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©Copyright 2015 Samuel Tabor Marionni Native Ion Mobility Mass Spectrometry: Characterizing Biological Assemblies and Modeling Their Structures
©Copyright 2015 Samuel Tabor Marionni Native Ion Mobility Mass Spectrometry: Characterizing Biological Assemblies and Modeling their Structures Samuel Tabor Marionni A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2015 Reading Committee: Matthew F. Bush, Chair Robert E. Synovec Dustin J. Maly James E. Bruce Program Authorized to Offer Degree: Chemistry University of Washington Abstract Native Ion Mobility Mass Spectrometry: Characterizing Biological Assemblies and Modeling their Structures Samuel Tabor Marionni Chair of the Supervisory Committee: Assistant Professor Matthew F. Bush Department of Chemistry Native mass spectrometry (MS) is an increasingly important structural biology technique for characterizing protein complexes. Conventional structural techniques such as X-ray crys- tallography and nuclear magnetic resonance (NMR) spectroscopy can produce very high- resolution structures, however large quantities of protein are needed, heterogeneity com- plicates structural elucidation, and higher-order complexes of biomolecules are difficult to characterize with these techniques. Native MS is rapid and requires very small amounts of sample. Though the data is not as high-resolution, information about stoichiometry, subunit topology, and ligand-binding, is readily obtained, making native MS very complementary to these techniques. When coupled with ion mobility, geometric information in the form of a collision cross section (Ω) can be obtained as well. Integrative modeling approaches are emerging that integrate gas-phase techniques — such as native MS, ion mobility, chemical cross-linking, and other forms of protein MS — with conventional solution-phase techniques and computational modeling. While conducting the research discussed in this dissertation, I used native MS to investigate two biological systems: a mammalian circadian clock protein complex and a series of engineered fusion proteins. -
Personal and Contact Details
CURRICULUM VITAE Carol Vivien Robinson DBE FRS FMedSci Personal and Contact Details Date of Birth 10th April 1956 Maiden Name Bradley Nationality British Contact details Department of Physical and Theoretical Chemistry University of Oxford South Parks Road Oxford OX1 3QZ Tel : +44 (0)1865 275473 E-mail : [email protected] Web : http://robinsonweb.chem.ox.ac.uk/Default.aspx Education and Appointments 2009 Professorial Fellow, Exeter College, Oxford 2009 Dr Lee’s Professor of Physical and Theoretical Chemistry, University of Oxford 2006 - 2016 Royal Society Research Professorship 2003 - 2009 Senior Research Fellow, Churchill College, University of Cambridge 2001 - 2009 Professor of Mass Spectrometry, Dept. of Chemistry, University of Cambridge 1999 - 2001 Titular Professor, University of Oxford 1998 - 2001 Research Fellow, Wolfson College, Oxford 1995 - 2001 Royal Society University Research Fellow, University of Oxford 1991 - 1995 Postdoctoral Research Fellow, University of Oxford. Supervisor: Prof. C. M. Dobson FRS 1991 - 1991 Postgraduate Diploma in Information Technology, University of Keele 1983 - 1991 Career break: birth of three children 1982 - 1983 MRC Training Fellowship, University of Bristol Medical School 1980 - 1982 Doctor of Philosophy, University of Cambridge. Supervisor: Prof. D. H. Williams FRS 1979 - 1980 Master of Science, University of Wales. Supervisor: Prof. J. H. Beynon FRS 1976 - 1979 Graduate of the Royal Society of Chemistry, Medway College of Technology, Kent 1972 - 1976 ONC and HNC in Chemistry, Canterbury -
Mass Spectrometry in Trace Organic Analysis
Pure & Appl. Chem.,Vol. 63, No. 11, pp. 1637-1646, 1991 Printed in Great Britain. @ 1991 IUPAC INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY ANALYTICAL CHEMISTRY DIVISION COMMISSION ON MICROCHEMICAL TECHNIQUES AND TRACE ANALYSIS* WORKING GROUP ON ORGANIC TRACE ANALYSIS ANALYTICAL TECHNIQUES FOR TRACE ORGANIC COMPOUNDS-I11 MASS SPECTROMETRY IN TRACE ORGANIC ANALYSIS Prepared for publication by KLAUS BIEMANN Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA *Membership of the Commission during the period (1985-89) when this report was prepared was as follows: Chairman: 1985-89 B. Griepink (Netherlands); Secretary: 1985-89 D. E. Wells (UK); Titular Members: K. Biemann (USA; 1985-89); W. H. Gries (FRG; 1987-89); E. Jackwerth (FRG; 1985-87); M. Leroy (France; 1987-89); A. Lamotte (France; 1985-87); Z. Marczenko (Poland; 1985-89); D. G. Westmoreland (USA; 1987-89); Yu. A. Zolotov (USSR; 1985-87); Associate Members: K. Ballschmiter (FRG; 1985-87); R. Dams (Belgium; 1985-89); K. Fuwa (Japan; 1985-89); M. Grasserbauer (Austria; 1985-87); W. H. Gries (FRG; 1985-87); M. W. Linscheid (FRG; 1985-89); M. Morita (Japan; 1987-89); M. Huntau (Italy; 1985-89); M. J. Pellin (USA; 1985-89); L. Reutergardh (Sweden; 1987-89); B. D. Sawicka (Canada; 1987-89); E. A. Schweikert (USA; 1987-89); G. Scilla (USA; 1987-89); B. Ya. Spivakov (USSR; 1985-89); A. Townshend (UK; 1985-87); W. Wegscheider (Austria; 1987-89); D. G. Westmoreland (USA; 1985-87); National Representatives: R. Gijbels (Belgium; 1985-89); Z.-M. Ni (Chinese Chemical Society; 1985-89); G. Werner (GDR; 1987-89); M. -
2Nd ANNUAL NORTH AMERICAN MASS SPECTROMETRY SUMMER SCHOOL
2nd ANNUAL NORTH AMERICAN MASS SPECTROMETRY SUMMER SCHOOL JULY 21-24, 2019 | MADISON, WISCONSIN Parabola of Neon (1913) Featured on the cover is an early 20th century parabola mass spectrograph. The early mass spectrometers, pioneered by J. J. Thomson, used electric and magnetic fields to disperse ion populations on photographic plates. Depending on their masses, the ions were dispersed along parabolic lines with those of the highest energy landing in the center and those with the least extending to the outermost edges. Positive ions are imaged on the upper half of the parabola while negative ions are deflected to the bottom half. Note that Ne produces two lines in the spectrum. Francis Aston, a former Thomson student, concluded from these data that stable elements also must have isotopes. These observations won Aston the Nobel Prize in Chemistry in 1922. Grayson, M.A. Measuring Mass: From Positive Rays to Proteins. 2002. Chemical Heritage Press, Philadelphia. Welcome to the 2nd Annual North American Mass Spectrometry Summer School We are proud to assemble world-leading experts in mass spectrometry for this second annual mass spectrometry summer school. We aim for you to experience an engaging and inspiring program covering the fundamentals of mass spectrometry and how to apply this tool to study biology. Also infused in the course are several workshops aimed to promote professional development. We encourage you to actively engage in discussion during all lectures, workshops, and events. This summer school is made possible through generous funding from the National Science Foundation (Plant Genome Research Program, Grant No. 1546742), the National Institutes of Health National Center for Quantitative Biology of Complex Systems (P41 GM108538), and the Morgridge Institute for Research. -
Focus on Proteomics in Honor of Ruedi Aebersold, 2002 Biemann Awardee
EDITORIAL Focus on Proteomics in Honor of Ruedi Aebersold, 2002 Biemann Awardee It is a pleasure to introduce this series of articles “Trypsin Catalyzed 16O-to-18O Exchange for Compara- honouring the achievements of Ruedi Aebersold, the tive Proteomics: Tandem Mass Spectrometry Compari- 2002 recipient of the ASMS Biemann Medal. During the son using MALDI-TOF, ESI-QTOF and ESI-Ion Trap last decade enormous progress has been made in the Mass Spectrometers” by Manfred Heller, Hassan Mat- application of mass spectrometry to proteomics, an area tou, Christoph Menzel, and Xudong Yao illustrates the to which Ruedi has contributed both generally and use of alternative labeling strategies involving 16Oto specifically with his isotope labelling strategies. In his 18O, in conjunction with enzymatic digestion for iden- opening Account and Perspective, “A Mass Spectromet- tifying proteins in human plasma. Of additional interest ric Journey into Protein and Proteome Research,” Ruedi in this article is the comparison of the many different poses the interesting question ‘does technology drive mass spectrometry platforms emerging for analysing biology or is the converse the case, where the biological such data including LC MALDI MS/MS approaches. question drives the technological development?’ This of Chromatographic separation is at the heart of many course remains an open question but the accompanying successful proteomic strategies, and an alternative ap- series of articles exemplify the tremendous synergy proach is exemplified by Figeys and colleagues in their between biology and methodological development. article, “On-line Strong Cation Exchange -HPLC-ESI- An important biological question prompts the first of MS/MS for Protein Identification and Process Optimi- the research articles; “Quantitative Proteomic Analysis zation.” Using a strong cation exchange micro LC of Chromatin-associated Factors” by Yuzuru Shiio, Eu- method for identification of proteins in mixtures, they gene C. -
Pittsburgh Conference
Journal of Automatic Chemistry, Vol. 16, No. 3 (May-June 1994), pp. 75-116 Abstracts of papers presented at the 1994 Pittsburgh Conference The following are the abstracts of the papers read at March 1994s Pittcon which are important to readers of 'Journal of Automatic Chemistry'. 1995s Pittcon will be held in New Orleans from 5 to 10 March. Details from The Pittsburgh Conference, 300 Penn Center Boulevard, Suite 332, Pittsburgh, PA 15235-5503, USA. Reflecting on the past; creating for the future interest in the determination of the structure of natural products. Therefore, no preconceived notions prevented Howard V. Malmstadt, University of the Nations, Kailua-Kona, him from applying mass spectrometry to the structure HI 96740 elucidation of new alkaloids, amino acids and peptides. A particularly field was the determination of Powerful and elegant analytical methods and instruments productive the structure of many indole alkaloids. By classical are used daily in industry, hospitals, R & D laboratories chemical methods this was difficult and very time and process control systems. Major improvements in but with the use of mass sensitivity, detectability, accuracy, speed and reliability consuming, spectrometry combined with a few chemical reactions, the task could provide the necessary data for dramatic breakthroughs in be accomplished quickly and with minimal material. science and technology. The speaker reflected on some of Thus, the early work brought mass spectrometry to the the developments on which he had helped pioneer. attention of the organic chemist. The story behind the story often starts with a simple In the 1960s, high resolution mass spectrometry was question or comment. -
Nature Milestones Mass Spectrometry October 2015
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. -
Aggregation, Dissemination, and Analysis of High- Throughput Scientific Data Sets in the Field of Proteomics
AGGREGATION, DISSEMINATION, AND ANALYSIS OF HIGH- THROUGHPUT SCIENTIFIC DATA SETS IN THE FIELD OF PROTEOMICS by Jayson A. Falkner A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Bioinformatics) in The University of Michigan 2008 Doctoral Committee Professor Philip C. Andrews, Chair Professor Daniel M. Burns Jr Assistant Professor Matthew A. Young Assistant Professor Alexey Nesvizhskii © Jayson A. Falkner 2008 I dedicate this to my parents and family for supporting me in pursuit of over-education to the fullest. Thankfully I've learned that academics, science, and the pursuit of intellect are of little to benefit an individual. Friends, family, and society give purpose to both work and life. One is not without the other. Thanks Mom and Dad. ii Acknowledgments Phil Andrews has been a constant source of ideas, enthusiasm, and support for my work. Pretty much every part of this thesis was inspired in one way or another by Phil, and I feel very fortunate to have had a mentor that wanted include me in most everything. Even sending me around the world for countless conferences, workshops, and meetings. I think that all mentors work in mysterious and unmeasurable ways, and I have been unbelievably lucky to have such a good mentor and friend. Pete Ulintz, Eric Simon, Anastasia Yocum, Bryan Smith, James “Augie” Hill, and the rest of Phil's lab have been great friends and contributed in many ways to my work. Dan Burns, David States, Brian Athey, Gil Omenn, Alexey Nesvizhskii, Matt Young, Heather Carlson, David Burke, and others in the program are all to thank for advice, guidance, and teaching me about what getting a PhD is really about. -
Original Filepdf
CHEMICAL HERITAGE FOUNDATION NICO M. NIBBERING Transcript of an Interview Conducted by Michael A. Grayson at Home of Michael Gross St. Louis Park, Minnesota on 7 and 8 June 2013 (With Subsequent Corrections and Additions) NICO M. NIBBERING ACKNOWLEDGMENT This oral history is one in a series initiated by the Chemical Heritage Foundation on behalf of the American Society for Mass Spectrometry. The series documents the personal perspectives of individuals related to the advancemen t of mass spectrometric instrumentation, and records the human dimensions of the growth of mass spectrometry in academic, industrial, and governmental laboratories during the twentieth century. This project is made possible through the generous support of the American Society for Mass Spectrometry This oral history is designated Free Access. Please note: Users citing this interview for purposes of publication are obliged under the terms of the Chemical Heritage Foundation (CHF) Center for Oral History to credit CHF using the format below: Nico M. Nibbering, interview by Michael A. Grayson at the home of Michael Gross St. Louis Park, Minnesota, 7 and 8 June 2013 (Philadelphia: Chemical Heritage Foundation, Oral History Transcript # 0709). Chemical Heritage Foundation Center for Oral History 315 Chestnut Street Philadelphia, Pennsylvania 19106 The Chemical Heritage Foundation (CHF) serves the community of the chemical and molecular sciences, and the wider public, by treasuring the past, educating the present, and inspiring the future. CHF maintains a world-class collection of materials that document the history and heritage of the chemical and molecular sciences, technologies, and industries; encourages research in CHF collections; and carries out a program of outreach and interpretation in order to advance an understanding of the role of the chemical and molecular sciences, technologies, and industries in shaping society. -
Ruedi Aebersold, Ph.D. Name
CURRICULUM VITAE Ruedi Aebersold, Ph.D. I. BIOGRAPHICAL DATA Name: Aebersold, Ruedi Current Position: Professor Place of Birth: Switzerland Date of Birth: September 12, 1954 Citizenship: Swiss, Canadian Curriculum Vitae – Ruedi Aebersold Page 2 of 50 II. EDUCATION Undergraduate: Biocenter, University of Basel, Switzerland. 1979 Diploma in Cellular Biology Graduate: Ph.D. in Cellular Biology, Biocenter, University of Basel, Switzerland, July 1983. Titles of theses written for graduate degrees: Diploma Thesis: Induction, expression and specificity of murine suppressor T-cells regulating antibody synthesis in vivo and in vitro . Supervisor: R.H. Gisler, Ph.D. Ph.D. Thesis: Structure-function relationships of hybridoma-derived monoclonal antibodies against streptococcal A group polysaccharide . Supervisor: Prof. D.G. Braun. III. Post-graduate training 1984-1986 Division of Biology, California Institute of Technology, Pasadena, CA. Postdoctoral Position. 1987-1988 Division of Biology, California Institute of Technology, Pasadena, CA. Senior Research Fellow IV. FACULTY POSITIONS 1989 -1993 Assistant Professor, Department of Biochemistry, University of British Columbia, Vancouver, B.C., Canada. 1993 -1998 Associate Professor, Department of Molecular Biotechnology, University of Washington, Seattle, WA 1998 - 2000 Professor, Department of Molecular Biotechnology, University of Washington, Seattle, WA 2000 - 2006 Affiliate Professor, Department of Molecular Biotechnology, University of Washington, Seattle, WA 2000 Co-Founder and Professor, -
Science History Institute Ronald D. Macfarlane
SCIENCE HISTORY INSTITUTE RONALD D. MACFARLANE Transcript of an Interview Conducted by Michael A. Grayson at Texas A&M University College Station, Texas on 26 May 2011 (With Subsequent Corrections and Additions) Ronald D. Macfarlane ACKNOWLEDGMENT This oral history is one in a series initiated by the Chemical Heritage Foundation on behalf of the American Society for Mass Spectrometry. The series documents the personal perspectives of individuals related to the advancement of mass spectrometric instrumentation, and records the human dimensions of the growth of mass spectrometry in academic, industrial, and governmental laboratories during the twentieth century. This project is made possible through the generous support of the American Society for Mass Spectrometry. This oral history is designated Free Access. Please note: Users citing this interview for purposes of publication are obliged under the terms of the Center for Oral History, Science History Institute, to credit the Science History Institute using the format below: Ronald D. MacFarlane, interview by Michael Grayson at Texas A&M University, College Station, Texas, 26 May 2011 (Philadelphia: Science History Institute, Oral History Transcript #0877). Formed by the merger of the Chemical Heritage Foundation and the Life Sciences Foundation, the Science History Institute collects and shares the stories of innovators and of discoveries that shape our lives. We preserve and interpret the history of chemistry, chemical engineering, and the life sciences. Headquartered in Philadelphia, with offices in California and Europe, the Institute houses an archive and a library for historians and researchers, a fellowship program for visiting scholars from around the globe, a community of researchers who examine historical and contemporary issues, and an acclaimed museum that is free and open to the public. -
Ronald A. Hites
RONALD A. HITES School of Public and Environmental Affairs Indiana University Bloomington, IN 47405 (812) 855-0193 [email protected] PROFESSIONAL EXPERIENCE Distinguished Professor, Indiana University, Bloomington, 1989-present Professor of Public and Environmental Affairs and of Chemistry, Indiana University, Bloomington, 1979-1989 Associate and Assistant Professor of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, 1972-1979 Research Staff, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, 1969-1972 National Academy of Sciences Postdoctoral Associate, Agricultural Research Service, Peoria, Illinois, 1968- 1969 EDUCATION Doctor of Philosophy in Analytical Chemistry, Massachusetts Institute of Technology, Cambridge, 1968; stud- ied with Professor Klaus Biemann (member of the National Academy of Sciences) Bachelor of Arts in Chemistry, Oakland University, Rochester, Michigan, 1964 HONORS (SELECTED) Lifetime Achievement Award, International Association for Great Lakes Research, 2016 “Ronald A. Hites Tribute Issue,” Environmental Science & Technology, 1 December 2015 Society of Environmental Toxicology and Chemistry Charter Fellow, 2014-present American Chemical Society Charter Fellow, 2009-present Ron Hites Award for an Outstanding Research Publication in the Journal of the American Society for Mass Spectrometry, named in Prof. Hites’ honor in November 2008 President, Board of Directors, International Association for Great Lakes Research, 2008-2009 Associate Editor, Environmental Science