October 2015 www.nature.com/milestones/mass-spec MILESTONES Mass Spectrometry Produced with support from: Produced by: Nature Methods, Nature, Nature Biotechnology, Nature Chemical Biology and Nature Protocols MILESTONES Mass Spectrometry MILESTONES COLLECTION 4 Timeline 5 Discovering the power of mass-to-charge (1910 ) NATURE METHODS: COMMENTARY 23 Mass spectrometry in high-throughput 6 Development of ionization methods (1929) proteomics: ready for the big time 7 Isotopes and ancient environments (1939) Tommy Nilsson, Matthias Mann, Ruedi Aebersold, John R Yates III, Amos Bairoch & John J M Bergeron 8 When a velocitron meets a reflectron (1946) 8 Spinning ion trajectories (1949) NATURE: REVIEW Fly out of the traps (1953) 9 28 The biological impact of mass-spectrometry- 10 Breaking down problems (1956) based proteomics 10 Amicable separations (1959) Benjamin F. Cravatt, Gabriel M. Simon & John R. Yates III 11 Solving the primary structure of peptides (1959) 12 A technique to carry a torch for (1961) NATURE: REVIEW 12 The pixelation of mass spectrometry (1962) 38 Metabolic phenotyping in clinical and surgical 13 Conquering carbohydrate complexity (1963) environments Jeremy K. Nicholson, Elaine Holmes, 14 Forming fragments (1966) James M. Kinross, Ara W. Darzi, Zoltan Takats & 14 Seeing the full picture of metabolism (1966) John C. Lindon 15 Electrospray makes molecular elephants fly (1968) 16 Signatures of disease (1975) 16 Reduce complexity by choosing your reactions (1978) 17 Enter the matrix (1985) 18 Dynamic protein structures (1991) 19 Protein discovery goes global (1993) 20 In pursuit of PTMs (1995) 21 Putting the pieces together (1999) CITING THE MILESTONES CONTRIBUTING JOURNALS UK/Europe/ROW (excluding Japan): The Nature Milestones: Mass Spectroscopy supplement has been published as Nature Methods, Nature, Nature Biotechnology, Nature Publishing Group, Subscriptions, a joint project between Nature Methods, Nature, Nature Biotechnology, Nature Chemical Biology and Nature Protocols. Brunel Road, Basingstoke, Hants RG21 6XS, UK. Nature Chemical Biology and Nature Protocols. However, most referencing for- Copyright © 2015 Nature America, Inc. 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One New York Plaza, Suite 4500, Tel: +81 3 3267 8751; Fax: +81 3 3267 8746 VISIT THE SUPPLEMENT ONLINE New York, NY 10004-1562 E-mail: [email protected] The Nature Milestones in Mass Spectrometry supplement can be T: (212) 726 9200 found at www.nature.com/milestones/mass-spec or +1 212 726 9223 (outside US/Canada). All Collection articles will be available free for six months. E-mail: [email protected] CUSTOMER SERVICE: [email protected] NATURE MILESTONES | MASS SPECTROMETRY OCTOBER 2015 | 1 ature Milestones are special supplements that aim to highlight the outstanding technological developments and scientific discoveries that have helped to define a particular field. Nature Milestones in Mass Spectrometry, a collaboration between five Nature Publishing Group journals, presents a historical look back at the key technical Ndevelopments in mass spectrometry and the chemical and biological applications that stemmed from these advances. Each short Milestone article, written by a Nature Publishing Group editor, covers one breakthrough, highlighting the main papers that contributed to the advance and discussing both their value at the time and their lasting influence on mass spectrometry today. The Milestone topics and papers were selected with the help of expert advisers, but the ultimate decisions on what to include were made by the editors. Nature Milestones in Mass Spectrometry is not meant to be a comprehensive overview of this field, and despite our and the advisers’ best efforts, omissions of important literature are inevitable. Our intent is to give readers a taste of the key advances in this technique, with a special focus on biological and biomedical applications, areas in which much of the research using mass spectrometry is currently concentrated. ▶ cover: Design by Erin Dewalt Original mass spectrum taken from Käll, L. et al., The seeds of mass spectrometry were planted just over a century ago with the pioneering Nat. Methods 4, 923–925 (2007). work of physicist J.J. Thomson (see Milestone 1). The development of ionization methods EDITORIAL OFFICES (Milestone 2) and instrumentation (see Milestones 4–6) was fueled in part by the Manhattan NEW YORK Project during the Second World War. The first applications of mass spectrometry in the field of Springer Nature One New York Plaza, Suite 4500, chemistry were reported soon after, and to this day, mass spectrometry serves as a workhorse New York, NY 10004-1562 technique for molecular and elemental analysis in laboratories worldwide (see Milestones 3, 7, T: (212) 726 9200 Coordinating editors: Allison Doerr, 10 and 12). Joshua Finkelstein, Irene Jarchum, Catherine Goodman and Bronwen Dekker The development of the soft ionization techniques of electrospray ionization (Milestone 15) production editor: Jennifer Gustavson and matrix-assisted laser desorption/ionization (MALDI; Milestone 18), and also of tandem Copy editorS: Rebecca Barr and Ashley Stevenson Editorial Assistant: Tanyeli Taze mass spectrometry (Milestone 13) and of the combination of chromatographic separation web production editorS: Jayce Childs and with mass spectrometry (Milestone 8), further revolutionized the field, allowing mass James McSweeney web Design: Sam Rios and Luke Stavenhagen spectrometry to become an essential tool not just in chemical research but also in the biological Manufacturing Production: Susan Gray arena. Today, mass spectrometry is the central technology employed in the field of proteomics marketing: Hannah Phipps Head of Publishing Services: Ruth Wilson (Milestone 20), enabling the analysis of post-translational modifications (Milestone 21) and editor-in-chief, Nature Publications: Philip Campbell protein interactions (Milestone 22), and it is also as an important tool in structural biology Sponsorship: David Bagshaw and Yvette Smith (Milestone 19). Copyright © 2015 Nature America, Inc. The supplement includes a Timeline that lists the key developments (by the year in which the first milestone paper pertinent to each breakthrough was published), a reprinted Commentary from Nature Methods and two reprinted Reviews from Nature (these articles will be made freely available online until March 2016). The Milestones website also includes an extensive Library listing of mass spectrometry–related papers published in Nature Publishing Group journals. We would like to sincerely thank our advisers and acknowledge support from SCIEX, Thermo Fisher Scientific Inc. and Waters Corporation. As always, Nature Publishing Group takes complete responsibility for the editorial content. Allison Doerr, Senior Editor, Nature Methods Joshua Finkelstein, Senior Editor, Nature Irene Jarchum, Associate Editor, Nature Biotechnology Catherine Goodman, Senior Editor, Nature Chemical Biology Bronwen Dekker, Senior Editor, Nature Protocols MILESTONES ADVISORS *Ruedi Aebersold, ETH Zürich, Switzerland *Fred W. McLafferty, Cornell University, USA *Peter Armentrout, University of Utah, USA Howard R. Morris, Imperial College London, UK Daniel Armstrong, University of Texas, USA David C. Muddiman, North Carolina State University, USA *H. Alex Brown, Vanderbilt University, USA Francis Pullen, University of Greenwich, UK *Richard Caprioli, Vanderbilt University, USA *Joshua Rabinowitz, Princeton University, USA Steven Carr, Broad Institute of MIT and Harvard, USA *Paula J. Reimer, Queen’s University Belfast, UK *Brian Chait, The Rockefeller University, USA *Carol Robinson, University of Oxford, UK David Clemmer, Indiana University, USA David H. Russell, Texas A&M University, USA *Anne Dell, Imperial College London, UK *Uwe Sauer, ETH Zürich, Switzerland *Rob Ellam, University of Glasgow, UK *Antonio Simonetti, University of Notre Dame, USA Michael H. Gelb, University of Washington, USA *Gary Siuzdak, The Scripps Research Institute, USA *Gary Glish, University of North Carolina at Chapel Hill, USA Luke Skinner, University of Cambridge, UK *Michael A. Grayson, American Society for Mass Spectrometry, USA Richard Smith, Pacific Northwest National Laboratory, USA *Jürgen H. Gross, University of Heidelberg, Germany *Giulio Superti-Furga, Research Center for Molecular Medicine of the Austrian Academy of Sciences, *Steven Gygi, Harvard Medical School, USA Austria Donald F. Hunt, University of Virginia, USA *Jonathan Sweedler, University of Illinois at Urbana-Champaign, USA *Akihiko Kameyama, National Institute of Advanced Industrial John Todd, University of Kent, UK Science and Technology, Japan *John Yates III, The Scripps Research Institute, USA Neil Kelleher, Northwestern University, USA *Richard Yost, University of Florida, USA *Bernhard Küster,