163
Views
41
CrossRef citations to date
0
Altmetric
Review

Population proteomics: addressing protein diversity in humans

Pages 315-324 | Published online: 09 Jan 2014

References

  • Hoyert DL, Kung H-C, Smith BL. Deaths: preliminary data for 2003. In: National Vital Statistics Reports, Center for Disease Control and Prevention, USA (2005).
  • Biomarkers DefinitionsWorking Group. Biomarkers and surrogate end points: preferred definitions and conceptual framework. Clin. Pharmacol. Ther. 69(3), 89–95 (2001).
  • Wasinger VC, Cordwell SJ, Cerpa-Poljak A et al. Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16(7), 1090–1094 (1995).
  • Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl Acad. Sci. USA 97(17), 9390–9395 (2000).
  • Page JS, Masselon CD, Smith RD. FTICR mass spectrometry for qualitative and quantitative bioanalyses. Curr. Opin. Biotechnol. 15(1), 3–11 (2004).
  • Washburn MP, Wolters D, Yates JR III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature Biotechnol. 19(3), 242–247 (2001).
  • Resing KA, Meyer-Arendt K, Mendoza AM et al. Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal. Chem. 76(13), 3556–3568 (2004).
  • Anderson NL, Polanski M, Pieper R et al. The human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol. Cell. Proteomics 3(4), 311–326 (2004).
  • •Presents a merger of four different views and data sets of the human proteome.
  • Yan W, Lee H, Deutsch EW et al. A data set of human liver proteins identified by protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. Mol. Cell. Proteomics 3(10), 1039–1041 (2004).
  • International HumanGenome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431(7011), 931–945 (2004).
  • Southan C. Has the yo-yo stopped? An assessment of human protein-coding gene number. Proteomics 4(6), 1712–1726 (2004).
  • Thorisson GA, Stein LD. The SNP Consortium Website: past, present and future. Nucleic Acids Res. 31(1), 124–127 (2003).
  • Petricoin EF, Zoon KC, Kohn EC, Barrett JC, Liotta LA. Clinical proteomics: translating benchside promise into bedside reality. Nature Rev. Drug Discov. 1(9), 683–695 (2002).
  • Liotta LA, Kohn EC, Petricoin EF. Clinical proteomics: personalized molecular medicine. JAMA 286(18), 2211–2214 (2001).
  • Krieg RC, Paweletz CP, Liotta LA, Petricoin EF. Clinical proteomics for cancer biomarker discovery and therapeutic targeting. Technol. Cancer Res. Treat. 1(4), 263–272 (2002).
  • Issaq HJ, Conrads TP, Prieto DA, Tirumalai R, Veenstra TD. SELDI-TOF MS for diagnostic proteomics. Anal. Chem. 75(7), 148A–155A (2003).
  • Tang N, Tornatore P, Weinberger SR. Current developments in SELDI affinity technology. Mass Spectrom. Rev. 23(1), 34–44 (2004).
  • Petricoin EF, Ardekani AM, Hitt BA et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359(9306), 572–577. (2002).
  • Ornstein DK, Rayford W, Fusaro VA et al. Serum proteomic profiling can discriminate prostate cancer from benign prostates in men with total prostate specific antigen levels between 2.5 and 15.0 ng/ml. J. Urol. 172(4 Pt 1), 1302–1305 (2004).
  • Koopmann J, Zhang Z, White N et al. Serum diagnosis of pancreatic adenocarcinoma using surface-enhanced laser desorption and ionization mass spectrometry. Clin. Cancer Res. 10(3), 860–868 (2004).
  • Chen YD, Zheng S, Yu JK, Hu X. Artificial neural networks analysis of surface-enhanced laser desorption/ionization mass spectra of serum protein pattern distinguishes colorectal cancer from healthy population. Clin. Cancer Res. 10(24), 8380–8385 (2004).
  • Junker K, Gneist J, Melle C et al. Identification of protein pattern in kidney cancer using ProteinChip arrays and bioinformatics. Int. J. Mol. Med. 15(2), 285–290 (2005).
  • Kang X, Xu Y, Wu X et al. Proteomic fingerprints for potential application to early diagnosis of severe acute respiratory syndrome. Clin. Chem. 51(1), 56–64 (2005).
  • Wulfkuhle JD, Liotta LA, Petricoin EF. Proteomic applications for the early detection of cancer. Nature Rev. Cancer 3(4), 267–275 (2003).
  • Petricoin E, Wulfkuhle J, Espina V, Liotta LA. Clinical proteomics: revolutionizing disease detection and patient tailoring therapy. J. Proteome Res. 3(2), 209–217 (2004).
  • Petricoin EF, Fishman DA, Conrads TP, Veenstra TD, Liotta LA. Lessons from Kitty Hawk: from feasibility to routine clinical use for the field of proteomic pattern diagnostics. Proteomics 4(8), 2357–2360 (2004).
  • Johann DJ Jr, McGuigan MD, Patel AR et al. Clinical proteomics and biomarker discovery. Ann. NY Acad. Sci. 1022, 295–305 (2004).
  • Sorace JM, Zhan M. A data review and re-assessment of ovarian cancer serum proteomic profiling. BMC Bioinformatics 4(1), 24 (2003).
  • Baggerly KA, Morris JS, Edmonson SR, Coombes KR. Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J. Natl Cancer Inst. 97(4), 307–309 (2005).
  • Diamandis EP. Point: proteomic patterns in biological fluids: do they represent the future of cancer diagnostics? Clin. Chem. 49(8), 1272–1275 (2003).
  • Diamandis EP. Analysis of serum proteomic patterns for early cancer diagnosis: drawing attention to potential problems. J. Natl Cancer Inst. 96(5), 353–356 (2004).
  • Diamandis EP. Mass spectrometry as a diagnostic and a cancer biomarker discovery tool: opportunities and potential limitations. Mol. Cell. Proteomics 3(4), 367–378 (2004).
  • Diamandis EP. Proteomic patterns to identify ovarian cancer: 3 years on. Expert Rev. Mol. Diagn. 4(5), 575–577 (2004).
  • Coombes KR, Morris JS, Hu J, Edmonson SR, Baggerly KA. Serum proteomics profiling – a young technology begins to mature. Nature Biotechnol. 23(3), 291–292 (2005).
  • Ransohoff DF. Lessons from controversy: ovarian cancer screening and serum proteomics. J. Natl Cancer Inst. 97(4), 315–319 (2005).
  • Petricoin EF, Liotta LA. Counterpoint: the vision for a new diagnostic paradigm. Clin. Chem. 49(8), 1276–1278 (2003).
  • Liotta LA, Lowenthal M, Mehta A et al. Importance of communication between producers and consumers of publicly available experimental data. J. Natl Cancer Inst. 97(4), 310–314 (2005).
  • Malyarenko DI, Cooke WE, Adam BL et al. Enhancement of sensitivity and resolution of surface-enhanced laser desorption/ionization time-of-flight mass spectrometric records for serum peptides using time-series analysis techniques. Clin. Chem. 51(1), 65–74 (2005).
  • Le L, Chi K, Tyldesley S et al. Identification of serum amyloid A as a biomarker to distinguish prostate cancer patients with bone lesions. Clin. Chem. 51(4), 695–707 (2005).
  • Cho WC, Yip TT, Yip C et al. Identification of serum amyloid A protein as a potentially useful biomarker to monitor relapse of nasopharyngeal cancer by serum proteomic profiling. Clin. Cancer Res. 10(1 Pt 1), 43–52 (2004).
  • Yip TT, Chan JW, Cho WC et al. 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(1), 47–55 (2005).
  • Hlavaty JJ, Partin AW, Shue MJ et al. Identification and preliminary clinical evaluation of a 50.8-kDa serum marker for prostate cancer. Urology 61(6), 1261–1265 (2003).
  • Ye B, Cramer DW, Skates SJ et al. Haptoglobin-α subunit as potential serum biomarker in ovarian cancer: identification and characterization using proteomic profiling and mass spectrometry. Clin. Cancer Res. 9(8), 2904–2911 (2003).
  • Zhang Z, Bast RC Jr, Yu Y et al. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res. 64(16), 5882–5890 (2004).
  • Paradis V, Degos F, Dargere D et al. Identification of a new marker of hepatocellular carcinoma by serum protein profiling of patients with chronic liver diseases. Hepatology 41(1), 40–47 (2005).
  • Howard BA, Wang MZ, Campa MJ et al. Identification and validation of a potential lung cancer serum biomarker detected by matrix-assisted laser desorption/ionization-time of flight spectra analysis. Proteomics 3(9), 1720–1724 (2003).
  • Koomen JM, Shih LN, Coombes KR et al. Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins. Clin. Cancer Res. 11(3), 1110–1118 (2005).
  • Liao H, Wu J, Kuhn E et al. Use of mass spectrometry to identify protein biomarkers of disease severity in the synovial fluid and serum of patients with rheumatoid arthritis. Arthritis Rheum. 50(12), 3792–3803 (2004).
  • Predki PF. Functional protein microarrays: ripe for discovery. Curr. Opin. Chem. Biol. 8(1), 8–13 (2004).
  • Templin MF, Stoll D, Schrenk M et al. Protein microarray technology. Trends Biotechnol. 20(4), 160–166 (2002).
  • Peter J, Unverzagt C, Krogh TN, Vorm O, Hoesel W. Identification of precursor forms of free prostate-specific antigen in serum of prostate cancer patients by immunosorption and mass spectrometry. Cancer Res. 61(3), 957–962 (2001).
  • Mikolajczyk SD, Marker KM, Millar LS et al. A truncated precursor form of prostate-specific antigen is a more specific serum marker of prostate cancer. Cancer Res. 61(18), 6958–6963 (2001).
  • Foster DB, Noguchi T, VanBuren P, Murphy AM, Van Eyk JE. C-terminal truncation of cardiac troponin I causes divergent effects on ATPase and force: implications for the pathophysiology of myocardial stunning. Circ. Res. 93(10), 917–924 (2003).
  • Yu ZB, Zhang LF, Jin JP. A proteolytic NH2-terminal truncation of cardiac troponin I that is upregulated in simulated microgravity. J. Biol. Chem. 276(19), 15753–15760 (2001).
  • Craig WY, Ledue TB, Ritchie RF. Plasma proteins: Clinical utility and interpretation. Foundation for Blood Research, ME, USA (2001).
  • Serum Proteins in Clinical Medicine. Ritchie RF (Ed.) Foundation for Blood Research, Scarborough, ME, USA (1999).
  • Wegner GJ, Lee HJ, Corn RM. Characterization and optimization of peptide arrays for the study of epitope–antibody interactions using surface plasmon resonance imaging. Anal. Chem. 74(20), 5161–5168 (2002).
  • Kanda V, Kariuki JK, Harrison DJ, McDermott MT. Label-free reading of microarray-based immunoassays with surface plasmon resonance imaging. Anal. Chem. 76(24), 7257–7262 (2004).
  • Chakraborty A, Regnier FE. Global internal standard technology for comparative proteomics. J. Chromatogr. A 949(1–2), 173–184 (2002).
  • Schmidt A, Kellermann J, Lottspeich F. A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5(1), 4–15 (2005).
  • Gygi SP, Rist B, Gerber SA et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol. 17(10), 994–999 (1999).
  • Steel LF, Haab BB, Hanash SM. Methods of comparative proteomic profiling for disease diagnostics. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 815(1–2), 275–284 (2005).
  • Villanueva J, Philip J, Entenberg D et al. Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry. Anal. Chem. 76(6), 1560–1570 (2004).
  • Zhang X, Leung SM, Morris CR, Shigenaga MK. Evaluation of a novel, integrated approach using functionalized magnetic beads, bench-top MALDI-TOF-MS with prestructured sample supports, and pattern recognition software for profiling potential biomarkers in human plasma. J. Biomol. Tech. 15(3), 167–175 (2004).
  • Stoeckli M, Chaurand P, Hallahan DE, Caprioli RM. Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nature Med. 7(4), 493–496 (2001).
  • Nelson RW, Krone JR, Bieber AL, Williams P. Mass-spectrometric immunoassay. Anal. Chem. 67(7), 1153–1158 (1995).
  • Dogruel D, Williams P, Nelson RW. Rapid tryptic mapping using enzymatically active mass spectrometer probe tips. Anal. Chem. 67(23), 4343–4348 (1995).
  • Krone JR, Nelson RW, Williams P. Mass spectrometric immunoassay. SPIE 2680, 415–421 (1996).
  • Nelson RW. The use of bioreactive probes in protein characterization. Mass Spectrom. Rev. 16(6), 353–376 (1997).
  • Niederkofler EE, Tubbs KA, Gruber K et al. Determination of β-2 microglobulin levels in plasma using a high-throughput mass spectrometric immunoassay system. Anal. Chem. 73(14), 3294–3299 (2001).
  • Kiernan UA, Black JA, Williams P, Nelson RW. High-throughput analysis of hemoglobin from neonates using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clin. Chem. 48(6 Pt 1), 947–949 (2002).
  • Kiernan UA, Tubbs KA, Gruber K et al. High-throughput protein characterization using mass spectrometric immunoassay. Anal. Biochem. 301(1), 49–56 (2002).
  • Kiernan UA, Tubbs KA, Nedelkov D, Niederkofler EE, Nelson RW. Detection of novel truncated forms of human serum amyloid A protein in human plasma. FEBS Lett. 537(1–3), 166–170 (2003).
  • Kiernan UA, Tubbs KA, Nedelkov D, Niederkofler EE, Nelson RW. Comparative phenotypic analyses of human plasma and urinary retinol binding protein using mass spectrometric immunoassay. Biochem. Biophys. Res. Commun. 297(2), 401–405 (2002).
  • Niederkofler EE, Tubbs KA, Kiernan UA, Nedelkov D, Nelson RW. Novel mass spectrometric immunoassays for the rapid structural characterization of plasma apolipoproteins. J. Lipid Res. 44(3), 630–639 (2003).
  • Kiernan UA, Nedelkov D, Tubbs KA, Niederkofler EE, Nelson RW. Proteomic characterization of novel serum amyloid P component variants from human plasma and urine. Proteomics 4(6), 1825–1829 (2004).
  • Kiernan UA, Tubbs KA, Nedelkov D et al. Comparative urine protein phenotyping using mass spectrometric immunoassay. J. Proteome Res. 2(2), 191–197 (2003).
  • Kiernan UA, Nedelkov D, Tubbs KA, Niederkofler EE, Nelson RW. Selected expression profiling of full-length proteins and their variants in human plasma. Clin. Proteomics. J. 1(1), 7–16 (2004).
  • Nedelkov D, Tubbs KA, Niederkofler EE, Kiernan UA, Nelson RW. High-throughput comprehensive analysis of human plasma proteins: a step toward population proteomics. Anal. Chem. 76(6), 1733–1737 (2004).
  • Theberge R, Connors L, Skinner M, Skare J, Costello CE. Characterization of transthyretin mutants from serum using immunoprecipitation, HPLC/electrospray ionization and matrix-assisted laser desorption/ionization mass spectrometry. Anal. Chem. 71(2), 452–459 (1999).
  • Lacey JM, Bergen HR, Magera MJ, Naylor S, O’Brien JF. Rapid determination of transferrin isoforms by immunoaffinity liquid chromatography and electrospray mass spectrometry. Clin. Chem. 47(3), 513–518 (2001).
  • Bergen HR III, Zeldenrust SR, Naylor S. An on-line assay for clinical detection of amyloidogenic transthyretin variants directly from serum. Amyloid 10(3), 190–197 (2003).
  • Sen JW, Bergen HR III, Heegaard NH. On-line immunoaffinity-liquid chromatography-mass spectrometry for identification of amyloid disease markers in biological fluids. Anal. Chem. 75(5), 1196–1202 (2003).
  • Connors LH, Lim A, Prokaeva T, Roskens VA, Costello CE. Tabulation of human transthyretin (TTR) variants, 2003. Amyloid 10(3), 160–184 (2003).
  • Kishikawa M, Sass JO, Sakura N et al. The peak height ratio of S-sulfonated transthyretin and other oxidized isoforms as a marker for molybdenum co-factor deficiency, measured by electrospray ionization mass spectrometry. Biochim. Biophys. Acta 1588(2), 135–138 (2002).

Websites

  • Human Proteome Organization www.hupo.org (Viewed May 2005)
  • HUPO 3rd World Congress on Proteomics. Beijing, China, October 25th, 2004. Plasma Proteome Session www.ushupo.org/roller/files/omennhupo 102504Beijing.pdf (Viewed May 2005)
  • The SNP Consortium, Ltd. Single Nucleotide Polymorphisms for Biomedical Research http://snp.cshl.org (Viewed May 2005)
  • International HapMap Project www.hapmap.org (Viewed May 2005)
  • UniProtKB/Swiss-Prot entry: P01344 http://au.expasy.org/ cgi-bin/niceprot.pl?P01344 (Viewed May 2005)

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.