Chapter 8: The Use of Mass Spectrometry in Proteomics—References
Adams L.R. and Roy J.A. 1984. A one dimensional numerical model of a drop-on-demand in jet. J. Appl. Mech. 53: 193–197.
Aebersold R. and Goodlett D.R. 2001. Proteomics and mass spectrometry. Chem. Rev. 101: 269–295.
Aitken A., Geisow M.J., Findlay J.B.C., Holmes C., and Yarwood A. 1989. Peptide preparation and characterization. In Protein sequencing: A practical approach (ed. J.B.C. Findlay and M.J. Geisow), pp. 43–68. IRL Press, New York.
Alpert A.J. and Andrews P.C. 1988. Cation-exchange chromatography of peptides on poly(2-sulfoethyl aspartamide)-silica. J. Chromatogr. 443: 85–96.
Amster I.J. 1996. Fourier transform mass spectrometry. J. Mass. Spectrom. 31: 1325–1337.
Arnott D., Henzel W.J., and Stults J.T. 1998. Rapid identification of comigrating gel-isolated proteins by ion trap-mass spectrometry. Electrophoresis 19: 968–980.
Attwood T.K. and Parry-Smith D.J. 1999. DNA sequence analysis In Introduction to bioinformatics, pp. 81–107. Addison-Wesley Longman, Harlow, Essex, United Kingdom.
Axen R. and Ernback S. 1971. Chemical fixation of enzymes to cyanogen halide activated polysaccharide carriers. Eur. J. Biochem. 18: 351–360.
Baldwin M.A., Medzihradszky K.F., Lock C.M., Fisher B., Settineri T.A., and Burlingame A.L. 2001. Matrix-assisted laser desorption/ionization coupled with quadrupole/orthogonal acceleration time-of-flight mass spectrometry for protein discovery, identification, and structural analysis. Anal. Chem. 73: 1707– 1720.
Ball C.A., Jin H., Sherlock G., Weng S., Matese J.C., Andrada R., Binkley G., Dolinski K., Dwight S.S., Harris M.A., Issel-Tarver L., Schroeder M., Botstein D., and Cherry J.M. 2001. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 29: 80–81.
Banks J.F. and Whitehouse C.M. 1996. Electrospray ionization mass spectrometry. Methods Enzymol. 270: 486–518.
Barber M., Bordoli R.S., Sedgwick R.D., and Tyler A.N. 1981. Fast atom bombardment of solids as an ion source in mass spectroscopy. Nature 293: 270–275.
Barber M., Bordoli R.S., Elliott G.J., Horoch N.J., and Green B.N. 1983. Fast atom bombardment mass spectrometry of human proinsulin. Biochem Biophys. Res Commun. 110: 753–757.
Barber M., Bordoli R.S., Elliot G.J., Sedgewick R.D., and Tyler A. 1982. Fast atom bombardment: Mass spectrometry. Anal. Chem. 54: 645–657.
Bateman R.H., Carruthers R., Hoyes J.B., Jones C., Langridge J.I., Millar A., and Vissers J.P.C. 2002. A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-flight (Q-TOF) mass spectrometer for studying protein phosphorylation. J. Am. Soc. Mass Spectrom. 13: 792–803.
Beavis R.C. and Chait B.T. 1989a. Matrix-assisted laser-desorption mass spectrometry using 355 nm radiation. Rapid Commun. Mass Spectrom. 3: 436–439.
_______. 1989b. Cinnamic acid derivatives as matrices for ultraviolet laser desorption mass spectrometry of proteins. Rapid Commun. Mass Spectrom. 3: 432–435.
_______. 1989c. Factors affecting the ultraviolet laser desorption of proteins. Rapid Commun. Mass Spectrom. 3: 233–237.
_______. 1996. Matrix-assisted laser desorption ionization mass spectrometry. Methods Enzymol. 270: 519–551.
Beavis R.C., Chaudhary T., and Chait B.T. 1992. Cyano-4-hydroxycinnamic acid as a matrix for matrix-assisted laser desorption mass spectrometry. Org. Mass. Spectrom. 27: 156–158.
Biemann K. 1962. Mass spectrometry: Organic chemical applications. McGraw-Hill, New York.
_______. 1978. Mass spectrometric sequencing of peptides and proteins. Pure Appl. Chem. 50: 149–158.
_______. 1988. Contributions of mass spectrometry to peptide and protein structure. Biomed. Environ. Mass Spectrom. 16: 99–111.
_______. 1990. Sequencing of peptides by tandem mass spectrometry and high energy collision-induced dissociation. Methods Enzymol. 193: 455–479.
_______. 1995. The coming of age of mass spectrometry in peptide and protein chemistry. Protein Sci. 4: 1920–1927.
Biemann K., Cone C., Webster B.R., and Arsenault G.P. 1966. Determination of the amino acid sequence in oligopeptides by computer interpretation of their high-resolution mass spectra. J. Am. Chem. Soc. 88: 5598–5606.
Biemann K., Martin S., Scoble H., Johnson R., Papayannopoulos I., Biller J., and Costello C. 1986. How to obtain and how to use mass spectral data at high mass. In Mass spectrometry in the analysis of large molecules (ed. C.J. McNeal), pp. 131–149. Wiley, Chichester, United Kingdom.
Bienvenut W.V., Deon C., Pasquarello C., Campbell J.M., Sanchez J.C., Vestal M.L., and Hochstrasser D.F. 2002. Matrix-assisted laser desorption/ionization-tandem mass spectrometry with high resolution and sensitivity for identification and characterization of proteins. Proteomics 2: 868–876.
Bienvenut W.V., Sanchez J.C., Karmime A., Rouge V., Rose K., Binz P.A., and Hochstrasser D.F. 1999. Toward a clinical molecular scanner for proteome research: Parallel protein chemical processing before and during western blot. Anal. Chem. 71: 4800–4807.
Bienvenut W.V., Müeller M., Palagi P.M., Heller M., Gasteiger E., Binz P.A., Giron M., Gay S., Jung E., Gras R., Hugues G.J., Sanchez J.C., Appel R.D., and Hochstrasser D.F. 2001. Proteomics and mass spectrometry: Some aspects and recent developments. In Mass spectrometry and genomic analysis (ed. N. Housby), pp. 1–53. Kluwer, The Netherlands.
Binz P.A., Muller M., Walther D., Bienvenut W.V., Gras R., Hoogland C., Bouchet G., Gasteiger E., Fabbretti R., Gay S., Palagi P., Wilkins M.R., Rouge V., Tonella L., Paesano S., Rossellat G., Karmime A., Bairoch A., Sanchez J.C., Appel R.D., and Hochstrasser D.F. 1999. A molecular scanner to automate proteomic research and to display proteome images. Anal. Chem. 71: 4981–4988.
Blais J.C., Nagnanlemeillour P., Bolbach G., and Tabet J.C. 1996. MALDI-TOFMS identification of odorant binding proteins (obps) electroblotted onto poly(vinylidene difluoride) membranes. Rapid Comm. Mass Spectrom. 10: 1–4.
Bogy D.B. and Talke F.E. 1984. Experimental and theoretical study of wave propagation phenomena in drop-on-demand in jet devices. IBM J. Res. Dev. 29: 314–321.
Bonner R. and Shushan B. 1995. The characterization of proteins and peptides by automated methods. Rapid Commun. Mass Spectrom. 9: 1067–1076.
Börnsen K.O. 2000. Influence of salts, buffers, detergents, solvents, and matrices on MALDI-MS protein analysis in complex mixtures. Methods Mol. Biol. 146: 387–404.
Bowers W.D., Delbert S.-S., Hunter R.L., and McIver R.T.J. 1984. Fragmentation of oligopeptide ions using ultraviolet laser radiation and Fourier transform mass spectrometry. J. Am. Chem. Soc. 106: 7288–7289.
Breen E.J., Hopwood F.G., Williams K.L., and Wilkins M.R. 2000. Automatic Poisson peak harvesting for high throughput protein identification. Electrophoresis 21: 2243–2251.
Brunnee C. 1987. The ideal mass analyzer: Fact or fiction? Int. J. Mass Spectrom. Ion Proc. 76: 121–237.
Bures E.J., Courchesne P.L., Douglass J., Chen K., Davis M.T., Jones M.D., McGinley M.D., Robinson J.H., Spahr C.S., Wahl R.C., and Patterson S.D. 2001. Identification of incompletely processed potential carboxypeptidase E substrates from CpEfat/CpEfatmice. Proteomics 1: 79–92.
Burke T.W., Mant C.T., Black J.A., and Hodges R.S. 1989. Strong cation-exchange high-performance liquid chromatography of peptides. Effect of non-specific hydrophobic interactions and linearization of peptide retention behaviour. J. Chromatogr. 476: 377–389.
Burlet O., Yang C.Y., and Gaskell S.J. 1992. Influence of cysteine to cysteic acid oxidation on the collision-activated decomposition of protonated peptides—Evidence for intraionic interactions. J. Am. Soc. Mass Spectrom. 3: 337–344.
Burlingame A.L. and Carr S.A., eds. 1996. Mass spectrometry in the biological sciences, p. 535. Humana Press, Totowa, New Jersey.
Busch K.L. 1995. Mass spectrometric detectors for samples separated by planar electrophoresis. J. Chromatogr. A 692: 275–290.
Busch K.L., Glish G.L., and McLuckey S.A. 1988. Mass spectrometry/mass spectrometry. Techniques and applications of tandem mass spectrometry. Wiley, New York.
Carr S.A. and Burlingame A.L. 1996. The meaning and usage of the terms monoisotopic mass, average mass, mass resolution, and mass accuracy for measurements of biomolecules. In Mass spectrometry in the biological sciences (ed. A.L. Burlingame and S.A. Carr), pp. 546–553. Humana Press, Totowa, New Jersey.
Chen X., Smith L.M., and Bradbury E.M. 2000. Site-specific mass tagging with stable isotopes in proteins for accurate and efficient protein identification. Anal. Chem. 72: 1134–1143.
Chin E.T. and Papac D.I. 1999. The use of a porous graphitic carbon column for desalting hydrophilic peptides prior to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal. Biochem. 273: 179–185.
Clauser K.R., Baker P., and Burlingame A.L. 1999. Role of accurate mass measurement (+/– 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71: 2871–2882.
Cohen S.L. and Chait B.T. 1996. Influence of matrix solution conditions on the MALDI-MS analysis of peptides and proteins. Anal. Chem. 68: 31–37.
Coligan J.E., Dunn B., Ploegh H., Speicher D., and Wingfield P., eds. 1999. Current protocols in protein science, p. A.1A. Wiley, New York.
Conrads T.P., Alving K., Veenstra T.D., Belov M.E., Anderson G.A., Anderson D.J., Lipton M.S., Pasa-Tolic L., Udseth H.R., Chrisler W.B., Thrall B.D., and Smith R.D. 2001. Quantitative analysis of bacterial and mammalian proteomes using a combination of cysteine affinity tags and 15N-metabolic labeling. Anal. Chem. 73: 2132–2139.
Corthals G.L., Wasinger V.C., Hochstrasser D.F., and Sanchez J.C. 2000. The dynamic range of protein expression: A challenge for proteomic research. Electrophoresis 21: 1104–1115.
Costanzo G., Camier S., Carlucci P., Burderi L., and Negri R. 2001a. RNA polymerase III transcription complexes on chromosomal 5S rRNA genes in vivo: TFIIIB occupancy and promoter opening. Mol. Cell. Biol. 21: 3166–3178.
Costanzo M.C., Crawford M.E., Hirschman J.E., Kranz J.E., Olsen P., Robertson L.S., Skrzypek M.S., Braun B.R., Hopkins K.L., Kondu P., Lengieza C., Lew-Smith J.E., Tillberg M., and Garrels J.I. 2001b. YPD, PombePD and WormPD: Model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res. 29: 75–79.
Cottrell J.S. and Frank B.H. 1985. Fast atom bombardment mass spectrometry of bovine proinsulin. Biochem. Biophys. Res. Commun. 127: 1032–1038.
Cox A.L., Skipper J., Chen Y., Henderson R.A., Darrow T.L., Shabanowitz J., Engelhard V.H., Hunt D.F., and Slingluff C.L., Jr. 1994. Identification of a peptide recognized by five melanoma-specific human cytotoxic T cell lines. Science 264: 716–719.
Daves G.D. 1979. Mass spectrometry of involatile and thermally unstable molecules. Accts. Chem. Res. 12: 359–365.
Davis M.T. and Lee T.D. 1997. Variable flow liquid chromatography-tandem mass spectrometry and the comprehensive analysis of complex protein digest mixtures. J. Am. Soc. Mass Spectrom. 8: 1059–1069.
Davis M., Stahl D., Hefta S., and Lee T. 1995. A microscale electrospray interface for on-line capillary liquid chromatography/tandem mass spectrometry of complex peptide mixtures. Anal. Chem. 67: 4549–4556.
de Hoffmann E. 1996. Tandem mass spectrometry: A primer. J. Mass. Spectrom. 31: 129–137.
Dell A. and Morris H.R. 1982. Fast atom bombardment—High field magnet mass spectrometry of 6000 dalton polypeptides. Biochem. Biophys. Res. Commun. 106: 1456–1462.
Desiderio D.M. and Katakuse I. 1983. Fast atom bombardment-collision activated dissociation-linked field scanning mass spectrometry of the neuropeptide substance P. Anal. Biochem. 129: 425–429.
Dijksman J.F. 1984. Hydrodynamics of small tubular pumps. J. Fluid Mech. 139: 173–191.
Dongre A.K., Somogyi A., and Wysocki V.H. 1996. Surface induced dissociation: An effective tool to probe structure, energetics and fragmentation mechanisms of protonated petpides. J. Mass Spectrom. 31: 339–350.
Eckerskorn C., Strupat K., Karas M., Hillenkamp F., and Lottspeich F. 1992. Mass spectrometric analysis of blotted proteins after gel electrophoretic separation by matrix-assisted laser desorption/ionization. Electrophoresis 13: 664–665.
Eckerskorn C., Strupat K., Kellermann J., Lottspeich F., and Hillenkamp F. 1997a. High-sensitivity peptide mapping by micro-LC with on-line membrane blotting and subsequent detection by scanning-IR-MALDI mass spectrometry. J. Protein Chem. 16: 349–362.
Eckerskorn C., Strupat K., Schleuder D., Hochstrasser D., Sanchez J.C., Lottspeich F., and Hillenkamp F. 1997b. Analysis of proteins by direct-scanning infrared-MALDI mass spectrometry after 2D-PAGE separation and electroblotting. Anal. Chem. 69: 2888–2892.
Egelhofer V., Bussow K., Luebbert C., Lehrach H., and Nordhoff E. 2000. Improvements in protein identification by MALDI-TOF-MS peptide mapping. Anal. Chem. 72: 2741–2750.
Emmett M.R. and Caprioli R.M.J. 1994. Micro-electrospray mass spectrometry: Ultra-high-sensitivity analysis of peptides and proteins. J. Am. Soc. Mass Spectrom. 5: 605–613.
Eng J.K., 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.
Erdjument-Bromage H., Lui M., Lacomis L., Grewal A., Annan R.S., McNulty D.E., Carr S.A., and Tempst P. 1998. Examination of micro-tip reversed-phase liquid chromatographic extraction of peptide pools for mass spectrometric analysis. J Chromatogr. A 826: 167–181.
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
Fenn J.B., Mann M., Meng C.K., Wong S.F., and Whitehouse C.M. 1989. Electrospray ionization for mass spectrometry of large biomolecules. Science 246: 64–71.
Fenyo D., Qin J., and Chait B.T. 1998. Protein identification using mass spectrometric information. Electrophoresis 19: 998–1005.
Figeys D., Gygi S.P., McKinnon G., and Aebersold R. 1998. An integrated microfluidics-tandem mass spectrometry system for automated protein analysis. Anal. Chem. 70: 3728–3734.
Fountoulakis M., Takacs M.F., and Takacs B. 1999a. Enrichment of low-copy-number gene products by hydrophobic interaction chromatography. J. Chromatogr. A 833: 157–168.
Fountoulakis M., Takacs M.F., Berndt P., Langen H., and Takacs B. 1999b. Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite chromatography. Electrophoresis 20: 2181–2195.
Garrels J.I., Futcher B., Kobayashi R., Latter G.I., Schwender B., Volpe T., Warner J.R., and McLaughlin C.S. 1994. Protein identifications for a Saccharomyces cerevisiae protein database. Electrophoresis 15: 1466–1486.
Gaskell S.J. 1997. Electrospray: Principles and practice. J. Mass Spectrom. 32: 677–688.
Gatlin C.L., Kleemann G.R., Hays L.G., Link A.J., and Yates J.R., III. 1998. Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry. Anal. Biochem. 263: 93–101.
Gauthier J.W., Trautman T.R., and Jacobson D.B. 1991. Sustained off-resonance irradiation for collision-activated dissoication involving Fourier transform mass spectrometry. Collision-activated dissociation technique that emulates infrared multiphoton dissociation. Anal. Chim. Acta 246: 211–225.
Gevaert K. and Vandekerckhove J. 2000. Protein identification methods in proteomics. Electrophoresis 21: 1145–1154.
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.
Giddings J.C. 1987. Concepts and comparisons in multidimensional chromatography. J. High Res. Chromatogr. 10: 319–323.
Gobom J., Nordhoff E., Ekman R. and Roepstorff P. 1997. Rapid micro-scale proteolysis of proteins for MALDI-MS peptide mapping using immobilized trypsin. Int. J. Mass Spectrom. Ion Proc. 169/170: 153–163.
Gobom J., Nordhoff E., Mirgorodskaya E., Ekman R., and Roepstorff P. 1999. Sample purification and preparation technique based on nano-scale reversed-phase columns for the sensitive analysis of complex peptide mixtures by matrix-assisted laser desorption/ionization mass spectrometry. J. Mass Spectrom. 34: 105–116.
Goffeau A., Barrell B.G., Bussey H., Davis R.W., Dujon B., Feldmann H., Galibert F., Hoheisel J.D., Jacq C., Johnston M., Louis E.J., Mewes H.W., Murakami Y., Philippsen P., Tettelin H., and Oliver S.G. 1996. Life with 6000 genes. Science 274: 546, 563–546, 567.
Goodlett D.R., Wahl J.H., Udseth H.R., and Smith R.D. 1993. Reduced elution speed detection for capillary electrophoresis-mass spectrometry. J. Microcol. Sep. 5: 57–62.
Goodlett D.R., Keller A., Watts J.D., Newitt R., Yi E.C., Purvine S., Eng J.K., von Haller P., Aebersold R., and Kolker E. 2001. Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation. Rapid Commun. Mass Spectrom. 15: 1214–1221.
Gorman J.J., Ferguson B.L., and Nguyen T.B. 1996. Use of 2,6-dihydroxyacetophenone for analysis of fragile peptides, disulphide bonding and small proteins by matrix-assisted laser desorption/ionization. Rapid Commun. Mass Spectrom. 10: 529–536.
Gras R., Müeller M., Gasteiger E., Gay S., Binz P.A., Bienvenut W., Hoogland C., Sanchez J.C., Bairoch A., Hochstrasser D.F., and Appel R.D. 1999. Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection. Electrophoresis 20: 3535–3550.
Grayson M.A., ed. 2002. Measuring mass: From positive rays to proteins. Chemical Heritage Press, Philadelphia, Pennsylvania.
Griffin P.R., MacCoss M.J., Eng J.K., Blevins R.A., Aaronson J.S., and Yates J.R. III. 1995. Direct database searching with MALDI-PSD spectra of peptides. Rapid Commun. Mass Spectrom. 9: 1546–1551.
Griffin P.R., Coffman J.A., Hood L.E., and Yates J.R., III. 1991. Structural analysis of proteins by capillary HPLC electrospray tandem mass spectrometry. Int. J. Mass Spectrom. Ion Processes 111: 131–149.
Griffin T.J., Han D.K., Gygi S.P., Rist B., Lee H., Aebersold R., and Parker K.C. 2001a. Toward a high-throughput approach to quantitative proteomic analysis: Expression-dependent protein identification by mass spectrometry. J. Am. Soc. Mass Spectrom. 12: 1238–1246.
Griffin T.J., Gygi S.P., Rist B., Aebersold R., Loboda A., Jilkine A., Ens W., and Standing K.G. 2001b. Quantitative proteomic analysis using a MALDI quadrupole time-of-flight mass spectrometer. Anal. Chem. 73: 978–986.
Gygi S.P. and Aebersold R. 1999. Absolute quantitation of 2-D protein spots. Methods Mol. Biol. 112: 417–421.
_______. 2000. Mass spectrometry and proteomics. Curr. Opin. Chem. Biol. 4: 489–494.
Gygi S.P., Rist B., and Aebersold R. 2000a. Measuring gene expression by quantitative proteome analysis. Curr. Opin. Biotechnol. 11: 396–401.
Gygi S.P., Corthals G.L., Zhang Y., Rochon Y., and Aebersold R. 2000b. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. 97: 9390–9395.
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.
Hanash S.M. 2000. Biomedical applications of two-dimensional electrophoresis using immobilized pH gradients: Current status. Electrophoresis 21: 1202–1209.
Harrison A.G. 1992. Chemical ionization mass spectrometry. CRC Press, Boca Raton, Florida.
Harrison A.G. and Cotter R.J. 1990. Methods of ionization. Methods Enzymol. 193: 3–36.
Hayes R.N. and Gross M.L. 1990. Collision-induced dissociation. Methods Enzymol. 193: 237–263.
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.
Hillenkamp F., Karas M., Beavis R.C., and Chait B.T. 1991. Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Anal. Chem. 63: 1193A–1203A.
Hong H.Y., Yoo G.S., and Choi J.K. 2000. Direct Blue 71 staining of proteins bound to blotting membranes. Electrophoresis 21: 841–845.
Horn D.M., Ge Y., and McLafferty F.W. 2000a. Activated ion electron capture dissociation for mass spectral sequencing of larger (42 kDa) proteins. Anal. Chem. 72: 4778–4784.
Horn D.M., Zubarev R.A., and McLafferty F.W. 2000b. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J. Am. Soc. Mass Spectrom. 11: 320–332.
Hummel B.C.W. 1959. A modified spectrophotometric determination of chymotrypsin, trypsin, and thrombin. Can. J. Biochem. Physiol. 37: 1393–1398.
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.
Hunt D.F., Bone W. M., Shabanowitz J., Rhodes J., and Ballard J.M. 1981. Sequence analysis of oligopeptides by secondary ion/collision activated dissociation mass spectrometry. Anal. Chem. 53: 1704–1706.
Hunt D.F., Alexander J.E., McCormack A.L., Martino P.A., Michel H., Shabanowitz J., Sherman N., Moseley M.A., Jorgenson J.W., and Tomer K.B. 1991. Techniques in protein chemistry II, p. 441. Academic Press, New York.
Hyver K.J., Campana J.E., Cotter R.J., and Fenselau C. 1985. Mass spectral analysis of murine epidermal growth factor. Biochem. Biophys. Res. Commun. 130: 1287–1293.
Ishii S., Yokosawa H., Kumazaki T., and Nakamura I. 1983. Immobilized anhydrotrypsin as a biospecific affinity adsorbent for tryptic peptides. Methods Enzymol. 91: 378–383.
Ishii S., Yokosawa H., Shiba S., and Kasai K. 1979. Specific isolation of biologically-active peptides by means of immobilized anhydrotrypsin and anhydrochymotrypsin. Adv. Exp. Med. Biol. 120A: 15–27.
James P., Quadroni M., Carafoli E., and Gonnet G. 1993. Protein identification by mass profile fingerprinting. Biochem. Biophys. Res. Commun. 195: 58–64.
_______. 1994. Protein identification in DNA databases by peptide mass fingerprinting. Protein Sci. 3: 1347–1350.
Jennings K.R. and Dolnikowski G.G. 1990. Mass analyzers. Methods Enzymol. 193: 37–60.
Jensen O.N., Podtelejnikov A., and Mann M. 1996a. Delayed extraction improves specificity in database searches by matrix-assisted laser desorption/ionization peptide maps. Rapid Commun. Mass Spectrom. 10: 1371–1378.
Jensen O.N., Kulkarni S., Aldrich J.V., and Barofsky D.F. 1996b. Characterization of peptide-oligonucleotide heteroconjugates by mass spectrometry. Nucleic Acids Res. 24: 3866–3872.
Ji H., Baldwin G.S., Burgess A.W., Moritz R.L., Ward L.D., and Simpson R.J. 1993. Epidermal growth factor induces serine phosphorylation of stathmin in a human colon carcinoma cell line (LIM 1215). J. Biol. Chem. 268: 13396–13405.
John N.E., Andersen H.U., Fey S.J., Larsen P.M., Roepstorff P., Larsen M.R., Pociot F., Karlsen A.E., Nerup J., Green I.C., and Mandrup-Poulsen T. 2000. Cytokine- or chemically derived nitric oxide alters the expression of proteins detected by two-dimensional gel electrophoresis in neonatal rat islets of Langerhans. Diabetes 49: 1819–1829.
Johnstone R.A.W. and Rose M.E. 1996. Mass spectrometry for chemists and biochemists, 2nd edition. Cambridge University Press.
Jones E.W. 1991. Tackling the protease problem in Saccharomyces cerevisiae. Methods Enzymol. 194: 428–453.
Karas M. and Hillenkamp F. 1988. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60: 2299–2301.
Karas M., Gluckmann M., and Schafer J. 2000. Ionization in matrix-assisted laser desorption/ionization: Singly charged molecular ions are the lucky survivors. J. Mass Spectrom. 35: 1–12.
Karas M., Ehring H., Nordhoff E., Stahl B., Stupat K., Grehl M., et al. 1993. Matrix-assisted laser desorption mass spectrometry with additives to 2.5-dihydroxy benzoic acid. Org. Mass Spectrom. 28: 1476–1481.
Kasai K. and Ishii S. 1975. Affinity chromatography of trypsin and related enzymes. I. Preparation and characteristics of an affinity adsorbent containing tryptic peptides from protamine as ligands. J. Biochem. 78: 653–662.
Katayama H., Nagasu T., and Oda Y. 2001. Improvement of in-gel digestion protocol for peptide mass fingerprinting by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 15: 1416–1421.
Kennedy R. and Jorgenson J.W. 1989. Preparation and evaluation of packed capillary liquid chromatography columns with inner diameter from 20 to 50 µm. Anal. Chem. 61: 1128–1135.
King R., Bonfiglio R., Fernandez-Metzler C., Miller-Stein C., and Olah T. 2000. Mechanistic investigation of ionization suppression in electrospray ionization. J. Am. Soc. Mass Spectrom. 11: 942–950.
Kumazaki T., Terasawa K., and Ishii S. 1987. Affinity chromatography on immobilized anhydrotrypsin: General utility for selective isolation of C-terminal peptides from protease digests of proteins. J. Biochem. 102: 1539–1546.
Kumazaki T., Nakako T., Arisaka F., and Ishii S. 1986. A novel method for selective isolation of C-terminal peptides from tryptic digests of proteins by immobilized anhydrotrypsin: Application to structural analysis of the tail sheath and the tube proteins from bacteriophage T4. Proteins Struct. Funct. Genet. 1: 100–107.
Kussmann M., Lassing U., Sturmer C.A., Przybylski M., and Roepstorff P. 1997. Matrix-assisted laser desorption/ionization mass spectrometric peptide mapping of the neural cell adhesion protein neurolin purified by sodium dodecyl sulfate polyacrylamide gel electrophoresis or acidic precipitation. J. Mass Spectrom. 32: 483–493.
Kussmann M. and Roepstorff P. 2000. Sample preparation techniques for peptides and proteins analyzed by MALDI-MS. Methods Mol. Biol. 146: 405–424.
Larsen M.R. and Roepstorff P. 2000. Mass spectrometric identification of proteins and characterization of their post-translational modifications in proteome analysis. Fresenius. J. Anal. Chem. 366: 677–690.
Larsen M.R., Cordwell S.J., and Roepstorff P. 2002a. Graphite powder as an alternative to reversed-phase material for desalting and concentration of peptide mixtures prior to mass spectrometric analysis. Proteomics 2: 1277–1287.
_______. 2002b. Characterization of modified proteins using graphite powder microcolumns in combination with gel electrophoresis and advanced mass spectrometry. In Proceedings of the 5th Siena Meeting: From Genome to Proteome: Functional Proteomics, Siena, Italy, p. 72.
Larsen M.R., Pedersen S.K., and Walsh B. 2001a. The use of GELoader tip microcolumn technology in combination with mass spectrometry. In Proceedings of the 49th ASMS Conference on Mass Spectrometry and Allied Topics, Chicago, Illinois, poster no. MPF146.
Larsen M.R., Larsen P.M., Fey S.J., and Roepstorff P. 2001b. Characterization of differently processed forms of enolase 2 from Saccharomyces cerevisiae by two-dimensional gel electrophoresis and mass spectrometry. Electrophoresis 22: 566–575.
Larsen M.R., Sorensen G.L., Fey S.J., Larsen P.M., and Roepstorff P. 2001c. Phospho-proteomics: Evaluation of the use of enzymatic de-phosphorylation and differential mass spectrometric peptide mass mapping for site specific phosphorylation assignment in proteins separated by gel electrophoresis. Proteomics 1: 223–238.
Larsen P.M., Fey S.J., Larsen M.R., Nawrocki A., Andersen H.U., Kahler H., Heilmann C., Voss M.C., Roepstorff P., Pociot F., Karlsen A.E., and Nerup J. 2001. Proteome analysis of interleukin-1beta-induced changes in protein expression in rat islets of Langerhans. Diabetes 50: 1056–1063.
Lazar J.M., Ramsey R.S., Sundberg S., and Ramsey J.M. 1999. Subattomole-sensitivity microchip nanoelectrospray source with time-of-flight mass spectrometry detection. Anal. Chem. 71: 3627–3631.
Licklider L.J., Thoreen C.C., Peng J., and Gygi S.P. 2002. Automation of nanoscale microcapillary liquid chromatograpy-tandem mass spectrometry with a vented column. Anal. Chem. 74: 3076–3083.
Link A.J., Eng J., Schieltz D.M., Carmack E., Mize G.J., Morris D.R., Garvik B.M., and Yates J.R., III. 1999. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17: 676–682.
Little D.P., Speir J.P., Senko M.W., O'Connor P.B., and McLafferty F.W. 1994. Infrared multiphoton dissociation of large multiply charged ions for biomolicule sequencing. Anal. Chem. 66: 2809–2815.
Loboda A.V., Krutchinsky A.N., Bromirski M., Ens W., and Standing K.G. 2000. A tandem quadrupole/time-of-flight mass spectrometer with a matrix-assisted laser desorption/ionization source: Design and performance. Rapid Commun. Mass Spectrom. 14: 1047–1057.
Mann M. 1994. Sequence database searching by mass spectrometric data. In Microcharacterisation of proteins (ed. R. Kellner et al.), pp. 223–245. VCH, Weinheim, Germany.
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.
Mant C.T. and Hodges R.S. 1985. Separation of peptides by strong cation-exchange high-performance liquid chromatography. J. Chromatogr. 327: 147–155.
March R.E. 1997. An introduction to quadrupole ion trap mass spectrometry. J. Mass Spectrom. 32: 351–369.
_______. 1998. Quadrupole ion trap mass spectrometry: Theory, simulation, recent developments and applications. Rapid. Commun. Mass Spectrom. 12: 1543–1554.
Marshall A.G. and Verdun F.R. 1990. Fourier transforms in NMR, optical and mass spectrometry: A user's handbook. Elsevier, New York.
Marshall A.G., Wang T.-C.L., and Ricca T.L. 1985. Tailored excitation for fourier transform ion cyclotron mass spectrometry. J. Am. Chem. Soc. 107: 7893–7897.
Marshall A.G., Senko M.W., Li W., Li M., Dillon S., Guan S., and Logan T.M. 1997. Protein molecular mass to 1 Da by 13C, 15N double-depletion and FT-ICR mass spectrometry. J. Am. Chem. Soc. 119: 433–434.
Martin S.E., Shabanowitz J., Hunt D.F., and Marto J.A. 2000. Subfemtomole MS and MS/MS peptide sequence analysis using nano-HPLC micro-ESI fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 72: 4266–4274.
Masselon C., Anderson G.A., Harkewicz R., Bruce J.E., Pasa-Tolic L., and Smith R.D. 2000. Accurate mass multiplexed tandem mass spectrometry for high-throughput polypeptide identification from mixtures. Anal. Chem. 72: 1918–1924.
Matsudaira P. 1987. Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. J. Biol. Chem. 262: 10035–10038.
McCormack A., Eng J., and Yates J.R. 1994. Peptide sequence analysis on quadrupole mass spectrometers. Methods 1994: 274–83.
McCormack A.L., Schieltz D.M., Goode B., Yang S., Barnes G., Drubin D., and Yates J.R., III. 1997. Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level. Anal. Chem. 69: 767–776.
McLafferty F.W., Fridriksson E.K., Horn D.M., Lewis M.A., and Zubarev R.A. 1999. Techview: Biochemistry. Biomolecule mass spectrometry. Science 284: 1289–1290.
McLuckey S.A. 1992. Principles of collisional activation in analytical mass spectrometry. J. Am. Soc. Mass Spectrom. 3: 599–614.
McLuckey S.A. and Goeringer D.E. 1997. Slow heating methods in tandem mass spectrometry. J. Mass Spectrom. 32: 461–474.
McLuckey S.A., Van Berkel G.J., Glish G.L., and Schwartz J.C. 1995. Electrospray and the quadrupole ion trap. In Practical aspects of ion trap mass spectrometry. II: Ion trap instrumentation (ed. R.E. March and J.F.J. Todd), pp. 89–141. CRC Press, Boca Raton, Florida.
Medzihradszky K.F., Campbell J.M., Baldwin M.A., Falick A.M., Juhasz P., Vestal M.L., and Burlingame A.L. 2000. The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. Anal. Chem. 72: 552–558.
Meeusen S., Tieu Q., Wong E., Weiss E., Schieltz D., Yates J.R., and Nunnari J. 1999. Mgm101p is a novel component of the mitochondrial nucleoid that binds DNA and is required for the repair of oxidatively damaged mitochondrial DNA. J. Cell Biol. 145: 291–304.
Meng F., Cargile B.J., Miller L.M., Forbes A.J., Johnson J.R., and Kelleher N.L. 2001. Informatics and multiplexing of intact protein identification in bacteria and the archaea. Nat. Biotechnol. 19: 952–957.
Mewes H.W., Frishman D., Gruber C., Geier B., Haase D., Kaps A., Lemcke K., Mannhaupt G., Pfeiffer F., Schuller C., Stocker S., and Weil B. 2000. MIPS: A database for genomes and protein sequences. Nucleic Acids Res. 28: 37–40.
Miranker A.D. 2000. Protein complexes and analysis of their assembly by mass spectrometry. Curr. Opin. Struct. Biol. 10: 601–606.
Molloy M.P. 2000. Two-dimensional electrophoresis of membrane proteins using immobilized pH gradients. Anal. Biochem. 280: 1–10.
Moore R.E., Young M.K., and Lee T.D. 2000. Method for screening peptide fragment ion mass spectra prior to database searching. J. Am. Soc. Mass Spectrom. 11: 422–426.
_______. 2002. Qscore: An algorithm for evaluating SEQUEST database search results. J. Am. Soc. Mass Spectrom. 13: 378–386.
Moritz R.L. and Simpson R.J. 1992a. Application of capillary reversed-phase high-performance liquid chromatography to high-sensitivity protein sequence analysis. J. Chromatogr. 599: 119–130.
_______. 1992b. Purification of proteins and peptides for sequence analysis using microcolumn liquid chromatography. J. Microcol. Sep. 4: 485–489.
_______. 1993. Capillary liquid chromatography: A tool for protein structural analysis. In Methods in protein sequence analysis (ed. K. Imahori and F. Sakiyama), pp. 3–10. Plenum Press, New York.
Moritz R.L., Eddes J.S., Reid G.E., and Simpson R.J. 1996. S-pyridylethylation of intact polyacrylamide gels and in situ digestion of electrophoretically separated proteins: A rapid mass spectrometric method for identifying cysteine-containing peptides. Electrophoresis 17: 907–917.
Morris H.R. 1972. Complete sequence determination of proteins by mass spectrometry. Rapid procedure for the successful permethylation of histidine-containing peptides. FEBS Lett. 22: 257–260.
Morris H.R., Dickinson R.J., and Williams D.H. 1973. Studies toward the complete sequence determination of proteins by mass spectrometry. Derivatization of methionine, cysteine, and arginine containing peptides. Biochem. Biophys. Res. Commum. 51: 247–255.
Morris H.R., Panico M., Barber M., Bordoli R.S., Sedgwick R.D., and Tyler A. 1981. Fast atom bombardment: A new mass spectrometric method for peptide sequence analysis. Biochem. Biophys. Res. Commun. 101: 623–631.
Morris H.R., Paxton T., Dell A., Langhorne J., Berg M., Bordoli R.S., Hoyes J., and Bateman R.H. 1996. High sensitivity collisionally-activated decomposition tandem mass spectrometry on a novel quadrupole/ orthogonal-acceleration time-of-flight mass spectrometer. Rapid Commun. Mass Spectrom. 10: 889–896.
Mortz E., Vorm O., Mann M., and Roepstorff P. 1994. Identification of proteins in polyacrylamide gels by mass spectrometric peptide mapping combined with database search. Biol. Mass. Spectrom. 23: 249–261.
Mortz E., O'Connor P.B., Roepstorff P., Kelleher N.L., Wood T.D., McLafferty F.W., and Mann M. 1996. Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases. Proc. Natl. Acad. Sci. 93: 8264–8267.
Moseley M.A., Deterding L.J., Tomer K.B., and Jorgenson J.W. 1991. Nanoscale packed-capillary liquid-chromatography coupled with mass-spectrometry using a coaxial continuous-flow fast-atom-bombardment interface. Anal. Chem. 63: 1467–1473.
Natsume T., Yamauchi Y., Nakayama H., Shinkawa T., Yanagida M., Takahashi N., and Isobe T. 2002. A direct nanoflow liquid chromatography-tandem mass spectrometry system for interaction proteomics. Anal. Chem. 74: 4725–4733.
Nawrocki A., Larsen M.R., Podtelejnikov A.V., Jensen O.N., Mann M., Roepstorff P., Gorg A., Fey S.J., and Larsen P.M. 1998. Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two-dimensional gel electrophoresis patterns based on mass spectrometric protein identification. Electrophoresis 19: 1024–1035.
Neubauer G. and Mann M. 1999. Mapping of phosphorylation sites of gel-isolated proteins by nanoelectrospray tandem mass spectrometry: Potentials and limitations. Anal. Chem. 71: 235–242.
Newton K.A., Chrisman P.A., Reid G.E., Wells J.M. and McLuckey S.A. 2001. Loss of charged versus neutral heme from gaseous holomyoglobin ions. Rapid Commun. Mass Spectrom. 15: 2334–2340.
Nilsson C.L. and Davidsson P. 2000. New separation tools for comprehensive studies of protein expression by mass spectrometry. Mass Spec. Rev. 19: 390–397.
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. 96: 6591–6596.
Oh-Ishi M., Satoh M., and Maeda T. 2000. Preparative two-dimensional gel electrophoresis with agarose gels in the first dimension for high molecular mass proteins. Electrophoresis 21: 1653–1669.
Pandey A. and Mann M. 2000. Proteomics to study genes and genomes. Nature 405: 837–846.
Pappin D.J., Hojrup P., and Bleasby A. 1993. Rapid identification of proteins by peptide-mass fingerprinting. Curr. Biol. 3: 327–332.
Papayannopoulos I.A. 1995. The interpretation of collision-induced dissociation tandem mass-spectra of peptides. Mass Spectrom. Rev. 14: 49–73.
Pasa-Tolic L., Jensen P.K., Anderson G.A., Lipton M.S., Peden K.K., Martinovic S., Tolic N., Bruce J.E., and Smith R.D. 1999. High throughput proteome-wide precision measurements of protein expression using mass spectrometry. J. Am. Chem. Soc. 12: 7949–7950.
Patterson S.D. 1995. Matrix-assisted laser-desorption/ionization mass spectrometric approaches for the identification of gel-separated proteins in the 5–50 pmol range. Electrophoresis 16: 1104–1114.
_______. 1997. Identification of low to subpicomolar quantities of electrophoretically separated proteins: Towards protein chemistry in the post-genome era. Biochem. Soc. Trans. 25: 255–262.
Pedersen S.K, Christiansen J., Hansen T.O., Larsen M.R., and Nielsen F.C. 2002. Human insulin-like growth factor II leader 2 mediates internal initiation of translation. Biochem. J. 363: 37–44.
Peng J. and Gygi S.P. 2001. Proteomics: The move to mixtures. J. Mass Spectrom. 36: 1083–1091.
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.
Price W.D. and Williams E.R. 1997. Activation of peptide ions by blackbody radiation: Factors that lead to dissociation kinetics in the rapid energy exchange limit. J. Phys. Chem. A. 101: 8844–8852.
Qin J., Fenyo D., Zhao Y., Hall W.W., Chao D.M., Wilson C.J., Young R.A, and Chait B.T. 1997. A strategy for rapid, high-confidence protein identification. Anal. Chem. 69: 3995–4001.
Rabilloud T. 1990. Mechanisms of protein silver staining in polyacrylamide gels: A 10-year synthesis. Electrophoresis 11: 785–794.
Reid G.E., Rasmussen R.K., Dorow D.S., and Simpson R.J. 1998. Capillary column chromatography improves sample preparation for mass spectrometric analysis: Complete characterization of human alpha-enolase from two-dimensional gels following in situ proteolytic digestion. Electrophoresis 19: 946–955.
Reid G.E. and McLuckey S.A. 2002. "Top down" protein characterization via tandem mass spectrometry. J. Mass Spectrom. 37: 663–675.
Roepstorff P. and Fohlman J. 1984. Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed. Mass Spectrom. 11: 601.
Santoni V., Molloy M., and Rabilloud T. 2000. Membrane proteins and proteomics: Un amour impossible? Electrophoresis 21: 1054–1070.
Schartz J.C. and Jardine I. 2000. Quadrupole ion trap mass spectrometry. Methods Enzymol. 270: 552–586.
Schleuder D., Hillenkamp F., and Strupat K. 1999. IR-MALDI-mass analysis of electroblotted proteins directly from the membrane: Comparison of different membranes, application to on-membrane digestion and protein identification by database searching. Anal. Chem. 71: 3238–3247.
Sechi S. and Chait B.T. 2000. A method to define the carboxyl terminal of proteins. Anal. Chem. 72: 3374–3378.
Seifert W.E. and Caprioli R.M. 1996. Fast atom bombardment mass spectrometry. Methods Enzymol. 270: 453–485.
Shaw A.C., Rossel L.M., Roepstorff P., Holm A., Christiansen G., and Birkelund S. 1999. Mapping and identification of HeLa cell proteins separated by immobilized pH-gradient two-dimensional gel electrophoresis and construction of a two-dimensional polyacrylamide gel electrophoresis database. Electrophoresis 20: 977–983.
Shevchenko A., Loboda A., Shevchenko A., Ens W., and Standing K.G. 2000. MALDI quadrupole time-of-flight mass spectrometry: A powerful tool for proteomic research. Anal. Chem. 72: 2132–2141.
Shevchenko A., Sunyaev S., Loboda A., Shevchenko A., Bork P., Ens W., and Standing K.G. 2001. Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching. Anal. Chem. 73: 1917–1926.
Simpson R.J. and Dorow D.S. 2001. Cancer proteomics: From signaling networks to tumor markers. Trends Biotechnol. 19: S40–S48.
Sloane A.J., Duff J.L., Wilson N.L., Gardhi P.S., Hill C.J., Hopwood F.G., Smith P.E., Thomas M.L., Cole R.A., Packer N.H., Breen E.J., Cooley P.W., Wallace D.B., Williams K.L., and Gooley A.A. 2002. High throughput peptide mass fingerprinting and protein macroarray analysis using chemical printing strategies. Mol. Cell. Proteomics 1: 490–499.
Spahr C.S., Susin S.A., Bures E.J., Robinson J.H., Davis M.T., McGinley M.D., Kroemer G., and Patterson S.D. 2000. Simplification of complex peptide mixtures for proteomic analysis: Reversible biotinylation of cysteinyl peptides. Electrophoresis 21: 1635–1650.
Spengler B., Kirsch D., and Kaufmann R. 1991. Metastable decay of peptides and proteins in matrix-assisted laser-desorption mass spectrometry. Rapid Commun. Mass Spectrom. 5: 198–202.
Spengler B., Kirsch D., Kaufmann R., and Jaeger E. 1992. Peptide sequencing by matrix-assisted laser-desorption mass spectrometry. Rapid Commun. Mass Spectrom 6: 105–108.
Strupat K., Karas M., and Hillenkamp F. 1991. 2,5-Dihydroxybenzoic acid: A new matrix for laser desorption-ionization mass spectrometry. Int. J. Mass Spectrom. Ion Processes 111: 89–102.
Strupat K., Karas M., Hillenkamp F., Eckerskorn C., and Lottspeich F. 1994. Matrix-assisted laser desorption ionization mass spectrometry of proteins electroblotted after polyacrylamide gel electrophoresis. Anal. Chem. 66: 464–470.
Tang C., Zhang W., Chait B.T., and Fenyö D. 2000. A method to evaluate the quality of database search results. ABRF Conference Proceedings. Bellevue, Washington.
Veenstra T.D., Martinovic S., Anderson G.A., Pasa-Tolic L., and Smith R.D. 2000. Proteome analysis using selective incorporation of isotopically labeled amino acids. J. Am. Soc. Mass Spectrom. 11: 78–82.
VerBerkmoes N.C., Bundy J.L., Hauser L., Asano K.G., Razumovskaya J., Larimer F., Hettich R.L., and Stephenson J.L. 2002. Integrating "top-down" and "bottom-up" mass spectrometric approaches for proteomic analysis of Shewanella oneidensis. J. Proteome Res. 1: 239–252.
Verma R., Chen S., Feldman R., Schieltz D., Yates J., Dohmen J., and Deshaies R.J. 2000. Proteasomal proteomics: Identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes. Mol. Biol. Cell 11: 3425–3439.
Vestling M.M. and Fenselau C. 1994. Polyvinylidene difluoride (PVDF): An interface for gel electrophoresis and matrix-assisted laser desorption/ionization mass spectrometry. Biochem. Soc. Trans. 22: 547–551.
Vorm O., Roepstorff P., and Mann M. 1994. Matrix surfaces made by fast evaporation yield improved resolution and very high sensitivity in MALDI TOF. Anal. Chem. 66: 3281–3287.
Wahl J.H., Gale D.C., and Smith R.D. 1994. Sheathless capillary electrophoresis-electrospray ionization mass spectrometry using 10 µm I.D. capillaries: Analyses of tryptic digests of cytochrome c. J. Chromatogr. A 659: 217–222.
Wahl J.H., Goodlett D.R., Udseth H.R., and Smith R.D. 1992. Attomole level capillary electrophoresis mass spectrometric protein analysis using 5 µm id capillaries. Anal. Chem. 64: 3194–3196.
_______. 1993. Use of small-diameter capillaries for increasing peptide and protein detection sensitivity in capillary electrophoresis-mass spectrometry. Electrophoresis 14: 448–457.
Wapstra A.H., Audi G., and Hoekstra R. 1985. The 1983 atomic mass evaluation. IV. Evaluation of input values, adjustment procedures. Nucl. Phys. A A432: 185–362.
Washburn M.P. and Yates J.R., III. 2000. Analysis of the microbial proteome. Curr. Opin. Microbiol. 3: 292–297.
Washburn M.P., Wolters D., and Yates J.R., III. 2001. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19: 242–247.
Wattenberg A., Organ A.J., Schneider K., Tyldesley R., Bordoli R., and Bateman R.H. 2002. Sequence dependent fragmentation of peptides generated by MALDI quadrupole time-of-flight (MALDI Q-TOF) mass spectrometry and its implications for protein identification. J. Am. Soc. Mass Spectrom. 13: 772–783.
Weast R.C., Lide D.R., Astle M.J., and Beyer W.H., eds. 1989. CRC handbook of chemistry and physics: A ready Reference book of chemical and physical data, 70th edition, p. B-227. CRC Press, Boca Raton, Florida.
Wilkins M.R., Lindskog I., Gasteiger E., Bairoch A., Sanchez J.C., Hochstrasser D.F., and Appel R.D. 1997. Detailed peptide characterization using PEPTIDEMASS—A World-Wide-Web-accessible tool. Electrophoresis 18: 403–408.
Wilm M.S. and Mann M. 1994. Electrospray and Taylor-Cone theory, Dole's beam of macromolecules at last? Int. J. Mass Spectrom. Ion Processes 136: 167–180.
_______. 1996. Analytical properties of the nanoelectrospray ion source. Anal. Chem. 68: 1–8.
Wysocki V.H. 1992. Triple quadrupole mass spectrometry. In Mass spectrometry in the biological sciences: A tutorial (ed. M.L.Gross), pp. 59–78. Kluwer, Dortrecht, The Netherlands.
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., Clauser K.R., and Burlingame A.L. 1996. Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides. J. Am. Soc. Mass Spectrom. 7: 1089–1098.
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.
Yokosawa H. and Ishii S. 1976. The effective use of immobilized anhydrotrypsin for the isolation of biologically active peptides containing L-arginine residues in C-termini. Biochem. Biophys. Res. Commun. 72: 1443–1449.
Yost R.A. and Boyd R.B. 1990. Tandem mass spectrometry: Quadrupole and hybrid instruments. Methods Enzymol. 193: 154–200.
Zhang W. and Chait B.T. 2000. ProFound: An expert system for protein identification using mass spectrometric peptide mapping information. Anal. Chem. 72: 2482–2489.
Zubarev R.A., Kelleher N.L., and McLafferty F.W. 1998. Electron capture dissociation of multiply charged protein cations. A nonergodic process. J. Am. Chem. Soc. 120: 3265–3266.
|