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Petroleomics
Petroleomics A barrel load of compounds As the world’s petroleum supply dries up, Phillip Broadwith goes hunting for oil armed with a mass spectrometer, a chromatography column and state-of-the-art data-mining software THINKSTOCK 46 | Chemistry World | May 2010 www.chemistryworld.org Petroleum, or crude oil, is one by 0.0005Da – about the mass of an biggest FT-ICR spectrometer In short of the most complex naturally electron. has a 14.5 Tesla superconducting occurring chemical mixtures on Rodgers explains why FT-ICR Oil companies are magnet, but they are expecting a the planet. Each drop can contain MS has the upper hand when it looking to oil shale and 21T machine to come online later hundreds of thousands of different comes to resolution: it’s down to tar sands, as supplies of this year. To put that in perspective, types of molecules, from simple the magnets. The magnet separates lightweight oils run low a fridge magnet has a field of hydrocarbons to highly structurally ions of different masses within the Oil is a very complex about 0.1T and a 500MHz NMR diverse carboxylic acids, sulfur and spectrometer – charged particles mixture of molecules, spectrometer’s magnet comes in at nitrogen heterocycles and metal in electromagnetic fields start to and mass spectrometry is just under 12T. ‘What we’ve found salts. whirl around, and the frequency of used to reveal these and is that you can never have enough Some of these compounds this spinning depends on both the assess the suitability of resolution,’ says Rodgers. ‘As you go – like the hydrocarbons – are mass of the ion and the strength of new oil supplies higher and higher you can see more relatively chemically benign, but the magnetic field. -
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 -
Novel Quadrupole Time-Of-Flight Mass Spectrometry for Shotgun Proteomics
DISSERTATION ZUR ERLANGUNG DES DOKTORGRADES DER FAKULTÄT FÜR CHEMIE UND PHARMAZIE DER LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Novel quadrupole time-of-flight mass spectrometry for shotgun proteomics von Scarlet Svenja Anna-Maria Beck aus Tettnang 2016 ii Erklärung Diese Dissertation wurde im Sinne von §7 der Promotionsordnung vom 28. November 2011 von Herrn Prof. Dr. Matthias Mann betreut. Eidesstattliche Versicherung Diese Dissertation wurde eigenständig und ohne unerlaubte Hilfe erarbeitet. München, den 25.04.2017 …………………………………………………………………………………………Scarlet Beck Dissertation eingereicht am 23.09.2016 1. Gutachter: Prof. Dr. Matthias Mann 2. Gutachter: Prof. Dr. Jürgen Cox Mündliche Prüfung am 04.11.2016 iii iv ABSTRACT Mass spectrometry (MS)-based proteomics has become a powerful technology for the identification and quantification of thousands of proteins. However, the coverage of complete proteomes is still very challenging due to the high sample complexity and the difference in protein concentrations. In data-dependent shotgun proteomics several peptides elute simultaneously from the column and are isolated by the quadrupole and fragmented by the collision cell one at a time. This method has two major disadvantages. On the one hand, a large number of eluting peptides cannot be targeted since the sequencing speeds of current instruments are too slow and on the other hand, peptides that only differ slightly in mass and elute together are co-isolated and co-fragmented, resulting in chimeric MS2 spectra. Therefore an urgent need for further developments and improvements of mass spectrometers remains. The aim of this thesis was to co-develop, evaluate and improve novel quadrupole time-of-flight (QTOF) mass spectrometers. In my first project I have described the developments and improvements of the hardware of the high-resolution QTOF mass spectrometer, the impact II, and have shown that this instrument can be used for very deep coverage of diverse proteomes as well as for accurate and reproducible quantification. -
Classifying Petroleum Samples with Waters SYNAPT HDMS and Omics
Classifying Petroleum Samples with Waters SYNAPT HDMS and Omics LLC PetroOrg Petroleomics Software Combines the value of Ion Mobility Mass Spectrometry (IM-MS) and accurate mass information with petroleomics data processing to easily characterize petroleum chemical composition ECONOMIC VALUE AND CHEMICAL COMPOSITION OF CRUDE OIL Benefits of using Waters The chemical composition of petroleum determines its economic value. Especially important SYNAPT HDMS and PetroOrg to economic value is the proportion of heteroatoms in crude oil, particularly molecules Petroleomics Software containing nitrogen, sulfur, and oxygen because these species contribute to solid deposition, ■■ Ion mobility in Waters SYNAPT flocculation, catalyst deactivation, storage instability, and refinery corrosion. Light sweet HDMS delivers enhanced crude are low in these heteroatoms, but the world supply of light sweet crude is diminishing, sample deconvolution thus resulting in a world-wide shift to heavier crudes that are rich in heteroatoms. Energy ■■ Easily classify petroleum samples companies seek better analytical methodologies to determine crude oil’s economic value using petroleomics methodology and the level of refining required in order to produce high-value products. and diagrams Analytical Characterization of Crude Oil ■■ Determining heteroatom Mass spectrometric analysis of petroleum is an attractive approach to fully characterizing composition of petroleum samples crude oils, including categorizing crude oil samples by their heteroatom content. Some aids in determining economic value of the earliest innovations in mass spectrometry were directed towards the petroleum ■■ Complementary to GC-MS and NMR industry. However, the extremely high complexity of crude oils offers a significant analyses of petroleum samples challenge to the analytical chemist. Added to that challenge is the difficulty of processing, ■■ The combination of Ion Mobility, visualizing, and interpreting the information rich mass spectral data. -
Yale School of Public Health Symposium on Lifetime Exposures and Human Health: the Exposome; Summary and Future Reflections Caroline H
Yale school of public health symposium on lifetime exposures and human health: the exposome; summary and future reflections Caroline H. Johnson, Yale School of Public Health Toby J. Athersuch, Imperial College London Gwen W. Collman, National Institutes of Health Suraj Dhungana, Waters Corporation David F. Grant, University of Connecticut Dean Jones, Emory University Chirag J. Patel, Harvard Medical School Vasilis Vasiliou, Yale School of Public Health Publisher: Biomed Central LTD Publication Date: 2017-12-08 Type of Work: Report Publisher DOI: 10.1186/s40246-017-0128-0 Permanent URL: https://pid.emory.edu/ark:/25593/s6w0w Final published version: http://dx.doi.org/10.1186/s40246-017-0128-0 Copyright information: © 2017 The Author(s). This is an Open Access work distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/). Accessed October 1, 2021 10:15 AM EDT Johnson et al. Human Genomics (2017) 11:32 DOI 10.1186/s40246-017-0128-0 MEETING REPORT Open Access Yale school of public health symposium on lifetime exposures and human health: the exposome; summary and future reflections Caroline H. Johnson1*, Toby J. Athersuch2,3, Gwen W. Collman4, Suraj Dhungana5, David F. Grant6, Dean P. Jones7, Chirag J. Patel8 and Vasilis Vasiliou1* Abstract The exposome is defined as “the totality of environmental exposures encountered from birth to death” and was developed to address the need for comprehensive environmental exposure assessment to better understand disease etiology. Due to the complexity of the exposome, significant efforts have been made to develop technologies for longitudinal, internal and external exposure monitoring, and bioinformatics to integrate and analyze datasets generated. -
Download on the Rawtools
PARSING AND ANALYSIS OF MASS SPECTROMETRY DATA OF COMPLEX BIOLOGICAL AND ENVIRONMENTAL MIXTURES by Kevin Kovalchik B.S., Oregon State University, 2014 B.M., The University of Idaho, 2007 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (CHEMISTRY) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) August 2019 © Kevin Kovalchik, 2019 The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, the dissertation entitled: PARSING AND ANALYSIS OF MASS SPECTROMETRY DATA OF COMPLEX BIOLOGICAL AND ENVIRONMENTAL MIXTURES submitted by Kevin A Kovalchik in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemistry Examining Committee: David DY Chen Co-supervisor John V Headley Co-supervisor Roman Krems Supervisory Committee Member Ed Grant University Examiner Keng Chou University Examiner ii Abstract The chemical characterization of biological and environmental samples are areas of research which involve the analysis of highly complex chemical mixtures. While the samples from these two fields differ greatly in composition, they present similar challenges. Complex mixtures provide a challenge to the analytical chemist as compounds in the mixture can have matrix effects which interfere with the analysis. Indeed, these interfering compounds may even be analytes themselves. High resolution mass spectrometry, which separates and detects ions based on their mass-to-charge ratio, is a powerful tool in the analysis of such mixtures. The amount of data resulting from such analyses, however, can be intractable to manual analysis, necessitating the use of computational tools. -
The 12Th North American FT MS Conference Program
Florida State University 1800 East Paul Dirac Drive Tallahassee, Florida 32310 nationalmaglab.org 10 April 2019 Colleagues, On behalf of the National High Magnetic Field Laboratory and Florida State University, we welcome you to the 12th North American FT MS Conference! We hope that your stay in Key West is both personally and professionally rewarding. Topics span a broad range of techniques and applications. Posters will remain up throughout the meeting, to encourage discussions. The primary effort for organizing the conference has been provided by the conference coordinator, Karol Bickett. She has done an excellent job with the many required logistical and personal arrangements. Should you need any assistance or have any issues that need to be resolved while at the conference, please see Karol at the registration table so that we can insure that your experience at this conference is a most enjoyable one. Your registration fee covers only a portion of the expenses of the conference. The generous contributions of our sponsors have kept the meeting costs affordable for participants, and made it possible for us to assist with the expenses of the invited speakers and the graduate student poster presenters. Please take an opportunity to thank our participating sponsors at their display tables. Thank you for joining us, and we look forward to a splendid conference! Sincerely, Christopher Hendrickson Director, Ion Cyclotron Resonance Program, NHMFL Christopher Hendrickson, Director, ICR Program 850.644.0711 | [email protected] Operated -
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. -
УДК 624.9 PETROLEOMICS Kazarian MV Scientific Supervisor
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Siberian Federal University Digital Repository УДК 624.9 PETROLEOMICS Kazarian M.V. Scientific supervisor: candidate of chemical science Orlovskaya N. F. Scientific instructor: lecturer Tsigankova Е.V. Siberian Federal University 1 What is the meaning of "petroleomics"? Prof. O. Mallinz (Schlumberger, 2007) introduced the concept of petroleomike as a new scientific direction in the study of petroleum systems, which by analogy with genomics in biology, is based on the concept of the development in each oil distribution system unique continuous series of different size and solubility of resin-asphaltene components in the hydrocarbon matrix. Petroleomics is a new field in petroleum chemistry engineering I am launching through my publication. "To understand function, study structure," said Francis Crick, Nobel Prize winner for revealing the chemical structure of DNA, a discovery that led to genomics. We envision petroleomics being to petroleum science what genomics is to medical science. In short, medicine traditionally treats patients based on symptoms, and the vision of genomics is to predict and treat medical concerns even before symptoms appear. Petroleum science has, similarly, been phenomenological. Establishing structure-function relationships has been precluded in petroleum science because nobody knew the petroleum chemical structure. This is all about to change. Petroleomics promises the ability to predict petroleum properties based on the foundation of elucidating the chemistry of all constituents in a crude oil. In addition, it is necessary to get information concerning Downhole Fluid Analysis in order to exploit petroleum chemistry to understand reservoir architecture. -
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.