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

Erol E. Gulcicek1, Christopher M. Colangelo1, Walter McMurray1, Kathryn Stone1, Kenneth Williams1, Terence Wu1, Hongyu Zhao1, Heidi Spratt2, Alexander Kurosky2, Baolin Wu3

1 Yale University, New Haven, Connecticut, 2 University of Texas Medical Branch, Galveston, Texas, 3 University of Minnesota, Minneapolis, Minnesota
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.1
DOI:  10.1002/0471250953.bi1301s10
Online Posting Date:  July, 2005
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library


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

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
PDF or HTML at Wiley Online Library


PDF or HTML at Wiley Online Library



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 coded affinity tag (cICAT) reagents: The yeast salinity stress response. Mol. Cell. Proteomics 2:1198‐1204.
   Lilien, R.H., Farid, H., and Donald, B.R. 2003. Probabilistic disease classification of expression‐dependent proteomic data from mass spectrometry of human serum. J. Comp. Biol. 10:925‐946.
   Lilley, K.S. 2002. Protein profiling using two‐dimensional difference gel electrophoresis (2‐D DIGE). In Current Protocols in Protein Science (J.E. Coligan, B.M. Dunn, D.W. Speicher, and P.T. Wingfield, eds.) pp. 22.2.1‐22.2.14. John Wiley & Sons, Hoboken, N.J.
   Link, A.J., Jennings, J.L., and Washburn, M.P. 2003. Analysis of protein composition using multidimensional chromatography and mass spectrometry. In Current Protocols in Protein Science (J.E. Coligan, B.M. Dunn, D.W. Speicher, and P.T. Wingfield, eds.) pp. 23.1.1‐23.1.25. John Wiley & Sons, Hoboken, N.J.
   Liu, Q., Krishnapuram, B., Pratapa, P., Liao, X., Hartemink, A., and Carin, L. 2003. Identification of differentially expressed proteins using MALDI‐TOF mass spectra. In Proceedings of Asilomar Conference: Biological Aspects of Signal Processing, November 2003. American Society for Mass Spectrometry, Santa Fe, N.M.
   Lowe, J.B. 2001. Glycosylation, immunity, and autoimmunity. Cell 104:809‐812.
   Ma, B., Zhang, K., Hendrie, C., Liang, C., Li, M., Doherty‐Kirby, A., and Lajoie, G. 2003. PEAKS: Powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom. 17:2337‐2342.
   MacBeath, G. and Schreiber, S.L. 2000. Printing proteins as microarrays for high‐throughput function determination. Science 289:1760‐1763.
   Madoz‐Gúrpide, J., Wang, H., Misek, D.E., Brichory, F., and Hanash, S.M. 2001. Protein based microarrays: A tool for probing the proteome of cancer cells and tissues. Proteomics 1:1279‐1287.
   Mann, M. and Wilm, M. 1994. Error‐tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 66:4390‐4399.
   Mann, M., Hojrup, P., and Roepstorff, P. 1993. Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol. Mass Spectrom. 22:338‐345.
   Marshall, A.G., Hendrickson, C.L., and Jackson, G.S. 1998. Fourier transform ion cyclotron resonance mass spectrometry: A primer. Mass Spectrom. Rev. 17:1‐35.
   McLachlin, D.T. and Chait, B.T. 2003. Improved beta‐elimination‐based affinity purification strategy for enrichment of phosphopeptides. Anal. Chem. 75:6826‐6836.
   Mechref, Y. and Novotny, M.V. 2002. Structural investigations of glycoconjugates at high sensitivity. Chem. Rev. 102:321‐369.
   Mian, S., Ball, G., Hornbuckle, J., Holding, F., Carmichael, J., Ellis, I., Ali, S., Li, G., McArdle, S., Creaser, C., and Rees, R. 2003. A prototype methodology combining surface‐enhanced laser desorption/ionization protein chip technology and artificial neural network algorithms to predict the chemoresponsiveness of breast cancer cell lines exposed to Paclitaxel and Doxorubicin under in vitro conditions. Proteomics 3:1725‐1737.
   Moritz, R.L., Ji, H., Schutz, F., Connolly, L.M., Kapp, E.A., Speed, T.P., and Simpson, R.J. 2004. A proteome strategy for fractionating proteins and peptides using continuous free‐flow electrophoresis coupled off‐line to reversed‐phase high‐performance liquid chromatography. Anal. Chem. 76:4811‐4824.
   Nesvizhskii, A.I., Keller, A., Kolker, E., and Aebersold, R. 2003. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75:4646‐4658.
   Nielsen, U.B., Cardone, M.H., Sinskey, A.J., MacBeath, G., and Sorger, P.K. 2003. Profiling receptor tyrosine kinase activation by using Ab microarrays. Proc. Natl. Acad. Sci. U.S.A. 100:9330‐9335.
   Nomura, F., Tomonaga, T., Sogawa, K., Ohashi, T., Nezu, M., Sunaga, M., Kondo, N., Iyo, M., Shimada, H., and Ochiai, T. 2004 Identification of novel and downregulated biomarkers for alcoholism by surface enhanced laser desorption/ionization‐mass spectrometry. Proteomics 4:1187‐1194.
   Oda, Y., Huang, K., Cross, F.R., Cowburn, D., and Chait, B.T. 1999. Accurate quantitation of protein expression and site‐specific phosphorylation. Proc. Natl. Acad. Sci. U.S.A. 96:6591‐6596.
   Oda, Y., Nagasu, T., and Chait, B.T. 2001. Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat. Biotechnol. 19:379‐382.
   Ong, S.E., Blagoev, B., Kratchmarova, I., Kristensen, D.B., Steen, H., Pandey, A., and Mann, M. 2002. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics. 1:376‐386.
   Ong, S.E., Kratchmarova, I., and Mann, M. 2003. Properties of 13C‐substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J. Proteome Res. 2:173‐181.
   Opiteck, G.J. and Jorgenson, J.W. 1997. Two‐dimensional SEC/RPLC coupled to mass spectrometry for the analysis of peptides. Anal. Chem. 69:2283‐2291.
   Opiteck, G.J., Ramirez, S.M., Jorgenson, J.W., and Moseley, M.A. 3rd. 1998. Comprehensive two‐dimensional high‐performance liquid chromatography for the isolation of overexpressed proteins and proteome mapping. Anal. Biochem. 258:349‐361.
   Papadopoulos, M.C., Abel, P.M., Agranoff, D., Stich, A., Tarelli, E., Bell, B.A., Planche, T., Loosemore, A., Saadoun, S., Wilkins, P., and Krishna, S. 2004. A novel and accurate diagnostic test for human African trypanosomiasis. Lancet 363:1358‐1363.
   Pappin, D.J.C., Hojrup, P., and Bleasby, A. 1993. Rapid identification of proteins by peptide‐mass fingerprinting. J. Curr. Biol. 3:327‐332.
   Pasa‐Tolic, L., Lipton, M.S., Masselon, C.D., Anderson, G.A., Shen, Y., Tolic, N., and Smith, R.D. 2002. Gene expression profiling using advanced mass spectrometric approaches. J. Mass. Spectrom. 37:1185‐1198.
   Patton, W.F. 2000. A thousand points of light: The application of fluorescence detection technologies to two‐dimensional gel electrophoresis and proteomics. Electrophoresis 6:1123‐1144.
   Patton, W.F. 2002. Detection technologies in proteome analysis. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 771:3‐31.
   Pawson, T. and Scott, J.D. 1997. Signaling through scaffold, anchoring, and adaptor proteins. Science 278:2075‐2080.
   Peng, J., Elias, J.E., Thoreen, C.C., Licklider, L.J., and Gygi, S.P. 2003. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC‐MS/MS) for large‐scale protein analysis: The yeast proteome. J. Proteome Res. 2:43‐50.
   Perkins, D.N., Pappin, J.C., Creasy, D.M., and Cottrell, J.S. 1999. Probability‐based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551‐3567.
   Petricoin, E.F., Ardekani, A.M., Hitt, B.A., Levine, P.J., Fusaro, V.A., Steinberg, S.M., Mills, G.B., Simone, C., Fishman, D.A., Kohn, E.C., and Liotta, L.A. 2002. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359:572‐577.
   Pinkse, M.W., Uitto, P.M., Hilhorst, M.J., Ooms, B., and Heck, A.J. 2004. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D‐NanoLC‐ESI‐MS/MS and titanium oxide precolumns. Anal. Chem. 76:3935‐3943.
   Posewitz, M.C. and Tempst, P. 1999. Immobilized gallium(III) affinity chromatography of phosphopeptides. Anal. Chem. 71:2883‐2892.
   Qian, W.J., Goshe, M.B., Camp, D.G. 2nd, Yu, L.R., Tang, K., and Smith, R.D. 2003. Phosphoprotein isotope‐coded solid‐phase tag approach for enrichment and quantitative analysis of phosphopeptides from complex mixtures. Anal. Chem. 75:5441‐5450.
   Qiu, Y., Sousa, E.A., Hewick, R.M., and Wang, J.H. 2002. Acid‐labile isotope‐coded extractants: A class of reagents for quantitative mass spectrometric analysis of complex protein mixtures. Anal. Chem. 74:4969‐4979.
   Qu, Y.S., Adam, B.L., Yasui, T., Ward, M.D., Cazares, L.H., Schellhammer, P.F., Feng, Z.D., Semmes, O.J., and Wright, G.L. 2002. Boosted decision tree analysis of surface‐enhanced laser desorption/ionization mass spectral serum profiles discriminates prostate cancer from noncancer patients. Clin. Chem. 48:1835‐1843.
   Rockhill, B. 2002. Proteomic patterns in serum and identification of ovarian cancer. Lancet 360:169‐171.
   Rush, J., Moritz, A., Lee, K.A., Goss, V.L., Guo, A., Zhang, H., Polakiewicz, R.D., and Comb, M.J. 2004. Immunoaffinity profiling of tyrosine phosphorylation. 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.
   Seberger, P.J. and Chaney, W.G. 1999. Control of metastasis by Asn‐linked, beta1‐6 branched oligosaccharides in mouse mammary cancer cells. Glycobiology 9:235‐241.
   Shi, Y., Xiang, R., Crawford, J.K., Colangelo, C.M., Horváth, C., and Wilkins, J.A. 2003. A simple solid phase mass tagging approach for quantitative proteomics. J. Proteome Res. 3:104‐111.
   Sorace, J.M. and Zhan, M. 2003. A data review and re‐assessment of ovarian cancer serum proteomic profiling. BMC Bioinformatics 4:24.
   Stears, R.L., Martinsky, T., and Schena, M. 2003. Trends in microarray analysis. Nature Med. 9:140‐145.
   Steen, H., Kuster, B., Fernandez, M., Pandey, A., and Mann, M. 2002. Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway. J. Biol. Chem. 277:1031‐1039.
   Suckau, D. and Resemann, A. 2003. T3‐sequencing: Targeted characterization of the N‐ and C‐termini of undigested proteins by mass spectrometry. Anal. Chem. 75:5817‐5824.
   Tabb, D.L., Saraf, A., and Yates, J.R. 3rd. 2003. GutenTag: High‐throughput sequence tagging via an empirically derived fragmentation model. Anal. Chem. 75:6415‐6421.
   Taylor, J.A. and Johnson, R.S. 2001. Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal. Chem. 73:2594‐2604.
   Taylor, S.W., Fahy, E., Zhang, B., Glenn, G.M., Warnock, D.E., Wiley, S., Murphy, A.N., Gaucher, S.P., Capaldi, R.A., Gibson, B.W., and Ghosh, S.S. 2003a. Characterization of the human heart mitochondrial proteome. Nat. Biotechnol. 21:281‐286.
   Taylor, G.K., Kim, Y.‐B., Forbes, A.J., Meng, F., McCarthy, R., and Kelleher, N.L. 2003b. Web and database software for identification of intact proteins using “Top Down” mass spectrometry. Anal. Chem. 75:4081‐4086.
   Tibshirani, R., Hastie, T., Narasimhan, B., Soltys, S., Shi, G., Koong, A. and Le, Q.T. 2004. Sample classification from protein mass spectrometry, by “peak probability contrasts.” Bioinformatics 20:3034‐3044.
   Tonge, R., Shaw, J., Middleton, B., Rowlinson, R., Rayner, S., Young, J., Pognan, F., Hawkins, E., Currie, I., and Davison, M. 2001. Validation and development of fluorescence two‐dimensional differential gel electrophoresis proteomics technology. Proteomics 1:377‐396.
   Unlu, M., Morgan, M.E., and Minden, J.S. 1997. Difference gel electrophoresis: A single gel method for detecting changes in protein extracts. Electrophoresis 18:2071‐2077.
   Van't Veer, L.J., Dai, H., van de Vijver, M.J., He, Y.D., Hart, A.A., Mao, M., Peterse, H.L., van der Kooy, K., Marton, M.J., Witteveen, A.T., Schreiber, G.J., Kerkhoven, R.M., Roberts, C., Linsley, P.S., Bernards, R., and Friend, S.H. 2002. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415:530‐536.
   Venable, J.D. and Yates, J.R. III. 2004. Impact of ion trap tandem mass spectra variability on the identification of peptides. Anal. Chem. 76:2928‐2937.
   Villanueva, J.P., Entenberg, J.D., Chaparro, C.A., Tanwar, M.K., Holland, E.C., and Tempst, P. 2004. Serum peptide profiling by magnetic particle‐assisted, automated sample processing and MALDI‐TOF mass spectrometry. Anal. Chem. 76:1560‐1570.
   Vlahou, A., Schorge, J.O., Gregory, B.W., and Coleman, R.L. 2003. Diagnosis of ovarian cancer using decision tree classification of mass spectral data. J. Biomed. Biotechnol. 5:308‐314.
   Wadsworth, J.T., Somers, K.D., Cazares, L.H., Malik, G., Adam, B.L., Stack, B.C., Wright, G.L., and Semmes, O.J. 2004. Serum protein profiles to identify head and neck cancer. Clin. Can. Res. 10:1625‐1632.
   Wall, D.B., Parus, S.J., and Lubman, D.M. 2002. Three‐dimensional protein map according to pI, hydrophobicity and molecular mass. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 774:53‐58.
   Wang, H., and Hanash, S. 2004. Intact‐protein based sample preparation strategies for proteome analysis in combination with mass spectrometry. Mass Spectrom. Rev. 24:413‐426.
   Wang, H., Kachman, M.T., Schwartz, D.R., Cho, K.R., and Lubman, D.M. 2002. A protein molecular weight map of ES2 clear cell ovarian carcinoma cells using a two‐dimensional liquid separations/mass mapping technique. Electrophoresis 23:3168‐3181.
   Washburn, M.P., Wolters, D., and Yates, J.R. 2001. Large‐scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19:242‐247.
   Washburn, M.P., Ulaszek, R., Deciu, C., Schieltz, D.M., and Yates, J.R. 3rd. 2002. Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal. Chem. 74:1650‐1657.
   Washburn, M.P., Koller, A., Oshiro, G., Ulaszek, R.R., Plouffe, D., Deciu, C., Winzeler, E., and Yates, J.R. 3rd. 2003. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 100:3107‐3112.
   Wolters, D.A., Washburn, M.P., and Yates, J.R. 3rd. 2001. An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73:5683‐5690.
   Wu, B., Abbott, T., Fishman, D., McMurray, W., Mor, G., Stone, K., Ward, D., Williams, K., and Zhao, H. 2003. Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics 19:1636‐1643.
   Yan, F., Sreekumar, A., Laxman, B., Chinnaiyan, A.M., Lubman, D.M., and Barder, T.J. 2003a. Protein microarrays using liquid phase fractionation of cell lysates. Proteomics 3:1228‐1235.
   Yan, F., Subramanian, B., Nakeff, A., Barder, T.J., Parus, S.J., and Lubman, D.M. 2003b. A comparison of drug‐treated and untreated HCT‐116 human colon adenocarcinoma cells using a 2‐D liquid separation mapping method based upon chromatofocusing PI fractionation. Anal. Chem. 75:2299‐2308.
   Yao, X., Freas, A., Ramirez, J., Demirev, P.A., and Fenselau, C. 2001. Proteolytic 18O labeling for comparative proteomics: Model studies with two serotypes of adenovirus. Anal. Chem. 73:2836‐2842.
   Yasui, Y., Pepe, M., Thompson, M.L., Adam, B.L., Wright, G.L. Jr., Qu, Y., Potter, J.D., Winget, M., Thornquist, M., and Feng, Z. 2003a. A data‐analytic strategy for protein biomarker discovery: Profiling of high‐dimensional proteomic data for cancer detection. Biostatistics 4:449‐463.
   Yasui, Y., McLerran, D., Adam, B.L., Winget, M., Thornquist, M., and Feng, Z.D. 2003b. An automated peak identification/calibration procedure for high‐dimensional protein measures from mass spectrometers. J. Biomed. Biotechnol. 4:242‐248.
   Yasui, Y., Pepe, M., Hsu, L., Adam, B.L., and Feng, Z.D. 2004. Partially supervised learning using an EM‐boosting algorithm. Biometrics 60:199‐206.
   Yu, Y., Wu, B., Liu, J., Li, X., Williams, K., and Zhao, H. 2005. MALDI‐MS data analysis for disease biomarker discovery. In Methods in Molecular Biology: New and Emerging Proteomics Techniques (D. Nedelkov and R. Nelson, eds.). Humana Press, Totowa, N.J. Submitted for publication.
   Zhang, H., Li, X.J., Martin, D.B., and Aebersold, R. 2003. Identification and quantification of N‐linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat. Biotechnol. 21:660‐666.
   Zhang, H., Yan, W., and Aebersold, R. 2004. Chemical probes and tandem mass spectrometry: A strategy for the quantitative analysis of proteomes and subproteomes. Curr. Opin. Chem. Biol. 8:66‐75.
   Zhou, H., Watts, J.D., and Aebersold, R. 2001. A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 19:375‐378.
   Zhou, G., Li, H., DeCamp, D., Chen, S., Shu, H., Gong, Y., Flaig, M., Gillespie, J.W., Hu, N., Taylor, P.R., Emmert‐Buck, M.R., Liotta, L.A., Petricoin, E.F. 3rd, and Zhao, Y. 2002a. 2D differential in‐gel electrophoresis for the identification of esophageal scans cell cancer‐specific protein markers. Mol. Cell. Proteomics 1:117‐124.
   Zhou, H., Ranish, J.A., Watts, J.D., and Aebersold, R. 2002b. Quantitative proteome analysis by solid‐phase isotope tagging and mass spectrometry. Nat. Biotechnol. 20:512‐515.
   Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T., Mitchell, T., Miller, P., Dean, D.A., Gerstein, M., and Snyder, M. 2001. Global analysis of protein activities using proteome chips. Science 293:2101‐2105.
   Zhu, K., Kim, J., Yoo, C., Miller, F.R., and Lubman, D.M. 2003a. High sequence coverage of proteins isolated from liquid separations of breast cancer cells using capillary electrophoresis‐time‐of‐flight MS and MALDI‐TOF MS mapping. Anal. Chem. 75:6209‐6217.
   Zhu, W., Wang, X.N., Ma, Y.M., Rao, M.L., Glimm, J., and Kovach, J.S. 2003b. Detection of cancer‐specific markers amid massive mass spectral data. Proc. Natl. Acad. Sci. U.S.A. 100:14666‐14671.
Internet Resources‐Protein/1023373HB_QXP_Phos_122002WW.pdf
  Information on Qiagen commercial phosphoprotein affinity kits
  Web sites for companies selling liquid‐based isoelectric focusing fractionation apparatus
  Institute for Systems Biology Web site specifically for proteomics project analysis and management
  A Global Proteome Machine (GPM) Organization Web site for proteomics project analysis and management
  Yale Protein Expression Database (YPED), a Yale University Web site for proteomics project analysis, management, and archiving (in development)
  Site for downloading a machine‐learned intensity‐based protein identification software application called SILVER
  Institute for Systems Biology Web site showcasing all of their Proteomics analysis tools
  BD Biosciences Clontech company Web site for protein antibody microarray products
  Web site forProtometrix, which developsg and sells protein microarrays (now part of Invitrogen)
PDF or HTML at Wiley Online Library