Nature Methods

A century of mass spectrometry: from atoms to proteomes

John R Yates III

Supplementary Figure 1: Referenced version of the timeline shown in Figure 1.

Nature Methods: doi:10.1038/nmeth.1659

Nature Methods: doi:10.1038/nmeth.1659

Supplementary Figure 1: Referenced version of the timeline shown in Figure 1. References 1) J.J. Thomson (1897), Cathode rays, Philosophical Magazine, 44, 293—The classic measurement of the electron mass and charge 2) Thomson J.J., On Rays of Positive Electricity, Phil. Mag. Series 6, 1907, 13(77), p.561 3) Dempster A.J., A new method of positive ray analysis, Phys. Rev., 1917, XI(4), p.316 4) Aston FW. 1920. The constitution of atmospheric neon. Phil Mag (Series 6), 39:449–455 5) J. Mattauch, R. Herzog, Über einen neuen Massenspektrographen, Zeitschrift fur Physik, 1934, 89, p.786 6) AO Nier and EA Gulbransen JACS 61, 697 (1939) 7) AO Nier Rev Sci Instrument 11, 212 (1940) 8) Wood HG, Werkman CH, Hemingway A, Nier AOC. Heavy carbon as a tracer in heterotropic carbon dioxide assimilation. J. Biol. Chem. 1941; 139: 365. 9) Time-of-Flight Mass Spectrometry Ref: Stephens W. Pulsed Mass Spectrometer with Time Dispersion Bull. Am. Phys. Soc., 1946, 21(2), p.22 10) Hipple J.A., Sommer H., Thomas H.A. A Precise Method of Determining the Faraday by Magnetic Resonance Phys. Rev., 1949, 76(12), p.1877 11) Johnson E.G., Nier A.O., Angular aberrations in sector-shaped electromagnetic lenses for focusing beams of charged particles, Phys. Rev., 1953, 91(1), p.10 12) W. Paul and H. Steinwedel, Z. f. Naturforschung 8a, 448 (1953) 13) Gohlke, R. S. (1959). "Time-of-Flight Mass Spectrometry and Gas-Liquid Partition Chromatography". Analytical Chemistry 31 (4): 535. 14) APPLICATION OF MASS SPECTROMETRY TO STRUCTURE PROBLEMS. I. AMINO ACID SEQUENCE IN PEPTIDES, K. Biemann, G. Gapp, J. Seibl, J. Am. Chem. Soc., 1959, 81 (9), pp 2274–2275 15) Jennings K.R., Collision-Induced Decompositions of Aromatic Molecular Ions Int. J. Mass Spec. Ion Physics, 1968, 1(3), p.227-235 16) Lederberg, Joshua. How Dendral Was Conceived and Born. ACM Symposium on the History of Medical Informatics, 5 November 1987, Rockefeller University. New York: National Library of Medicine, 1987.

Nature Methods: doi:10.1038/nmeth.1659

17) Futrell J.H., Miller C.D. Tandem Mass Spectrometer for the Study of Ion-Molecule Reactions Review of Scientific Instruments, 1966, 37, p.1521 18) Munson, M.S.B.; Field, F.H. J. Am. Chem. Soc. 1966, 88, 2621-2630. Chemical Ionization Mass Spectrometry. I. General Introduction 19) Dole M., Mack L.L., Hines R.L., Mobley R.C., Ferguson L.D., Alice M.B., Molecular beams of macroions , Journal of Chemical Physics, 1968, 49(5), p.2240 20) M.B. Comisarow and A.G. Marshall, Chem. Phys. Lett. 25, 282 (1974) 21) Nau H, Kelley JA, Biemann K., J Am Chem Soc. Determination of the amino acid sequence of the C-terminal cyanogen bromide fragment of actin by computer-assisted gas chromatography--mass spectrometry. 1973 Oct 17;95(21):7162-4 22) O'Farrell PH. High resolution two-dimensional electrophoresis of proteins. J Biol Chem. 1975 May 25;250(10):4007-21.; Klose J., Humangenetik. 1975;26(3):231-43., Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. 23) R. A. Yost, C. G. Enke, J. Am. Chem. Soc., Selected ion fragmentation with a tandem quadrupole mass spectrometer. 1978, 100 (7), pp 2274–2275 24) A new method for sequencing DNA., Maxam AM, Gilbert W., Proc Natl Acad Sci U S A. 1977 Feb;74(2):560-4.; DNA sequencing with chain-terminating inhibitors. Sanger F, Nicklen S, Coulson AR., Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7. 25) Mass spectra of partial protein hydrolysates as a multiple phase check for long polypeptides deduced from DNA sequences: NH2-terminal segment of alanine tRNA synthetase., Herlihy WC, Royal NJ, Biemann K, Putney SD, Schimmel PR., Proc Natl Acad Sci U S A. 1980 Nov;77(11):6531-5. 26) Barber, M. et al., Fast Atom Bombardment of Solids as an Ion Source in Mass Spectrometry, Nature 293, 270-5, 1981 27) International Journal of Mass Spectrometry and Ion Processes, Volume 60, Issue 1, 7 September 1984, Pages 85-98, Recent improvements in and analytical applications of advanced ion trap technology, G.C. Stafford Jr., P.E. Kelley, J.E.P. Syka, W.E. Reynolds and J.F.J. Todd 28) Proc Natl Acad Sci U S A. 1984 Apr;81(7):1956-60., Strategy for the mass spectrometric verification and correction of the primary structures of proteins deduced from their DNA sequences., Gibson BW, Biemann K. 29) Introduced with the TSQ70 by Finnigan MAT 30) Tandem quadrupole-Fourier transform mass spectrometry of oligopeptides., Hunt DF, Shabanowitz J, Yates JR 3rd, MeIver RT Jr, Hunter RL, Syka JE, Amy J., Anal Chem. 1985 Nov;57(13):2728-33.

Nature Methods: doi:10.1038/nmeth.1659

31) Protein Sequencing by Tandem Mass Spectrometry, D. F. Hunt, J. R. Yates, III, J. Shabanowitz, S. Winston, C. R. Hauer, Proc. Natl. Acad. Sci. USA 1986, 83, 6233. 32) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons., Karas M, Hillenkamp F.,Anal Chem. 1988 Oct 15;60(20):2299-301. 33) JB Fenn, M Mann, CK Meng, SF Wong, CM Whitehouse.Electrospray ionization for mass spectrometry of large biomolecules. Science 1989;246:64–71. 34) Henry KD, Williams ER, Wang BH, McLafferty FW, Shabanowitz J, Hunt DF. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9075-8. Fourier-transform mass spectrometry of large molecules by electrospray ionization. 35) Tandem time-of-flight mass spectrometer, Timothy J. Cornish, Robert J. Cotter, Anal. Chem., 1993, 65 (8), pp 1043–1047 36) Peptide mass maps: A highly informative approach to protein identification. J. R. Yates, III, S. Speicher, P. R. Griffin, and T. Hunkapiller, Analytical Biochemistry 214, 397-408 (1993).; Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases., Henzel WJ, Billeci TM, Stults JT, Wong SC, Grimley C, Watanabe C., Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5011-5.; Rapid identification of proteins by peptide-mass fingerprinting., Pappin DJ, Hojrup P, Bleasby AJ., Curr Biol. 1993 Jun 1;3(6):327-32. Erratum in: Curr Biol. 1993 Jul 1;3(7): 487.; Protein identification by mass profile fingerprinting., James P, Quadroni M, Carafoli E, Gonnet G., Biochem Biophys Res Commun. 1993 Aug 31;195(1):58-64. 37) An approach to correlate MS/MS data to amino acid sequences in a protein database, J. K. Eng, A. L. McCormack, and J. R. Yates, III, J. American Soc. Mass Spectrom. 5, 976-989 (1994). 38) American Society of Mass Spectrometry Conference 1995 39) Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database., Yates JR 3rd, Eng JK, McCormack AL, Schieltz D., Anal Chem. 1995 Apr 15;67(8):1426-36. 40) Morris et al. (1996), Rapid Commun. Mass Spectrom. 10, 889-896 41) Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases. Proc Natl Acad Sci U S A 93(16):8264-8267. 42) A strategy for the identification of proteins localized to in subcellular spaces: application to E. coli periplasmic proteins, A. Link, E. Carmack, and J. R. Yates, III, Int. J. Mass Spectrom. Ion Processes 160, 303-316, 1997. 43) Anal Chem. 1997 Feb 15;69(4):767-76., Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level., McCormack AL, Schieltz DM, Goode B, Yang S, Barnes G, Drubin D, Yates JR 3rd.

Nature Methods: doi:10.1038/nmeth.1659

44) Zubarev R.A., Kelleher N.L., McLafferty F.W., Electron Capture Dissociation of Multiply Charged Protein Cations - a Nonergodic Process, J. Am. Chem. Soc., 1998, 120(13), p.3265 45) Anal Chem. 1998 Jun 1;70(11):2236-42. Three-dimensional ion mobility/TOFMS analysis of electrosprayed biomolecules.Hoaglund CS, Valentine SJ, Sporleder CR, Reilly JP, Clemmer DE. 46) Kelleher, N. L.; Lin, H. Y.; Valaskovic, G. A.; Aaserud, D. J.; Fridriksson, E. K.; McLafferty, F. W. (1999) Top Down versus Bottom Up Protein Characterization by Tandem High-Resolution Mass Spectrometry. J Am Chem Soc 121:806-812. 47) Direct analysis of protein complexes using mass spectrometry., Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM, Yates JR 3rd., Nat Biotechnol. 1999 Jul;17(7):676-82. 48) Proc Natl Acad Sci U S A. 1999 Jun 8;96(12):6591-6., Accurate quantitation of protein expression and site-specific phosphorylation., Oda Y, Huang K, Cross FR, Cowburn D, Chait BT. 49) Makarov A. (2000). "Electrostatic axially harmonic orbital trapping: A high-performance technique of mass analysis". Analytical Chemistry : AC 72 (6): 1156–62 50) The sequence of the human genome., Venter JC, et al, Science. 2001 Feb 16;291(5507):1304-51; Initial sequencing and analysis of the human genome., Lander ES, et al, Nature. 2001 Feb 15;409(6822):860-921. 51) Meng, F.; Cargile, B. J.; Miller, L. M.; Forbes, A. J.; Johnson, J. R.; Kelleher, N. L. (2001) Informatics and multiplexing of intact protein identification in bacteria and the archaea. Nat Biotechnol 19(10):952-957. 52) Nat Biotechnol. 2001 Mar;19(3):242-7., Large-scale analysis of the yeast proteome by multidimensional protein identification technology, Washburn MP, Wolters D, Yates JR 3rd. 53) Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Ficarro SB, McCleland ML, Stukenberg PT, Burke DJ, Ross MM, Shabanowitz J, Hunt DF, White FM., Nat Biotechnol. 2002 Mar;20(3):301-5. 54) Meng, F.; Cargile, B. J.; Patrie, S. M.; Johnson, J. R.; McLoughlin, S. M.; Kelleher, N. L. (2002) Processing complex mixtures of intact proteins for direct analysis by mass spectrometry. Anal Chem 74(13):2923-2929. 55) American Society of Mass Spectrometry Conference 2003 56) American Society of Mass Spectrometry Conference 2003 57) Introduced at Pittcon 2003; Novel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modifications., Syka JE, Marto JA, Bai DL, Horning S, Senko MW, Schwartz

Nature Methods: doi:10.1038/nmeth.1659

JC, Ueberheide B, Garcia B, Busby S, Muratore T, Shabanowitz J, Hunt DF., J Proteome Res. 2004 May-Jun;3(3):621-6. 58) Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci U S A. 2004;101:9528–33. 59) Ruotolo BT, Giles K, Campuzano I, Sandercock AM, Bateman RH, Robinson CV. Evidence for macromolecular protein rings in the absence of bulk water. Science. 2005 Dec 9;310(5754):1658-61. 60) Introduced as a product ASMS 2005 61) Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons. Han X, Jin M, Breuker K, McLafferty FW. Science. 2006 Oct 6;314(5796):109-12.) 62) ASMS 2006 in Seattle

Nature Methods: doi:10.1038/nmeth.1659