Proteomics and the Analysis of Proteomic Data: An Overview of Current Protein‐Profiling Technologies实验方法详情页

实验方法> 生物信息学技术> 数据库>Proteomics and the Analysis of Proteomic Data: An Overview of Current Protein‐Profiling Technologies

Proteomics and the Analysis of Proteomic Data: An Overview of Current Protein‐Profiling Technologies

关键词： proteomic data来源：互联网

Abstract
Table of Contents
Figures
Literature Cited

Abstract

In recent years, several proteomic methodologies have been developed that now make it possible to identify, characterize, and comparatively quantify the relative level of expression of hundreds of proteins that are coexpressed in a given cell type or tissue, or that are found in biological fluids such as serum. These advances have resulted from the integration of diverse scientific disciplines including molecular and cellular biology, protein/peptide chemistry, bioinformatics, analytical and bioanalytical chemistry, and the use of instrumental and software tools such as multidimensional electrophoretic and chromatographic separations and mass spectrometry. In this unit, some of the common protein?profiling technologies are reviewed, along with the accompanying data?analysis tools.

Keywords: Proteomics; Protein profiling; protein analysis; protein identification; serum biomarkers; computational tools; database searches

GO TO THE FULL PROTOCOL: PDF or HTML at Wiley Online Library Table of Contents

Gel‐Based Approaches
Non‐Gel Based Approaches
SELDI/MALDI‐MS‐Based Disease Biomarkers
Protein Microarrays
Analysis of Protein Profiling Data
Gel‐Based Data Analysis
MS‐Based Protein Profiling Software Analysis
Disease Biomarker Analysis
Conclusions
Acknowledgements
Literature Cited
Figures
Tables

GO TO THE FULL PROTOCOL: PDF or HTML at Wiley Online Library Materials

GO TO THE FULL PROTOCOL: PDF or HTML at Wiley Online Library Figures

Figure 13.1.1 Increasing complexity from the genome to the proteome (adapted from National Heart, Lung, and Blood Institute; courtesy, Susan Old and Tom Kodadek).

View Image

Figure 13.1.2 Declining rate of introduction of new plasma protein analytes in FDA‐approved clinical tests (adapted from Anderson and Anderson, , with permission from the American Society for Biochemistry and Molecular Biology).

View Image

Figure 13.1.3 Block diagram of commonly used protein profiling workflows in mass spectrometry. The workflow is divided in to three basic categories and generally flows from proteins to peptides, and to LC and MS strategies. Examples of individual techniques within the categories are described in blocks, and possible workflow combinations are connected with arrows. Refer to Table for a list of abbreviations.

View Image

Figure 13.1.4 Block diagram of commonly used proteomics bioinformatic workflows in mass spectrometry. The blocks highlight the algorithmic steps taken to process mass spectral data, to obtain protein sequence, identification, or quantitation, or to evaluate disease markers, and to manage and store data, experimental information, and results. Refer to Table for a list of abbreviations.

View Image

Videos

Literature Cited

	Adam, B.L., Qu, Y., Davis, J.W., Ward, M.D., Clements, M.A., Cazares, L.H., Semmes, O.J., Schellhammer, P.F., Yasui, Y., Feng, Z., and Wright, G.L. Jr. 2002. Serum protein fingerprinting coupled with a pattern‐matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res. 62:3609‐3614.
	Aebersold, R. 2003a. Constellations in a cellular universe. Nature 422:115‐116.
	Aebersold, R. 2003b. A mass spectrometric journey into protein and proteome research. J. Am. Soc. Mass. Spectrom. 14:685‐695.
	Ahmed, N., Argirov, O.K., Minhas, H.S., Cordeiro, C.A., and Thornalley, P.J. 2002. Assay of advanced glycation endproducts (AGEs): Surveying AGEs by chromatographic assay with derivatization by 6‐aminoqunolyl‐N‐hydroxysuccinimidyl‐carbamate and application to N epsilon‐carboxymethyl‐lysine‐ and N epsilon‐(1‐carboxyethyl)lysine‐modified albumin. Biochem. J. 364:1‐14.
	Alexe, G., Alexe, S., Liotta, L.A., Petricoin, E., Reiss, M., and Hammer, P.L. 2004. Ovarian cancer detection by logical analysis of proteomic data. Proteomics 4:766‐783.
	Anderson, N.L. and Anderson, N.G. 2002. The human plasma proteome: History, character, and diagnostic prospects. Mol. Cell. Proteomics 1:845‐867.
	Erratum 2003; 2:50.
	Baggerly, K.A., Morris, J.S., Wang, J., Gold, D., Xiao, L.C., and Coombes, K.R. 2003. A comprehensive approach to the analysis of matrix‐assisted laser desorption/ionization‐time of flight proteomics spectra from serum samples. Proteomics 3:1667‐1672.
	Baggerly, K.A., Morris, J.S., and Coombes, K.R. 2004. Reproducibility of SELDI‐TOF protein patterns in serum: Comparing datasets from different experiments. Bioinformatics 20:777‐785.
	Banks, J.F. and Gulcicek, E.E. 1997. Rapid peptide mapping by reversed‐phase liquid chromatography on nonporous silica with on‐line electrospray time‐of‐flight mass spectrometry. Anal. Chem. 69:3973‐3978.
	Beausoleil, S.A., Jedrychowski, M., Schwartz, D., Elias, J.E., Villen, J., Li, J., Cohn, M.A., Cantley, L.C., and Gygi, S.P. 2004. Large‐scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci. U.S.A. 101:12130‐12135.
	Bergen, H.R. 3rd, Vasmatzis, G., Cliby, W.A., Johnson, K.L., Oberg, A.L., and Muddiman, D.C. 2003. Discovery of ovarian cancer biomarkers in serum using NanoLC electrospray ionization TOF and FT‐ICR mass spectrometry. Dis. Markers 19:239‐249.
	Betgovargez, E. and Simonian, M.H. 2003. Reproducibility and Dynamic Range Characteristics of the Proteome PF 2D System. Beckman Coulter Application Information Bulletin A‐1964A. BD Biosciences, San Jose, Calif.
	Bischoff, R. and Luider, T.M. 2004. Methodological advances in the discovery of protein and peptide disease markers. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 803:27‐40.
	Bobbitt, J.M. 1956. Periodate oxidation of carbohydrates. Adv. Carbohyr. Chem. Biochem. 11:1‐41.
	Bonenfant, D., Schmelzle, T., Jacinto, E., Crespo, J.L., Mini, T., Hall, M.N., and Jenoe, P. 2003. Quantitation of changes in protein phosphorylation: A simple method based on stable isotope labeling and mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 100:880‐885.
	Bushey, M.M. and Jorgenson, J.W. 1990. Automated instrumentation for comprehensive two‐dimensional high‐performance liquid chromatography of proteins. Anal. Chem. 62:161‐167.
	Chong, B.E., Yan, F., Lubman, D.M., and Miller, F.R. 2001. Chromatofocusing nonporous reversed‐phase high‐performance liquid chromatography/electrospray ionization time‐of‐flight mass spectrometry of proteins from human breast cancer whole cell lysates: A novel two‐dimensional liquid chromatography/mass spectrometry method. Rapid Commun. Mass Spectrom. 15:291‐296.
	Cohen, P. 1982. The role of protein phosphorylation in neural and hormonal control of cellular activity. Nature 296:613‐620.
	Cohen, P. 1992. Signal integration at the level of protein kinases, protein phosphatases and their substrates. Trends Biochem. Sci. 17:408‐413.
	Coombes, K.R., Fritsche, H.A., Clarke, C., Chen, J.N., Baggerly, K.A., Morris, J.S., Xiao, L.C., Hung, M.C., and Kuerer, H.M. 2003. Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface‐enhanced laser desorption and ionization. Clin. Chem. 49:1615‐1623.
	Dančık, V., Addona, T.A., Clauser, K.R., Vath, J.E., and Pevzner, P.A. 1999. De novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol. 6:327‐342.
	Daniels, S., Pappin, D., Stanick, W., Ross, P., Huang, Y., Williamson, B., and Purkayastha, B. 2004. Optimization of a protocol for labeling peptides and protein digests with tags for relative and absolute quantification. In Proceedings of the 52nd ASMS Conference on Mass Spectrometry and Allied Topics, Nashville, Tennessee, May 23–27. American Society for Mass Spectrometry, Santa Fe, N.M.
	de Jager, W., te Velthuis, H., Prakken, B.J., Kuis, W., and Rijkers, G.T. 2003. Simultaneous detection of 15 human cytokines in a single sample of stimulated peripheral blood mononuclear cells. Clin. Diagn. Lab. Immun. 10:133‐139.
	Diamandis, E.P. 2004. Mass spectrometry as a diagnostic and a cancer biomarker discovery tool opportunities and potential limitations. Mol. Cell. Proteomics 3:367‐378.
	Edmondson, R.D., Vondriska, T.M., Biederman, K.J., Zhang, J., Jones, R.C., Zheng, Y., Allen, D.L., Xiu, J.X., Cardwell, E.M., Pisano, M.R., and Ping, P. 2002. Protein kinase C epsilon signaling complexes include metabolism‐ and transcription/translation‐related proteins: complimentary separation techniques with LC/MS/MS. Mol. Cell. Proteomics 1:421‐433.
	Edmondson, R.D., Jones, R.C., and Dragan, Y.P. 2004. Strategy to map the liver proteome. In Proceedings of the 52nd ASMS Conference on Mass Spectrometry and Allied Topics, Nashville, Tennessee, May 23‐27. American Society for Mass Spectrometry, Santa Fe, N.M.
	Elias, J.E., Gibbons, F.D., King, O.D., Roth, F.P., and Gygi, S.P. 2004. Intensity‐based protein identification by machine learning from a library of tandem mass spectra. Nat. Biotechnol. 22:214‐219.
	Endo, T. and Toda, T. 2003. Glycosylation in congenital muscular dystrophies. Biol. Pharm. Bull. 26:1641‐1647.
	Eng, J., McCormack, A.L., and Yates, J.R. 3rd. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass. Spectrom. 5:976‐989.
	Fernandez de Cossio, J., Gonzalez, J., Satomi, Y., Shima, T., Okumura, N., Besada, V., Betancourt, L., Padron, G., Shimonishi, Y., and Takao, T. 2000. Automated interpretation of low‐energy collision‐induced dissociation spectra by SeqMS, a software aid for de novo sequencing by tandem mass spectrometry. Electrophoresis 21:1694‐1699.
	Ficarro, S.B., McCleland, M.L., Stukenberg, P.T., Burke, D.J., Ross, M.M., Shabanowitz, J., Hunt, D.F., and White, F.M. 2002. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 20:301‐305.
	Forbes, A.J., Patrie, S.M., Taylor, G.K., Kim, Y.B., Jiang, L., and Kelleher, N.L. 2004. Targeted analysis and discovery of posttranslational modifications in proteins from methanogenic archaea by top‐down MS. Proc. Natl. Acad. Sci. U.S.A. 101:2678‐2683.
	Futcher, B., Latter, G.I., Monardo, P., McLaughlin, C.S., and Garrels, J.I. 1999. A sampling of the yeast proteome. Mol. Cell. Biol. 19:7357‐7368.
	Gharbi, S., Gaffney, P., Yang, A., Zvelebil, M.J., Cramer, R., Waterfield, M.D., and Timms, J.F. 2002. Evaluation of two‐dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system. Mol. Cell. Proteomics 1:91‐98.
	Gibbons, F.D., Elias, J.E., Gygi, S.P., and Roth, F.P. 2004. SILVER helps assign peptides to tandem mass spectra using intensity‐based scoring. J. Am. Soc. Mass Spectrom. 15:910‐912.
	Goshe, M.B., Conrads, T.P., Panisko, E.A., Angell, N.H., Veenstra, T.D., and Smith, R.D. 2001. Phosphoprotein isotope‐coded affinity tag approach for isolating and quantitating phosphopeptides in proteome‐wide analyses. Anal. Chem. 73:2578‐2586.
	Goshe, M.B., Veenstra, T.D., Panisko, E.A., Conrads, T.P., Angell, N.H., and Smith, R.D. 2002. Phosphoprotein isotope‐coded affinity tags: Application to the enrichment and identification of low‐abundance phosphoproteins. Anal. Chem. 74:607‐616.
	Greenbaum, D., Colangelo, C., Williams, K., and Gerstein, M. 2003. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol. 4:117.
	Gronborg, M., Kristiansen, T.Z., Stensballe, A., Andersen, J.S., Ohara, O., Mann, M., Jensen, O.N., and Pandey, A. 2002. A mass spectrometry–based proteomic approach for identification of serine/threonine‐phosphorylated proteins by enrichment with phospho‐specific antibodies: Identification of a novel protein, Frigg, as a protein kinase A substrate. Mol. Cell. Proteomics 7:517‐527.
	Gygi, S.P., Rochon, Y., Franza, B.R., and Aebersold, R. 1999a. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19:1720‐1730.
	Gygi, S.P., Rist, B., Gerber, S.A., Turecek, F., Gelb, M.H., and Aebersold, R. 1999b. Quantitative analysis of complex protein mixtures using isotope‐coded affinity tags. Nat. Biotechnol. 17:994‐999.
	Gygi, S.P., Corthals, G.L., Zhang, Y., Rochon, Y., and Aebersold, R. 2000. Evaluation of two‐dimensional gel electrophoresis‐based proteome analysis technology. Proc. Natl. Acad. Sci. U.S.A. 97:9390‐9395.
	Haab, B.B., Dunham, M.J., and Brown, P.O. 2001. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 2:1‐13.
	Hagglund, P., Bunkenborg, J., Elortza, F., Jensen, O.N., and Roepstorff, P. 2004. A new strategy for identification of N‐glycosylated proteins and unambiguous assignment of their glycosylation sites using HILIC enrichment and partial deglycosylation. J. Proteome Res. 3:556‐566.
	Hamler, R.L., Zhu, K., Buchanan, N.S., Kreunin, P., Kachman, M.T., Miller, F.R., and Lubman, D.M. 2004. A two‐dimensional liquid‐phase separation method coupled with mass spectrometry for proteomic studies of breast cancer and biomarker identification. Proteomics 4:562‐577.
	Han, D.K., Eng, J., Zhou, H., and Aebersold, R. 2001. Quantitative profiling of differentiation‐induced microsomal proteins using isotope‐coded affinity tags and mass spectrometry. Nat. Biotechnol. 19:946‐951.
	Harper, S., Mozdzanowski, J., and Speicher, D. 1998. Two‐dimensional gel electrophoresis. In Current Protocols in Protein Science. (J.E. Coligan, B.M. Dunn, D.W. Speicher, and P.T. Wingfield, eds.) pp. 10.4.1‐10.4.36. John Wiley & Sons, Hoboken, N.J.
	He, T., Alving, K., Feild, B., Norton, J., Joseloff, E.G., Patterson, S.D., and Domon, B. 2004. Quantitation of phosphopeptides using affinity chromatography and stable isotope labeling. J. Am. Soc. Mass Spectrom. 15:363‐373.
	Helenius, A. and Aebi, M. 2001. Intracellular functions of N‐linked glycans. Science 291:2364‐2369.
	Henzel, W.J. and Stults, J.T. 1996. Matrix‐assisted laser desorption/ionization time‐of‐flight mass analysis of peptides. In Current Protocols in Protein Science. (J.E. Coligan, B.M. Dunn, D.W. Speicher, and P.T. Wingfield, eds.) pp. 16.2.1‐16.2.11. John Wiley & Sons, Hoboken, N.J.
	Henzel, W.J., Billeci, T.M., Stults, J.T., Wong, S.C., Grimley, C., and Watanabe, C. 1993. Identifying proteins from two‐dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. U.S.A. 90:5011‐5015.
	Henzel, W.J., Watanabe, C. and Stults, J.T. 2003. Protein identification: The origins of peptide mass fingerprinting. J. Am. Soc. Mass Spectrom. 14:931‐942.
	Hoving, S., Voshol, H., and van Oostrum, J. 2000. Towards high performance two‐dimensional gel electrophoresis using ultrazoom gels. Electrophoresis 21:2617‐2621.
	Huang, Y., Ross, P.L., Pillai, S., Purkayastha, B., Martin, S., and Pappin, D. 2004. Protein expression measurements using multiplexed isobaric tagging technology. In Proceedings of the 52nd ASMS Conference on Mass Spectrometry and Allied Topics, Nashville, Tennessee, May 23–27. American Society for Mass Spectrometry, Santa Fe, N.M.
	Hubbard, M.J. and Cohen, P. 1993. On target with a new mechanism for the regulation of protein phosphorylation. Trends Biochem. Sci. 18:172‐177.
	Issaq, H.J., Veenstra, T.D., Conrads, T.P., and Felschow, D. 2002. The SELDI‐TOF MS approach to proteomics: Protein profiling and biomarker identification. Biochem. Biophys. Res. Commun. 292:587‐592.
	Julka, S. and Regnier, F. 2004. Quantification in proteomics through stable isotope coding: A review. J. Proteome Res. 3:350‐363.
	Kalkum, M., Lyon, G.J., and Chait, B.T. 2003. Detection of secreted peptides by using hypothesis‐driven multistage mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 100:2795‐2800.
	Kelleher, N.L. 2004. Top‐down proteomics. Anal. Chem. 76:197A‐203A.
	Keller, A., Nesvizhskii, A.I., Kolker, E., and Aebersold, R. 2002. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74:5383‐5392.
	Knight, Z.A., Schilling, B., Row, R.H., Kenski, D.M., Gibson, B.W., and Shokat, K.M. 2003. Phosphospecific proteolysis for mapping sites of protein phosphorylation. Nat. Biotechnol. 21:1047‐1054. [Published erratum appears in Nat. Biotechnol. 21:1396].
	Kuster, B., Krogh, T.N., Mortz, E., and Harvey, D.J. 2001. Glycosylation analysis of gel‐separated proteins. Proteomics 1:350‐361.
	Li, J., Zhang, Z., Rosenzweig, J., Wang, Y.Y., and Chan, D.W. 2002. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin. Chem. 48:1296‐1304.
	Li, J., Steen, H., and Gygi, S.P. 2003. Protein profiling with cleavable isotope c

推荐方法