbent Assay

SISCAPA:

Stable Isotope Standards with Capture by Anti-Peptide Antibody

AQUA:

Absolute Quantitative Analysis. Commercial brands are also shown

MARS:

Multiple Affinity Removal System (Agilent Palo Alto CA USA)

Enchant™:

Enchant™ Multi-protein Affinity Separation Kit (Pall Life Sciences Ann Arbor MI USA)

Gradiflow™:

Gradiflow™ Separation (Life Bioprocess Frenchs Forest, Australia)

FFE™:

BD Free Flow Electrophoresis System (BD Diagnostics, Martinsried/Planegg, Germany)

Zoom® :

Zoom® Benchtop Proteomics System (Invitrogen Corporation, Carlsbad, CA, USA)

Rotofor:

Bio-Rad Rotofor® Prep IEF Ccll (Bio-Rad, Hercules, CA, USA)

PF2D:

ProteomeLab™ PF2D Protein Fractionation System (Beckman Coulter, Inc., Fullerton, CA, USA)

DIGE:

Ettan™ DIGE System (GE Healthcare Bio-Sciences AB, Uppsala, Sweden)

Deep Purple™:

Deep Purple™ Total Pprotein Stain (GE Healthcare Bio-Sciences AB, Uppsala, Sweden)

ICAT™:

Isotope-coded affinity tags (Applied Biosystems, Foster City, CA, USA)

iTRAQ™:

iTRAQ™ Reagents (Applied Biosystems, Foster City, CA, USA)

Q-TRAP™:

(Applied Biosystems, Foster City, CA, USA)

References

  1. Etzioni, R., Urban, N., Ramsey, S., McIntosh, M., Schwartz, S., Reid, B., Radich, J., Anderson, G., and Hartwell, L. (2003) The case for early detection. Nat. Rev. Cancer 3, 1–10.

    Article  Google Scholar 

  2. Ludwig, J. A. and Weinstein, J. N. (2005) Biomarkers in cancer staging, prognosis and treatment selection. Nat. Rev. Cancer 5, 845–856.

    Article  PubMed  CAS  Google Scholar 

  3. Xiao, Z., Prieto, D., Conrads, T. P., Veenstra, T. D., and Issaq, H. J. (2005) Proteomic patterns: their potential for disease diagnosis. Mol. Cell Endocrinol. 230, 95–106.

    Article  PubMed  CAS  Google Scholar 

  4. Rifai, N., Gillette, M. A., and Carr, S. A. (2006) Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. 24, 97–983.

    Article  Google Scholar 

  5. Emmert-Buck, M. R., Bonner, R. F., Smith, P. D., Chuaqui, R. F., Zhuang, Z., Goldstein, S. R., Weiss, R. A., and Liotta, L. A. (1996) Laser capture microdissection. Science 274, 998–1001.

    Article  PubMed  CAS  Google Scholar 

  6. Gillespie, J. W., Ahram, M., Best, C. J., Swalwell, J. I., Krizman, D. B., Petricoin, E. F., Liotta, L. A., and Emmert-Buck, M. R. (2001) The role of tissue microdissection in cancer research. Cancer J. 7, 32–39.

    PubMed  CAS  Google Scholar 

  7. Craven, R. A. and Banks, R. E. (2002) Use of laser capture microdissection to selectively obtain distinct populations of cells for proteomic analysis. Methods Enzymol. 356, 33–49.

    Article  PubMed  CAS  Google Scholar 

  8. Vincourt, J. B., Lionneton, F., Kratassiouk, G., Guillemin, F., Netter, P., Mainard, D., and Magdalou, J. (2006) Establishment of a reliable method for direct proteome characterization of human articular cartilage. Mol. Cell Proteomics 5, 1984–1995.

    Article  PubMed  CAS  Google Scholar 

  9. Platt, M. S., Agamanolis, D. P., Krill, C. E. Jr., Boeckman, C., Potter, J. L., Robinson, H., and Lloyd, J. (1983) Occult hepatic sinusoid tumor of infancy simulating neuroblastoma. Cancer 52, 1183–1189.

    Article  PubMed  CAS  Google Scholar 

  10. Mahadevia, P. J., Fleisher, L. A., Frick, K. D., Eng, J., Goodman, S. N., and Powe, N. R. (2003) Lung cancer screening with helical computed tomography in older adult smokers: a decision and cost-effectiveness analysis. JAMA 289, 313–322.

    Article  PubMed  Google Scholar 

  11. Hood, B. L., Darfler, M. M., Guiel, T. G., Furusato, B., Lucas, D. A., Ringeisen, B. R., Sesterhenn, I. A., Conrads, T. P., Veenstra, T. D., and Krizman, D. B. (2005) Proteomic analysis of formalin-fixed prostate cancer tissue. Mol. Cell Proteomics 4, 1741–1753.

    Article  PubMed  CAS  Google Scholar 

  12. Alaiya, A., Al-Mohanna, M., and Linder, S. (2005) Clinical cancer proteomics: promises and pitfalls. J. Proteome Res. 4, 1213–1222.

    Article  PubMed  CAS  Google Scholar 

  13. Gericke, B., Raila, J., Sehouli, J., Haebel, S., Konsgen, D., Mustea, A., and Schweigert, F. J. (2005) Microheterogeneity of transthyretin in serum and ascitic fluid of ovarian cancer patients. BMC Cancer 17, 133–141.

    Article  Google Scholar 

  14. Swisher, E. M., Wollan, M., Mahtani, S. M., Willner, J. B., Garcia, R., Goff, B. A., and King, M. C. (2005) Tumor-specific p53 sequences in blood and peritoneal fluid of women with epithelial ovarian cancer. Am. J. Obstet. Gynecol. 193, 662–667.

    Article  PubMed  CAS  Google Scholar 

  15. Pisitkun, T., Johnstone, R., and Knepper, M. A. (2006) Discovery of urinary biomarkers. Mol. Cell Proteomics 5, 1760–1771.

    Article  PubMed  CAS  Google Scholar 

  16. Ghafouri, B., Irander, K., Lindbom, J., Tagesson, C., and Lindahl, M. (2006) Comparative proteomics of nasal fluid in seasonal allergic rhinitis. J. Proteome Res. 5, 330–338.

    Article  PubMed  CAS  Google Scholar 

  17. Koo, B. S., Lee, D. Y., Ha, H. S., Kim, J. C., and Kim, C. W. (2005) Comparative analysis of the tear protein expression in blepharitis patients using two-dimensional electrophoresis. J. Proteome Res. 4, 719–724.

    Article  PubMed  CAS  Google Scholar 

  18. Grus, F. H., Podust, V. N., Bruns, K., Lackner, K., Fu, S., Dalmasso, E. A., Wirthlin, A., and Pfeiffer, N. (2005) SELDI-TOF-MS ProteinChip array profiling of tears from patients with dry eye. Invest. Ophthalmol. Vis. Sci. 46, 863–876.

    Article  PubMed  Google Scholar 

  19. Amado, F. M., Vitorino, R. M., Domingues, P. M., Lobo, M. J., and Duarte, J. A. (2005) Analysis of the human saliva proteome. Expert Rev. Proteomics 2, 521–539.

    Article  PubMed  CAS  Google Scholar 

  20. Wang, T. H., Chang, Y. L., Peng, H. H., Wang, S. T., Lu, H. W., Teng, S. H., Chang, S. D., and Wang, H. S. (2005) Rapid detection of fetal aneuploidy using proteomics approaches on amniotic fluid supernatant. Prenat. Diagn. 25, 559–566.

    Article  PubMed  CAS  Google Scholar 

  21. Ruetschi, U., Rosen, A., Karlsson, G., Zetterberg, H., Rymo, L., Hagberg, H., and Jacobsson, B. (2005) Proteomic analysis using protein chips to detect biomarkers in cervical and amniotic fluid in women with intra-amniotic inflammation. J. Proteome Res. 4, 2236–2242.

    Article  PubMed  Google Scholar 

  22. Kim, Y. S., Kim, M. S., Lee, S. H., Choi, B. C., Lim, J. M., Cha, K. Y., and Baek, K. H. (2006) Proteomic analysis of recurrent spontaneous abortion: identification of an inadequately expressed set of proteins in human follicular fluid. Proteomics 6, 3445–3454.

    Article  PubMed  CAS  Google Scholar 

  23. Pilch, B. and Mann, M. (2006) Large-scale and high-confidence proteomic analysis of human seminal plasma. Genome Biol. 7, R40

    Article  PubMed  Google Scholar 

  24. Varnum, S. M., Covington, C. C., Woodbury, R. L., Petritis, K., Kangas, L. J., Abdullah, M. S., Pounds, J. G., Smith, R. D., and Zangar, R. C. (2003) Proteomic characterization of nipple aspirate fluid: identification of potential biomarkers of breast cancer. Breast Cancer Res. Treat. 80, 87–97.

    Article  PubMed  CAS  Google Scholar 

  25. Zheng, P. P., Luider, T. M., Pieters, R., Avezaat, C. J., van den Bent, M. J., Sillevis Smitt, P. A., and Kros, J. M. (2003) Identification of tumor-related proteins by proteomic analysis of cerebrospinal fluid from patients with primary brain tumors. J. Neuropathol. Exp. Neurol. 62, 855–862.

    PubMed  CAS  Google Scholar 

  26. Gibson, D. S., Blelock, S., Brockbank, S., Curry, J., Healy, A., McAll ister, C., and Rooney, M. E. (2006) Proteomic analysis of recurrent joint inflammation in juvenile idiopathic arthritis. J. Proteome Res. 5, 1988–1995.

    Article  PubMed  CAS  Google Scholar 

  27. Merkel, D., Rist, W., Seither, P., Weith, A., and Lenter, M. C. (2005) Proteomic study of human bronchoalveolar lavage fluids from smokers with chronic obstructive pulmonary disease by combining surface-enhanced laser desorption/ionization-mass spectrometry profiling with mass spectrometric protein identification. Proteomics 5, 2972–2980.

    Article  PubMed  CAS  Google Scholar 

  28. Wu, J., Kobayashi, M., Sousa, E. A., Liu, W., Cai, J., Goldman, S. J., Dorner, A. J., Projan, S. J., Kavuru, M. S., Qiu, Y., and Thomassen, M. J. (2005) Differential proteomic analysis of bronchoalveolar lavage fluid in asthmatics following segmental antigen challenge. Mol. Cell Proteomics 4, 1251–1264.

    Article  PubMed  CAS  Google Scholar 

  29. Tyan, Y. C., Wu, H. Y., Lai, W. W., Su, W. C., and Liao, P. C. (2005) Proteomic profiling of human pleural effusion using two-dimensional nano liquid chromatography tandem mass spectrometry. J. Proteome Res. 4, 1274–1286.

    Article  PubMed  CAS  Google Scholar 

  30. Khalil, A. A. and James, P. (2007) Biomarker discovery: a proteomic approach for brain cancer profiling. Cancer Sci. 98, 201–213.

    Article  PubMed  CAS  Google Scholar 

  31. Khodavirdi, A. C., Song, Z., Yang, S., Zhong, C., Wang, S., Wu, H., Pritchard, C., Nelson, P. S., and Roy-Burman, P. (2006) Increased expression of osteopontin contributes to the progression of prostate cancer. Cancer Res. 66, 883–888.

    Article  PubMed  CAS  Google Scholar 

  32. Vincourt, J. B., Lionneton, F., Kratassiouk, G., Guillemin, F., Netter, P., Mainard, D., and Magdalou, J. (2006) Establishment of a reliable method for direct proteome characterization of human articular cartilage. Mol. Cell Proteomics 5, 1984–1995.

    Article  PubMed  CAS  Google Scholar 

  33. Lee, Y. J., Rice, R. H., and Lee, Y. M. (2006) Proteome analysis of human hair shaft: from protein identification to post-translational modification. Mol. Cell Proteomics 5, 789–800.

    Article  PubMed  CAS  Google Scholar 

  34. Cho, S. Y., Lee, E. Y., Lee, J. S., Kim, H. Y., Park, J. M., Kwon, M. S., Park, Y. K., Lee, H. J., Kang, M. J., Kim, J. Y., Yoo, J. S., Park, S. J., Cho, J. W., Kim, H. S., and Paik, Y. K. (2005) Efficient prefractionation of low-abundance proteins in human plasma and construction of a two-dimensional map. Proteomics 5, 3386–3396.

    Article  PubMed  CAS  Google Scholar 

  35. Lathrop, J. T., Hayes, T. K., Carrick, K., and Hammond, D. J. (2005) Rarity gives a charm: evaluation of trace proteins in plasma and serum. Expert Rev. Proteomics 2, 393–406.

    Article  PubMed  CAS  Google Scholar 

  36. Lee, H. J., Lee, E. Y., Kwon, M. S., and Paik, Y. K. (2006) Biomarker discovery from the plasma proteome using multidimensional fractionation proteomics. Curr. Opin. Chem. Biol. 10, 42–49.

    Article  PubMed  CAS  Google Scholar 

  37. Anderson, N. L. and Anderson, N. G. (2002) The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell Proteomics 1, 845–867.

    Article  PubMed  CAS  Google Scholar 

  38. Hu, S., Loo, J. A., and Wong, D. T. (2006) Human body fluid proteome analysis. Proteomics 6, 6326–6353.

    Article  PubMed  CAS  Google Scholar 

  39. Park, M. R., Wang, E. H., Jin, D. C., Cha, J. H., Lee, K. H., Yang, C. W., Kang, C. S., and Choi, Y. J. (2006) Establishment of a 2-D human urinary proteomic map in IgA nephropathy. Proteomics 6, 1066–1076.

    Article  PubMed  CAS  Google Scholar 

  40. Tammen, H., Schutle, I., Hess, R., Menzel, C., Kellmann, M., and Schulz-Knappe, P. (2005) Prerequisites for peptidomic analysis of blood samples: I. Evaluation of blood specimen qualities and determination of technical performance characteristics. Comb. Chem. High Trhoughput Screen 8, 725–733.

    Article  CAS  Google Scholar 

  41. Rai, A. J., Gelfand, C. A., Haywood, B. C., Warunek, D. J., Yi, J., Schuchard, M. D., Mehigh, R. J., Cockrill, S. L., Scott, G. B., Tammen, H., Schulz-Knappe, P., Speicher, D. W., Vitzthum, F., Haab, B. B., Siest, G., and Chan, D. W. (2005) HUPO plasma proteome project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 5, 3262–3277.

    Article  PubMed  CAS  Google Scholar 

  42. Zhou, M., Lucas, D. A., Chan, K. C., Issaq, H. J., Petricoin, E. F. 3rd, Liotta, L. A., Veenstra, T. D., and Conrads, T. P. (2004) An investigation into the human serum “interactome”. Electrophoresis 25, 1289–1298.

    Article  PubMed  CAS  Google Scholar 

  43. Findeisen, P., Sismanidis, D., Riedl, M., Costina, V., and Neumaier, M. (2005) Preanalytical impact of sample handling on proteome profiling experiments with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clin. Chem. 51, 2409–2411.

    Article  PubMed  CAS  Google Scholar 

  44. Park, K. S., Kim, H., Kim, N. G., Cho, S. Y., Choi, K. H., Seong, J. K., and Paik, Y. K. (2002) Proteomic analysis and molecular characterization of tissue ferritin light chain in hepatocellular carcinoma. Hepatology 35, 1459–1466.

    Article  PubMed  CAS  Google Scholar 

  45. Park, K. S., Cho, S. Y., Kim, H., and Paik, Y. K. (2002) Proteomic alterations of the variants of human aldehyde dehydrogenase isozymes correlate with hepatocellular carcinoma. Int. J. Cancer 97, 261–265.

    Article  PubMed  CAS  Google Scholar 

  46. Marko-Varga, G., Berglund, M., Malmstrom, J., Lindberg, H., and Fehniger, T. E. (2003) Targeting hepatocytes from liver tissue by laser capture microdissection and proteomics expression profiling. Electrophoresis 24, 3800–3805.

    Article  PubMed  CAS  Google Scholar 

  47. Paradis, V., Degos, F., Dargere, D., Pham, N., Belghiti, J., Degott, C., Janeau, J. L., Bezeaud, A., Delforge, D., Cubizolles, M., Laurendeau, I., and Bedossa, P. (2005) Identification of a new biomarker of hepatocellular carcinoma by serum protein profiling of patients with chronic liver diseases. Hepatology 41, 40–47.

    Article  PubMed  CAS  Google Scholar 

  48. Ru, Q. C., Zhu, L. A., Silberman, J., and Shriver, C. D. (2006) Label-free semiquantitative peptide feature profiling of human breast cancer and breast disease sera via two-dimensional liquid chromatography–mass spectrometry. Mol. Cell Proteomics 5, 1095–1104.

    Article  PubMed  CAS  Google Scholar 

  49. Azad, N. S., Rasool, N., Annuziata, C. M., Minasian, L., Whiteley, G., and Kohn, E. C. (2006) Prot eomics in clinical trials and practice: present uses and future promise. Mol. Cell Proteomics 5, 1819–1829.

    Article  PubMed  CAS  Google Scholar 

  50. Gunter, E. W. (1997) Biological and environmental specimen banking at the Centers for Disease Control and Prevention. Chemosphere 34, 1945–1953.

    Article  PubMed  CAS  Google Scholar 

  51. Strauss, G. H. and Kelly, S. J. (1990) The development of the U.S. EPA health effects research laboratory frozen blood cell repository program. Mutat. Res. 234, 349–354.

    PubMed  CAS  Google Scholar 

  52. Romeo, M. J., Espina, V., Lowenthal, M., Espina, B. H., Petricoin, E. F. 3rd, and Liotta, L. A. (2005) CSF proteome: a protein repository for potential biomarker identification. Expert Rev. Proteomics 2, 57–70.

    Article  PubMed  CAS  Google Scholar 

  53. Conrads, T. P., Hood, B. L., Petricoin, E. F. 3rd, Liotta, L. A., and Veenstra, T. D. (2005) Cancer proteomics: many technologies, one goal. Expert Rev. Proteomics 2, 693–703.

    Article  PubMed  CAS  Google Scholar 

  54. Schrader, M. and Selle, H. (2006) The process chain for peptidomic biomarker discovery. Dis. Markers 22, 27–37.

    PubMed  CAS  Google Scholar 

  55. Danna, E. A. and Nolan, G. P. (2006) Transcending the biomarker mindset: deciphering disease mechanisms at the single cell level. Curr. Opin. Chem. Biol. 10, 20–27.

    Article  PubMed  CAS  Google Scholar 

  56. De Masi, S., Tosti, M. E., and Mele, A. (2005) Screening for hepatocellular carcinoma. Dig. Liver Dis. 37, 260–268.

    Article  PubMed  Google Scholar 

  57. Yamaguchi, K., Nagano, M., Torada, N. Hamasaki, N., Kawakita, M., and Tanaka, M. (2004) Urine diacetylspermine as a novel tumor marker for pancreatobiliary carcinomas. Rinsho. Byori. 52, 336–339

    PubMed  CAS  Google Scholar 

  58. Dabrowska, M., Grubek-Jaworska, H., Domagala-Kulawik, J., Bartoszewicz, Z., Kondracka, A., Krenke, R., Nejman, P., and Chazan, R. (2004) Diagnostic usefulness of selected tumor markers (CA125, CEA, CYFRA 21–1) in bronchoalveolar lavage fluid in patients with non-small cell lung cancer. Pol. Arch. Med. Wewn 111, 659–665.

    PubMed  CAS  Google Scholar 

  59. Gann, P. H., Hennekens, C. H., and Stampfer, M. J. (1995) A prospective evaluation of plasma prostate-specific antigen for detection of prostatic cancer. JAMA 273, 289–294

    Article  PubMed  CAS  Google Scholar 

  60. Ciambellotti, E., Coda, C., and Lanza, E. (1993) Determination of CA 15–3 in the control of primary and metastatic breast carcinoma. Minerva Med. 84, 107–112.

    PubMed  CAS  Google Scholar 

  61. Linkov, F., Lisovich, A., Yurkovetsky, Z., Marrangoni, A., Velikokhatnaya, L., Nolen, B., Winans, M., Bigbee, W., Siegfried, J., Lokshin, A., and Ferris, R. L. (2007) Early detection of head and neck cancer: development of a novel screening tool using multiplexed immunobead-based biomarker profiling. Cancer Epidemiol. Biomarkers Prev. 16, 102–107.

    Article  PubMed  CAS  Google Scholar 

  62. Casiano, C. A., Mediavilla-Varela, M., and Tan, E. M. (2006) Tumor-associated antigen arrays for the serological diagnosis of cancer. Mol. Cell Proteomics 5, 1745–1759.

    Article  PubMed  CAS  Google Scholar 

  63. Nissom, P. M., Lo, S. L., Lo, J. C., Ong, P. F., Lim, J. W., Ou, K., Liang, R. C., Seow, T. K., and Chung, M. C. (2006) Hcc-2, a novel mammalian ER thioredoxin that is differentially expressed in hepatocellular carcinoma. FEBS Lett. 580, 2216–2226.

    Article  PubMed  CAS  Google Scholar 

  64. Feng, J. T., Liu, Y. K., Song, H. Y., Dai, Z., Qin, L. X., Almofti, M. R., Fang, C. Y., Lu, H. J., Yang, P. Y., and Tang, Z. Y. (2005) Heat-shock protein 27: a potential biomarker for hepatocellular carcinoma identified by serum proteome analysis. Proteomics 5, 4581–1588.

    Article  PubMed  CAS  Google Scholar 

  65. Li, D. Q., Wang, L., Fei, F., Hou, Y. F., Luo, J. M., Wei-Chen, Zeng, R., Wu, J., Lu, J. S., Di, G. H., Ou, Z. L., Xia, Q. C., Shen, Z. Z., and Shao, Z. M. (2006) Identification of breast cancer metastasis-associated proteins in an isogenic tumor metastasis model using two-dimensional gel electrophoresis and liquid chromatography-ion trap-mass spectrometry. Proteomics 6, 3352–3368.

    Article  PubMed  CAS  Google Scholar 

  66. Lee, I. N., Chen, C. H., Sheu, J. C., Lee, H. S., Huang, G. T., Yu, C. Y., Lu, F. J., and Chow, L. P. (2005) Identification of human hepatocellular carcinoma-related biomarkers by two-dimensional difference gel electrophoresis and mass spectrometry. J. Proteome Res. 4, 2062–2069.

    Article  PubMed  CAS  Google Scholar 

  67. Righetti, P. G., Castagna, A., Antonucci, F., Piubelli, C., Cecconi, D., Campostrini, N., Rustichelli, C., Antonioli, P., Zanusso, G., Monaco, S., Lomas, L., and Boschetti, E. (2005) Proteome analysis in the clinical chemistry laboratory: myth or reality? Clin. Chim. Acta 357, 123–139.

    Article  PubMed  CAS  Google Scholar 

  68. Jang, J. S., Cho, H. Y., Lee, Y. J., Ha, W. S., and Kim, H. W. (2004) The differential proteome profile of stomach cancer: identification of the biomarker candidates. Oncol. Res. 14, 491–499.

    PubMed  CAS  Google Scholar 

  69. Steel, L. F., Shumpert, D., Trotter, M., Seeholzer, S. H., Evans, A. A., London, W. T., Dwek, R., and Block, T. M. (2003) A strategy for the comparative analysis of serum proteomes for the discovery of biomarkers for hepatocellular carcinoma. Proteomics 3, 601–609.

    Article  PubMed  CAS  Google Scholar 

  70. Yip, T. T., Chan, J. W., Cho, W. C., Yip, T. T., Wang, Z., Kwan, T. L., Law, S. C., Tsang, D. N., Chan, J. K., Lee, K. C., Cheng, W. W., Ma, V. W., Yip, C., Lim, C. K., Ngan, R. K., Au, J. S., Chan, A., Lim, W. W., and Ciphergen SARS Proteomics Study Group (2005) Protein chip array profiling analysis in patients with severe acute respiratory syndrome identified serum amyloid a protein as a biomarker potentially useful in monitoring the extent of pneumonia. Clin. Chem. 51, 47–55.

    Article  PubMed  CAS  Google Scholar 

  71. Anderson, L. and Hunter, C. L. (2005) Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell Proteomics 5, 573–588.

    Article  PubMed  Google Scholar 

  72. Lee, J. W., Figeys, D., and Vasilescu, J. (2007) Biomarker assay translation from discovery to clinical studies in cancer drug development: quantification of emerging protein biomarkers. Adv. Cancer Res. 96, 269–298.

    Article  PubMed  CAS  Google Scholar 

  73. Zolg, W. (2006) The proteomic search for diagnostic biomarkers: lost in translation? Mol. Cell Proteomics 5, 1720–1726.

    Article  PubMed  CAS  Google Scholar 

  74. Bensmail, H., Golek, J., Moody, M. M., Semmes, J. O., and Haoudi, A. (2005) A novel approach for clustering proteomics data using Bayesian fast Fourier transform. Bioinformatics 21, 2210–2224.

    Article  PubMed  CAS  Google Scholar 

  75. Ward, D. G., Cheng, Y., N'Kontchou, G., Thar, T. T., Barget, N., Wei, W., Billingham, L. J., Martin, A., Beaugrand, M., and Johnson, P. J. (2006) Changes in the serum proteome associated with the development of hepatocellular carcinoma in hepatitis C-related cirrhosis. Br. J. Cancer 94, 287–292.

    Article  PubMed  CAS  Google Scholar 

  76. Lin, N. and Zhao, H. (2005) Are scale-free networks robust to measurement errors? BMC Bioinformatics 6, 119.

    Article  PubMed  Google Scholar 

  77. Castagna, A., Cecconi, D., Sennels, L., Rappsilber, J., Guerrier, L., Fortis, F., Boschetti, E., Lomas, L., and Righetti, P. G. (2005) Exploring the hidden human urinary proteome via ligand library beads. J. Proteome Res. 4, 1917–1930.

    Article  PubMed  CAS  Google Scholar 

  78. Rauch, A., Bellew, M., Eng, J., Fitzgibbon, M., Holzman, T., Hussey, P., Igra, M., Maclean, B., Lin, C. W., Detter, A., Fang, R., Faca, V., Gafken, P., Zhang, H., Whiteaker, J., States, D., Hanash, S., Paulovich, A., and McIntosh, M. W. (2006) Computational proteomics analysis system (CPAS): an extensible open source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J. Proteome Res. 5, 112–121.

    Article  PubMed  CAS  Google Scholar 

  79. Lilley, K. S. and Friedman, D. B. (2004) All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev. Proteomics 1, 401–409.

    Article  PubMed  CAS  Google Scholar 

  80. Qian, W. J., Jacobs, J. M., Liu, T., Camp, D. G. 2nd, and Smith, R. D. (2006) Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Mol. Cell Proteomics 5, 1727–1744.

    Article  PubMed  CAS  Google Scholar 

  81. Powell, D. W., Merchant, M. L., and Link, A. J. (2006) Discovery of regulatory molecular events and biomarkers using 2D capillary chromatography and mass spectrometry. Expert Rev. Proteomics 3, 63–74.

    Article  PubMed  CAS  Google Scholar 

  82. Andre, M., Le Caer, J. P., Greco, C., Planchon, S., El Nemer, W., Boucheix, C., Rubinstein, E., Chamot-Rooke, J., and Le Naour, F. (2006) Proteomic analysis of the tetraspanin web using LC-ESI-MS/MS and MALDI-FTICR-MS. Proteomics 6, 1437–1449.

    Article  PubMed  CAS  Google Scholar 

  83. Greengauz-Roberts, O., Stoppler, H., Nomura, S., Yamaguchi, H., Goldenring, J. R., Podolsky, R. H., Lee, J. R., and Dynan, W. S. (2005) Saturation labeling with cysteine-reactive cyanine fluorescent dyes provides increased sensitivity for protein expression profiling of laser-microdissected clinical specimens. Proteomics 5, 1746–1757.

    Article  PubMed  CAS  Google Scholar 

  84. Heck, A. J. and Krijgsveld, J. (2004) Mass spectrometry-based quantitative proteomics. Expert Rev. Proteomics 1, 317–326.

    Article  PubMed  CAS  Google Scholar 

  85. Schneider, L. V. and Hall, M. P. (2005) Stable isotope methods for high-precision proteomics. Drug Discov. Today 10, 353–363.

    Article  PubMed  CAS  Google Scholar 

  86. Zhang, J., Goodlett, D. R., Peskind, E. R., Quinn, J. F., Zhou, Y., Wang, Q., Pan, C., Yi, E., Eng, J., Aebersold, R. H., and Montine, T. J. (2005) Quantitative proteomic analysis of age-related changes in human cerebrospinal fluid. Neurobiol Aging 26, 207–227.

    Article  PubMed  CAS  Google Scholar 

  87. Liu, T., Qian, W. J., Strittmatter, E. F., Camp, D. G. 2nd, Anderson, G. A., Thrall. B. D., and Smith, R. D. (2004) High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology. Anal. Chem. 76, 5345–5353.

    Article  PubMed  CAS  Google Scholar 

  88. Li, C., Hong, Y., Tan, Y. X., Zhou, H., Ai, J. H., Li, S. J., Zhang, L., Xia, Q. C., Wu, J. R., Wang, H. Y., and Zeng, R. (2004) Accurate qualitative and quantitative proteomic analysis of clinical hepatocellular carcinoma using laser capture microdissection coupled with isotope-coded affinity tag and two-dimensional liquid chromatography mass spectrometry. Mol. Cell Proteomics 3, 399–409.

    Article  PubMed  CAS  Google Scholar 

  89. Sheehan, K. M., Calvert, V. S., Kay, E. W., Lu, Y., Fishman, D., Espina, V., Aquino. J., Speer, R., Araujo, R., Mills, G. B., Liotta, L. A., Petricoin, E. F. 3rd, and Wulfkuhle, J. D. (2005) Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol. Cell Proteomics 4, 346–355.

    Article  PubMed  CAS  Google Scholar 

  90. Knezevic, V., Leethanakul, C., Bichsel, V. E., Worth, J. M., Prabhu, V. V., Gutkind, J. S., Liotta, L. A., Munson, P. J., Petricoin, E. F. 3rd, and Krizman, D. B. (2001) Proteomic profiling of the cancer microenvironment by antibody arrays. Proteomics 1, 1271–1278.

    Article  PubMed  CAS  Google Scholar 

  91. Sharma-Oates, A., Quirke, P., Westhead, D. R. (2005) TmaDB: a repository for tissue microarray data. BMC Bioinformatics 6, 218.

    Article  PubMed  Google Scholar 

  92. Rai, A. J., Stemmer, P. M., Zhang, Z., Adam, B. L., Morgan, W. T., Caffrey, R. E., Podust, V. N., Patel, M., Lim, L. Y., Shipulina, N. V., Chan, D. W., Semmes, O. J., and Leung, H. C. (2005) Analysis of human proteome organization plasma proteome project (HUPO PPP) reference specimens using surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry: multi-institution correlation of spectra and identification of biomarkers. Proteomics 5, 3467–3474.

    Article  PubMed  CAS  Google Scholar 

  93. Engwegen, J. Y., Gast, M. C., Schellens, J. H., and Beijnen, J. H. (2006) Clinical proteomics: searching for better tumour markers with SELDI-TOF mass spectrometry. Trends Pharmacol. Sci. 27, 251–259.

    Article  PubMed  CAS  Google Scholar 

  94. Domon, B. and Aebersold, R. (2006) Mass spectrometry and protein analysis. Science 312, 212–217.

    Article  PubMed  CAS  Google Scholar 

  95. Domon, B. and Aebersold, R. (2006) Challenges and opportunities in proteomics data analysis. Mol. Cell Proteomics 5, 1921–1926.

    Article  PubMed  CAS  Google Scholar 

  96. Uhlen, M. and Ponten, F. (2005) Antibody-based proteomics for human tiss ue profiling. Mol. Cell Proteomics 4, 384–393.

    Article  PubMed  CAS  Google Scholar 

  97. Taussig, M. J., Stoevesandt, O., Borrebaeck, C. A., Bradbury, A. R., Cahill, D., Cambillau, C., de Daruvar, A., Dubel, S., Eichler, J., Frank, R., Gibson, T. J., Gloriam, D., Gold, L., Herberg, F. W., Hermjakob, H., Hoheisel, J. D., Joos, T. O., Kallioniemi, O., Koegll, M., Konthur, Z., Korn, B., Kremmer, E., Krobitsch, S., Landegren, U., van der Maarel, S., McCafferty, J., Muyldermans, S., Nygren, P. A., Palcy, S., Pluckthun, A., Polic, B., Przybylski, M., Saviranta, P., Sawyer, A., Sherman, D. J., Skerra, A., Templin, M., Ueffing, M., and Uhlen, M. (2007) ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat. Methods 4, 13–17.

    Article  PubMed  CAS  Google Scholar 

  98. Ilyin, S. E., Belkowski, S. M., and Plata-Salaman, C. R. (2004) Biomarker discovery and validation: technologies and integrative approaches. Trends Biotechnol. 22, 411–416.

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This study was supported by a grant from the Korea Health 21 R&D project, Ministry of Health & Welfare, Republic of Korea (A030003 to YKP).

Author information

Authors and Affiliations

  1. Department of Biochemistry, Yonsei Proteome Research Center & Biomedical Proteome Research Center, Seoul, Korea

    Young-Ki Paik

  2. Department of Pathology, College of Medicine, Yonsei University, Seoul, Korea

    Hoguen Kim

  3. Department of Biochemistry, College of Sciences, Yonsei Biomedical Proteome Research Center, Seoul, Korea

    Eun-Young Lee

  4. Department of Biochemistry, College of Sciences, Yonsei Biomedical Proteome Research Center, Seoul, Korea

    Min-Seok Kwon

  5. Department of Biochemistry, College of Sciences, Yonsei Biomedical Proteome Research Center, Seoul, Korea

    Sang Yun Cho

Authors
  1. Young-Ki Paik
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hoguen Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Eun-Young Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Min-Seok Kwon
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Sang Yun Cho
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Biomedical Research Foundation, Academy of Athens, Athens, Greece

    Antonia Vlahou

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Paik, YK., Kim, H., Lee, EY., Kwon, MS., Cho, S.Y. (2008). Overview and Introduction to Clinical Proteomics. In: Vlahou, A. (eds) Clinical Proteomics. Methods in Molecular Biology™, vol 428. Humana Press. https://doi.org/10.1007/978-1-59745-117-8_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-117-8_1

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-837-9

  • Online ISBN: 978-1-59745-117-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation