Pyopenms: a Python-Based Interface to the Openms Mass-Spectrometry Algorithm Library
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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 -
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. -
Introduction to Label-Free Quantification
SeqAn and OpenMS Integration Workshop Temesgen Dadi, Julianus Pfeuffer, Alexander Fillbrunn The Center for Integrative Bioinformatics (CIBI) Mass-spectrometry data analysis in KNIME Julianus Pfeuffer, Alexander Fillbrunn OpenMS • OpenMS – an open-source C++ framework for computational mass spectrometry • Jointly developed at ETH Zürich, FU Berlin, University of Tübingen • Open source: BSD 3-clause license • Portable: available on Windows, OSX, Linux • Vendor-independent: supports all standard formats and vendor-formats through proteowizard • OpenMS TOPP tools – The OpenMS Proteomics Pipeline tools – Building blocks: One application for each analysis step – All applications share identical user interfaces – Uses PSI standard formats • Can be integrated in various workflow systems – Galaxy – WS-PGRADE/gUSE – KNIME Kohlbacher et al., Bioinformatics (2007), 23:e191 OpenMS Tools in KNIME • Wrapping of OpenMS tools in KNIME via GenericKNIMENodes (GKN) • Every tool writes its CommonToolDescription (CTD) via its command line parser • GKN generates Java source code for nodes to show up in KNIME • Wraps C++ executables and provides file handling nodes Installation of the OpenMS plugin • Community-contributions update site (stable & trunk) – Bioinformatics & NGS • provides > 180 OpenMS TOPP tools as Community nodes – SILAC, iTRAQ, TMT, label-free, SWATH, SIP, … – Search engines: OMSSA, MASCOT, X!TANDEM, MSGFplus, … – Protein inference: FIDO Data Flow in Shotgun Proteomics Sample HPLC/MS Raw Data 100 GB Sig. Proc. Peak 50 MB Maps Data Reduction 1 -
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. -
Openms – a Framework for Computational Mass Spectrometry
OpenMS { A framework for computational mass spectrometry Dissertation der Fakult¨atf¨urInformations- und Kognitionswissenschaften der Eberhard-Karls-Universit¨atT¨ubingen zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) vorgelegt von Dipl.-Inform. Marc Sturm aus Saarbr¨ucken T¨ubingen 2010 Tag der m¨undlichen Qualifikation: 07.07.2010 Dekan: Prof. Dr. Oliver Kohlbacher 1. Berichterstatter: Prof. Dr. Oliver Kohlbacher 2. Berichterstatter: Prof. Dr. Knut Reinert Acknowledgments I am tremendously thankful to Oliver Kohlbacher, who aroused my interest in the field of computational proteomics and gave me the opportunity to write this thesis. Our discussions where always fruitful|no matter if scientific or technical. Furthermore, he provided an enjoyable working environment for me and all the other staff of the working group. OpenMS would not have been possible without the joint effort of many people. My thanks go to all core developers and students who contributed to OpenMS and suffered from the pedantic testing rules. I especially thank Eva Lange, Andreas Bertsch, Chris Bielow and Clemens Gr¨oplfor the tight cooperation and nice evenings together. Of course, I'm especially grateful to my parents and family for their support through- out my whole life. Finally, I thank Bettina for her patience and understanding while I wrote this thesis. iii Abstract Mass spectrometry coupled to liquid chromatography (LC-MS) is an analytical technique becoming increasingly popular in biomedical research. Especially in high-throughput proteomics and metabolomics mass spectrometry is widely used because it provides both qualitative and quantitative information about analytes. The standard protocol is that complex analyte mixtures are first separated in liquid chromatography and then analyzed using mass spectrometry. -
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. -
June 5, 2017 Bioinformatics MS Interest Group Your Hosts
Open Source Software Packages: Using and Making your conbributions June 5, 2017 Bioinformatics MS Interest Group Your hosts Meena Choi Samuel Payne Post doc. Scientist Northeastern University Pacific Northwest National Lab Statistical methods for Integrative Omics quantitative proteomics Outline • General Intro – Meena Choi • mzRefinery/proteowizard - Sam Payne • openMS - Oliver Kohlbacher • Skyline - Brendan MacLean • General discussion on open source • Ask questions for the General Discussion http://bit.ly/2qNZVBU • Shout-out for Open Source tool http://bit.ly/2qVHVo7 Oliver Kohlbacher • The chair of Applied Bioinformatics at University of Tübingen & fellow at the Max Plank Institute • OpenMS ( openms.de ) Brendan MacLean • Principal developer for Skyline ( skyline.ms ) • University of Washington Ask questions or comments : http://bit.ly/2qNZVBU • Why have open source? • What are the advantages and disadvantages between open source and private closed-source software? • How should a developer consider the question of making a project open source or not? • What is appropriate level of guide/documentation to help new developers? • How to incentivize people to contribute to open source software? Bioconductor.org biocViews search R package development • Provide the framework for developing package : basic structure, requirements… • Requirements : 1. pass check or BiocCheck on all supported platforms (their own checking system) 2. Documents • DESCRIPTION, NAMESPACE, vignette, help file, NEWS 3. Review process (2-5 weeks) • submit a GitHub repository • a reviewer will be assigned and a detailed package review is returned. • the process is repeated until the package is accepted to Bioconductor. • Maintaining the packages across release cycles (twice a year) + deprecate packages • Import or depend on other packages in Bioconductor or CRAN R package as software • Easy to make open source software for new method development. -
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 .................................................................................................................... -
Dissertation / Doctoral Thesis
DISSERTATION / DOCTORAL THESIS Titel der Dissertation /Title of the Doctoral Thesis „Proteomic studies on Chlamydomonas reinhardtii“ verfasst von / submitted by Dipl.-Biochem. Luis Recuenco-Muñoz angestrebter akademischer Grad / in partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) Wien, 2017 / Vienna 2017 Studienkennzahl lt. Studienblatt / A 794 685 437 degree programme code as it appears on the student record sheet: Dissertationsgebiet lt. Studienblatt / Biologie field of study as it appears on the student record sheet: Betreut von / Supervisors: Univ.-Prof. Dr. Wolfram Weckwerth Ass.-Prof. Dipl.-Biol. Dr. Stefanie Wienkoop, Privatdoz. 2 Declaration of authorship I, Luis Recuenco-Muñoz, declare that this thesis, titled ‘Proteomic studies on Chlamydomonas reinhardtii’ and the work presented in it are my own. I confirm that: • This work was done wholly or mainly while in candidature for a research degree at this University. • Where I have consulted the published work of others, this is always clearly attributed. • Where I have quoted from the work of others, the source is always given. With the exception of such quotations, this thesis is entirely my own work. • I have acknowledged all main sources of help. • Where the thesis is based on work done by myself jointly with others, I have made clear exactly what was done by others and what I have contributed myself. Signed: Date: 3 4 Equal goes it loose (Ernst Goyke) 5 Aknowledgements • I wish to thank Prof. Dr. Wolfram Weckwerth and Dr. habil. Stefanie Wienkoop for giving me the chance to work in this utterly interesting field, tutoring and mentoring me throughout my PhD Thesis, and for all the teaching, support, advice and fun I have had both on a working and on a personal level during my whole stint in Vienna.