2Nd ANNUAL NORTH AMERICAN MASS SPECTROMETRY SUMMER SCHOOL
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Curriculum Vitae LINGJUN LI
Curriculum Vitae LINGJUN LI University of Wisconsin-Madison School of Pharmacy & Department of Chemistry 777 Highland Avenue Madison, WI 53705-2222 E-mail: [email protected] Phone : (608)265-8491 Fax : (608)262-5345 EDUCATION Ph.D. University of Illinois at Urbana-Champaign, 1995-2000 May 2000 Chemistry major (analytical and biomolecular) B.E. Beijing University of Technology, Beijing, China, 1987-1992 July 1992 Chemistry major (environmental analytical chemistry) EXPERTISE AND RESEARCH INTERESTS Bioanalytical chemistry, neurochemistry, biological mass spectrometry, neuropeptides, proteomics, peptidomics Research in my laboratory is focused on developing and implementing an array of novel mass spectrometry (MS) based methodologies to answer questions about the most complex and elusive set of signaling molecules, the neuropeptides, and gain new insights into the roles of peptide hormones and neurotransmitters play in the plasticity of neural circuits and behavior. Emphasis has been placed on constructing a multi-faceted and integrated platform that include high resolution in-situ peptide mapping, high sensitivity micro-separation techniques coupled with tandem MS de novo sequencing, isotopic labeling strategies, and new bioinformatics tools to allow large-scale discovery and functional analysis of novel neuropeptides. Furthermore, both mass spectrometric imaging technologies and in vivo microdialysis sampling tools have been implemented to follow neuropeptide distribution and secretion in unprecedented details. Towards the goal of -
©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 -
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. -
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. -
University of California, San Diego
UC San Diego UC San Diego Electronic Theses and Dissertations Title Novel proteomics methods for increased sensitivity, greater proteome coverage, and global profiling of endogenous SUMO modification sites Permalink https://escholarship.org/uc/item/4xq3v9wd Author Meyer, Jesse Gerard Publication Date 2015 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Novel proteomics methods for increased sensitivity, greater proteome coverage, and global profiling of endogenous SUMO modification sites A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Chemistry by Jesse Gerard Meyer Committee in charge: Professor Elizabeth A. Komives, Chair Professor Nuno Bandeira, Co-Chair Professor Jack Dixon Professor Randy Hampton Professor Judy Kim Professor Wei Wang 2015 Copyright Jesse Gerard Meyer, 2015 All rights reserved The dissertation of Jesse Gerard Meyer is approved, and it is acceptable in quality and form for publication on microfilm: Co-Chair Chair University of California, San Diego 2015 iii DEDICATION I dedicate this work to my family and friends. iv TABLE OF CONTENTS Signature Page…….……..………………………………………………………… iii Dedication……………………………………………………..…………………… iv Table of Contents………………………………………………………………... …v List of Abbreviations ……………………………………………………………… xi Lists of Figures……………………………………………….………….………… xiv Lists of Tables…………………………………………………...…….…………… xvii Acknowledgements………………………………………………………………… -
The Human Proteome
Vidal et al. Clinical Proteomics 2012, 9:6 http://www.clinicalproteomicsjournal.com/content/9/1/6 CLINICAL PROTEOMICS MEETING REPORT Open Access The human proteome – a scientific opportunity for transforming diagnostics, therapeutics, and healthcare Marc Vidal1, Daniel W Chan2, Mark Gerstein3, Matthias Mann4, Gilbert S Omenn5*, Danilo Tagle6, Salvatore Sechi7* and Workshop Participants Abstract A National Institutes of Health (NIH) workshop was convened in Bethesda, MD on September 26–27, 2011, with representative scientific leaders in the field of proteomics and its applications to clinical settings. The main purpose of this workshop was to articulate ways in which the biomedical research community can capitalize on recent technology advances and synergize with ongoing efforts to advance the field of human proteomics. This executive summary and the following full report describe the main discussions and outcomes of the workshop. Executive summary human proteome, including the antibody-based Human A National Institutes of Health (NIH) workshop was Protein Atlas, the NIH Common Fund Protein Capture convened in Bethesda, MD on September 26–27, 2011, Reagents, the mass spectrometry-based Peptide Atlas with representative scientific leaders in the field of pro- and Selected Reaction Monitoring (SRM) Atlas, and the teomics and its applications to clinical settings. The main Human Proteome Project organized by the Human purpose of this workshop was to articulate ways in which Proteome Organization. Several leading laboratories the biomedical research community can capitalize on re- have demonstrated that about 10,000 protein products, cent technology advances and synergize with ongoing of the about 20,000 protein-coding human genes, can efforts to advance the field of human proteomics. -
Top-Down Proteomics: Applications, Recent Developments and Perspectives
JOURNAL OF APPLIED BIOANALYSIS, Apr. 2016, p. 52-75. http://dx.doi.org/10.17145/jab.16.009 Vol. 2, No. 2 REVIEW Top-down proteomics: applications, recent developments and perspectives Annapurna Pamreddy1, Nagender Reddy Panyala2,* 1Department of chemistry, Masaryk University, Brno, Czech Republic, 2Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA (Received: 30 December 2015, Revised 22 March 2016, Accepted 4 April 2016 ) Now-a-days, top-down proteomics (TDP) is a booming approach for the analysis of intact pro- teins and it is attaining significant interest in the field of protein biology. The term has emerged as an alternative to the well-established, bottom-up strategies for analysis of peptide fragments de- rived from either enzymatically or chemically digestion of intact proteins. TDP is applied to mass spectrometric analysis of intact large biomolecules that are constituents of protein complexes and assemblies. This article delivers an overview of the methodologies in top-down mass spec- trometry, mass spectrometry instrumentation and an extensive review of applications covering the venomics, biomedical research, protein biology including the analysis of protein post-transla- tional modifications (PTMs), protein biophysics, and protein complexes. In addition, limitations of top-down proteomics, challenges and future directions of TDP are also discussed. Keywords: Top-down, protein biology, mass spectrometry, fragmentation techniques, data analysis. Introduction specificity at the expense of far higher experimental re- In recent years the mass spectrometry (MS) ionization quirements by directly introducing the proteins into the techniques such as ESI [1] and MALDI [2] have been mass spectrometer. The top-down method is being de- applied for the detection of a wide variety of large bio- veloped progressively in specific applications, with 18% polymers, such as proteins [3,4], lipids, and nucleic ac- of proteomics papers/posters at the 2007 meetings of ids. -
Abstract Book
ABSTRACT BOOK 16th ANNUAL US HUPO Conference Novel Proteomic Perspectives on Aging, Cancer and Disease March 8–11, 2020 The Westin Seattle, Seattle Washington, USA 16th Annual US HUPO Conference The Co-chairs would like to express their sincere gratitude to the following sponsors for their generous financial support: PLATINUM SPONSORS ADDITIONAL SUPPORT *Funding for this conference was made possible (in part) by 1R13CA250291-01 from the National Cancer Institute. The views expressed in written conference materials or publications and by speakers and moderators do not necessarily reflect the official policies of the Department of Health and Human Services; nor does mention by trade names, commercial practices, or organizations imply endorsement by the U.S. Government. Bruker at US HUPO timsTOF Pro and PASEF The New Standard for Shotgun Proteomics timsTOF Pro with PASEF technology delivers revolutionary improvements in scan speed, coupled with enhanced specificity and high sensitivity. Near 100% duty cycle using dual TIMS technology Unrivalled MS/MS speed >100Hz Discover more proteins using PASEF Meet the Experts Booth #204 Bruker Lunch Seminar Monday, March 9th, 12:15pm – 1:30pm; Cascade Room #2 diaPASEF: combining improved ion usage efficiency with data independent acquisition to quantify proteomes Dr. Ben Collins, Reader in the School of Biological Sciences at Queen’s University Belfast Building protein interaction networks to understand KRAS lung cancer Dr. Peter Jackson, Professor, Stanford University School of Medicine Register here -
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. -
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, -
Investigating Alternative Informatics Approaches for Protein Identification and Quantification Via SWATH-MS
Investigating alternative informatics approaches for protein identification and quantification via SWATH-MS A thesis submitted to the University of Manchester for the degree of Master of Philosophy in the Faculty of Biology, Medicine and Health 2020 Paul Brack School of Biological Sciences / Division of Evolution & Genomic Sciences Contents Index of figures and tables ...................................................................................................................... 4 Abstract ................................................................................................................................................... 6 Copyright statement................................................................................................................................... 7 Declaration .............................................................................................................................................. 7 Chapter 1: The path towards rapid, high resolution acquisition and analysis of the human proteome for biomarker discovery ................................................................................................................................... 8 Introduction ............................................................................................................................................ 8 Background: from genes to protein biomarkers ................................................................................... 11 Lessons from genomics ....................................................................................................................