Chapter 18: Identification of Novel Protein Complexes and Protein–Protein Interactions by Mass Spectrometry—References

Anderson D.C., Li W., Payan D.G., and Noble W.S. 2003. A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: Support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J. Proteome Res. 2: 137–146.

Berndt P., Hobohm U., and Langen H. 1999. Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints. Electrophoresis 20: 3521–3526.

Chamnongpol S. and Li X. 2004. SH3 domain protein-binding arrays. Methods Mol. Biol. 264: 183–189.

Cheeseman I.M., Niessen S., Anderson S., Hyndman F., Yates J.R., III, Oegema K., and Desai A. 2004. A conserved protein network controls assembly of the outer kinetochore and its ability to sustain tension. Genes Dev. 18: 2255–2268.

Cho S., Park S.G., Lee D.H., and Park B.C. 2004. Protein–protein interaction networks: From interactions to networks. J. Biochem. Mol. Biol. 37: 45–52.

Eng J., McCormack A.L., and Yates J.R., III. 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.

Eriksson J., Chait B.T., and Fenyo D. 2000. A statistical basis for testing the significance of mass spectrometric protein identification results. Anal. Chem. 72: 999–1005.

Fields S. and Song O. 1989. A novel genetic system to detect protein–protein interactions. Nature 340: 245–246.

Franke A., DeCamillis M., Zink D., Cheng N., Brock H.W., and Paro R. 1992. Polycomb and polyhomeotic are constituents of a multimeric protein complex in chromatin of Drosophila melanogaster. EMBO J. 11: 2941–2950.

Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., Schultz J., Rick J.M., Michon A.M., Cruciat C.M., et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141–147.

Gibson B.W. and Biemann K. 1984. Strategy for the mass spectrometric verification and correction of the primary structures of proteins deduced from their DNA sequences. Proc. Natl. Acad. Sci. 81: 1956–1960.

Gygi S.P., Rist B., Griffin T.J., Eng J., and Aebersold R. 2002. Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. J. Proteome Res. 1: 47–54.

Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., and Aebersold R. 1999. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17: 994–999.

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.

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. 90: 5011–5015.

Ho Y., Gruhler A., Heilbut A., Bader G. D., Moore L., Adams S. L., Millar A., Taylor P., Bennett K., Boutilier K., et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180–183.

Hunt D.F., Yates J.R., III, Shabanowitz J., Winston S., and Hauer C. R. 1986. Protein sequencing by tandem mass spectrometry. Proc. Natl. Acad. Sci. 83: 6233–6237.

Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., and Sakaki Y. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. 98: 4569–4574.

James P., Quadroni M., Carafoli E., and Gonnet G. 1993. Protein identification by mass profile fingerprinting. Biochem. Biophys. Res. Commun. 195: 58–64.

Jensen O.N., Podtelejnikov A.V., and Mann M. 1997. Identification of the components of simple protein mixtures by high-accuracy peptide mass mapping and database searching. Anal. Chem. 69: 4741–4750.

Jurica M.S. and Moore M.J. 2003. Pre-mRNA splicing: Awash in a sea of proteins. Mol. Cell 12: 5–14.

Karas M. and Hillenkamp F. 1988. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60: 2299–2301.

Knappik A. and Pluckthun A. 1994. An improved affinity tag based on the FLAG peptide for the detection and purification of recombinant antibody fragments. BioTechniques 17: 754–761.

Lessard J., Baban S., and Sauvageau G. 1998. Stage-specific expression of polycomb group genes in human bone marrow cells. Blood 91: 1216–1224.

Lim H., Eng J., Yates J.R., III, Tollaksen S.L., Giometti C.S., Holden J.F., Adams M.W., Reich C.I., Olsen G.J., and Hays L.G. 2003. Identification of 2D-gel proteins: A comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 14: 957–970.

Lopez F., Pichereaux C., Burlet-Schiltz O., Pradayrol L., Monsarrat B., and Esteve J.P. 2003. Improved sensitivity of biomolecular interaction analysis mass spectrometry for the identification of interacting molecules. Proteomics 3: 402–412.

MacCoss M.J., Wu C.C., and Yates J.R., III. 2002a. Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal. Chem. 74: 5593–5599.

MacCoss M.J., Wu C.C., Liu H., Sadygov R., and Yates J.R., III. 2003. A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal. Chem. 75: 6912–6921.

MacCoss M.J., McDonald W.H., Saraf A., Sadygov R., Clark J.M., Tasto J.J., Gould K.L., Wolters D., Washburn M., Weiss A., Clark J.I., and Yates J.R., III. 2002b. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl. Acad. Sci. 99: 7900–7905.

Matsuoka T.A., Zhao L., Artner I., Jarrett H.W., Friedman D., Means A., and Stein R. 2003. Members of the large Maf transcription family regulate insulin gene transcription in islet β cells. Mol. Cell Biol. 23: 6049–6062.

Morris H.R., Panico M., and Taylor G.W. 1983. FAB-mapping of recombinant-DNA protein products. Biochem. Biophys. Res. Commun. 117: 299–305.

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.

O'Hair L. 2000. The role of nucleophile-electrophile interactions in the unimolecular and bimolecular gas-phase ion chemistry of peptides and related systems. J. Mass Spectrom. 35: 1377–1381.

Papayannopoulos I. 1995. The interpretation of collision-induced dissociation tandem mass spectra of peptides. Mass Spectrom. Rev. 14: 49–73.

Pappin D.J.C., Hojrup P., and Beasly A.J. 1993. Rapid identification of proteins by peptide-mass fingerprinting. Curr. Biol. 3: 327–332.

Perkins D.N., Pappin D.J., Creasy D.M., and Cottrell J.S. 1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551–3567.

Polce M.J., Ren D., and Wesdemiotis C. 2000. Dissociation of the peptide bond in protonated peptides. J. Mass Spectrom. 35: 1391–1398.

Radulovic D., Jelveh S., Ryu S., Hamilton T.G., Foss E., Mao Y., and Emili A. 2004. Informatics platform for global proteomic profiling and biomarker discovery using liquid-chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 3: 984–997.

Rigaut G., Shevchenko A., Rutz B., Wilm M., Mann M., and Seraphin B. 1999. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17: 1030–1032.

Sadygov R.G. and Yates J.R., III. 2003. A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases. Anal. Chem. 75: 3792–3798.

Sato S., Tomomori-Sato C., Parmely T.J., Florens L., Zybailov B., Swanson S.K., Banks C.A., Jin J., Cai Y., Washburn M.P., Conaway J.W., and Conaway R.C. 2004. A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. Mol. Cell 14: 685–691.

Saurin A.J., Shao Z., Erdjument-Bromage H., Tempst P., and Kingston R.E. 2001. A Drosophila Polycomb group complex includes Zeste and dTAFII proteins. Nature 412: 655–660.

Schlosser A. and Lehmann W.D. 2000. Five-membered ring formation in unimolecular reactions of peptides: A key structural element controlling low-energy collision-induced dissociation of peptides. J. Mass Spectrom. 35: 1382–1390.

Screaton R.A., Conkright M.D., Katoh Y., Best J.L., Canettieri G., Jeffries S., Guzman E., Niessen S., Yates J.R., III, Takemori H., Okamoto M., and Montminy M. 2004. The CREB coactivator TORC2 functions as a calcium- and cAMP-sensitive coincidence detector. Cell 119: 61–74.

Shevchenko A., Wilm M., Vorm O., and Mann M. 1996. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 68: 850–858.

Suizdak G. 2003. The expanding role of mass spectrometry in biotechnology. MCC Press, San Diego, California.

Tabb D.L., McDonald W.H., and Yates J.R., III. 2002. DTASelect and Contrast: Tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 1: 21–26.

Tabb D.L., Huang Y., Wysocki V.H., and Yates J.R., III. 2004. Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 76: 1243–1248.

Tanaka K., Waki H., Ido Y., Akita S., Yoshida Y., and Yoshida T. 1988. Protein and polymer analysis up to m/z 100,000 by laser ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 2: 151–159.

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.

Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., Lockshon D., Narayan V., Srinivasan M., Pochart P., Qureshi-Emili A., Li Y., Godwin B., Conover D., Kalbfleisch T., Vijayadamodar G., Yang M., Johnston M., Fields S., and Rothberg J.M. 2000. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature 403: 623–627.

Walhout A.J., Boulton S.J., and Vidal M. 2000. Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast 17: 88–94.

Whitehouse C.M., Dreyer R.N., Yamashita M., and Fenn J.B. 1985. Electrospray interface for liquid chromatographs and mass spectrometers. Anal. Chem. 57: 675–679.

Wu K., Bottazzi M.E., de la Fuente C., Deng L., Gitlin S.D., Maddukuri A., Dadgar S., Li H., Vertes A., Pumfery A., and Kashanchi F. 2004. Protein profile of tax-associated complexes. J. Biol. Chem. 279: 495–508.

Wysocki V.H., Tsaprailis G., Smith L.L., and Breci L. A. 2000. Mobile and localized protons: A framework for understanding peptide dissociation. J. Mass Spectrom. 35: 1399–1406.

Yates J.R., III. 1998. Database searching using mass spectrometry data. Electrophoresis 19: 893–900.

Yates J.R., III, Eng J.K., and McCormack A.L. 1995a. Mining genomes: Correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal. Chem. 67: 3202–3210.

Yates J.R., III, Eng J.K., McCormack A.L., and Schieltz D. 1995b. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 67: 1426–1436.

Yates J.R., III, Speicher S., Griffin P.R., and Hunkapiller T. 1993. Peptide mass maps: A highly informative approach to protein identification. Anal. Biochem. 214: 397–408.

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 R.A., Gerstein M., and Snyder M. 2001. Global analysis of protein activities using proteome chips. Science 293: 2101–2105.

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