Thomas O Metz

Thomas O Metz

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Thomas O Metz

Thomas O Metz

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Evaluation of Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples.

J Chem Inf Model 2019 Sep 20;59(9):4052-4060. Epub 2019 Aug 20.

Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States.

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http://dx.doi.org/10.1021/acs.jcim.9b00444DOI Listing
September 2019

The role of proteomics in assessing beta-cell dysfunction and death in type 1 diabetes.

Expert Rev Proteomics 2019 Jul 24;16(7):569-582. Epub 2019 Jun 24.

a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA.

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http://dx.doi.org/10.1080/14789450.2019.1634548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628911PMC
July 2019

Extending Classification Algorithms to Case-Control Studies.

Biomed Eng Comput Biol 2019 15;10:1179597219858954. Epub 2019 Jul 15.

Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.

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http://dx.doi.org/10.1177/1179597219858954DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6630079PMC
July 2019

ISiCLE: A Quantum Chemistry Pipeline for Establishing in Silico Collision Cross Section Libraries.

Anal Chem 2019 Apr 6;91(7):4346-4356. Epub 2019 Mar 6.

Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States.

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http://dx.doi.org/10.1021/acs.analchem.8b04567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6526953PMC
April 2019

P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data.

J Proteome Res 2019 Mar 6;18(3):1426-1432. Epub 2019 Feb 6.

Computing & Analytics Division , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99352 , United States.

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http://dx.doi.org/10.1021/acs.jproteome.8b00840DOI Listing
March 2019

Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards.

J Proteome Res 2019 Feb 19;18(2):694-699. Epub 2018 Dec 19.

Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States.

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http://dx.doi.org/10.1021/acs.jproteome.8b00688DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537873PMC
February 2019

Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease.

N Engl J Med 2018 11 10;379(22):2131-2139. Epub 2018 Oct 10.

From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.).

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http://www.nejm.org/doi/10.1056/NEJMoa1714458
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http://dx.doi.org/10.1056/NEJMoa1714458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6481166PMC
November 2018

Measurement of Fructose-Asparagine Concentrations in Human and Animal Foods.

J Agric Food Chem 2018 Jan 29;66(1):212-217. Epub 2017 Dec 29.

Department of Microbial Infection and Immunity, The Ohio State University , Columbus, Ohio 43210, United States.

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http://dx.doi.org/10.1021/acs.jafc.7b04237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6191295PMC
January 2018

Characterizing the lipid and metabolite changes associated with placental function and pregnancy complications using ion mobility spectrometry-mass spectrometry and mass spectrometry imaging.

Placenta 2017 12 29;60 Suppl 1:S67-S72. Epub 2017 Mar 29.

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.placenta.2017.03.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5620120PMC
December 2017

Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis.

Cell Host Microbe 2017 Dec 16;22(6):817-829.e8. Epub 2017 Nov 16.

Department of Pathobiological Sciences, University of Wisconsin - Madison (UW-Madison), Madison, WI 53706, USA; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science (IMS), University of Tokyo, Tokyo 108-8639, Japan; International Research Center for Infectious Diseases, IMS, University of Tokyo, Tokyo 108-8639, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2017.10.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5730472PMC
December 2017

Sexual dimorphism in the fetal cardiac response to maternal nutrient restriction.

J Mol Cell Cardiol 2017 07 19;108:181-193. Epub 2017 Jun 19.

Center for Pregnancy and Newborn Research, Department of Obstetrics and Gynecology, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA. Electronic address:

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http://dx.doi.org/10.1016/j.yjmcc.2017.06.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5548301PMC
July 2017

Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in .

MBio 2017 06 20;8(3). Epub 2017 Jun 20.

Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden

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http://dx.doi.org/10.1128/mBio.00857-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478895PMC
June 2017

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Authors:
Mingxun Wang Jeremy J Carver Vanessa V Phelan Laura M Sanchez Neha Garg Yao Peng Don Duy Nguyen Jeramie Watrous Clifford A Kapono Tal Luzzatto-Knaan Carla Porto Amina Bouslimani Alexey V Melnik Michael J Meehan Wei-Ting Liu Max Crüsemann Paul D Boudreau Eduardo Esquenazi Mario Sandoval-Calderón Roland D Kersten Laura A Pace Robert A Quinn Katherine R Duncan Cheng-Chih Hsu Dimitrios J Floros Ronnie G Gavilan Karin Kleigrewe Trent Northen Rachel J Dutton Delphine Parrot Erin E Carlson Bertrand Aigle Charlotte F Michelsen Lars Jelsbak Christian Sohlenkamp Pavel Pevzner Anna Edlund Jeffrey McLean Jörn Piel Brian T Murphy Lena Gerwick Chih-Chuang Liaw Yu-Liang Yang Hans-Ulrich Humpf Maria Maansson Robert A Keyzers Amy C Sims Andrew R Johnson Ashley M Sidebottom Brian E Sedio Andreas Klitgaard Charles B Larson Cristopher A Boya P Daniel Torres-Mendoza David J Gonzalez Denise B Silva Lucas M Marques Daniel P Demarque Egle Pociute Ellis C O'Neill Enora Briand Eric J N Helfrich Eve A Granatosky Evgenia Glukhov Florian Ryffel Hailey Houson Hosein Mohimani Jenan J Kharbush Yi Zeng Julia A Vorholt Kenji L Kurita Pep Charusanti Kerry L McPhail Kristian Fog Nielsen Lisa Vuong Maryam Elfeki Matthew F Traxler Niclas Engene Nobuhiro Koyama Oliver B Vining Ralph Baric Ricardo R Silva Samantha J Mascuch Sophie Tomasi Stefan Jenkins Venkat Macherla Thomas Hoffman Vinayak Agarwal Philip G Williams Jingqui Dai Ram Neupane Joshua Gurr Andrés M C Rodríguez Anne Lamsa Chen Zhang Kathleen Dorrestein Brendan M Duggan Jehad Almaliti Pierre-Marie Allard Prasad Phapale Louis-Felix Nothias Theodore Alexandrov Marc Litaudon Jean-Luc Wolfender Jennifer E Kyle Thomas O Metz Tyler Peryea Dac-Trung Nguyen Danielle VanLeer Paul Shinn Ajit Jadhav Rolf Müller Katrina M Waters Wenyuan Shi Xueting Liu Lixin Zhang Rob Knight Paul R Jensen Bernhard O Palsson Kit Pogliano Roger G Linington Marcelino Gutiérrez Norberto P Lopes William H Gerwick Bradley S Moore Pieter C Dorrestein Nuno Bandeira

Nat Biotechnol 2016 08;34(8):828-837

Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.

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http://dx.doi.org/10.1038/nbt.3597DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5321674PMC
August 2016

Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica.

BMC Genomics 2016 Feb 25;17:138. Epub 2016 Feb 25.

Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.

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http://dx.doi.org/10.1186/s12864-016-2471-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4766638PMC
February 2016

The succinated proteome.

Mass Spectrom Rev 2014 Mar-Apr;33(2):98-109. Epub 2013 Sep 30.

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.

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http://dx.doi.org/10.1002/mas.21382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4038156PMC
September 2014

The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation.

Environ Microbiol Rep 2014 Aug 27;6(4):389-95. Epub 2014 Apr 27.

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.

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http://dx.doi.org/10.1111/1758-2229.12163DOI Listing
August 2014

Decreased abundance of type III secretion system-inducing signals in Arabidopsis mkp1 enhances resistance against Pseudomonas syringae.

Proc Natl Acad Sci U S A 2014 May 21;111(18):6846-51. Epub 2014 Apr 21.

Division of Biochemistry, Christopher S. Bond Life Sciences Center, and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211.

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http://dx.doi.org/10.1073/pnas.1403248111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4020108PMC
May 2014

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data.

Bioinformatics 2013 Nov 23;29(22):2900-8. Epub 2013 Aug 23.

Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093-0412, USA and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt493DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810847PMC
November 2013

Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes.

J Exp Med 2013 Jan 31;210(1):191-203. Epub 2012 Dec 31.

Biological Sciences Division and the 2 Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA.

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http://dx.doi.org/10.1084/jem.20111843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549705PMC
January 2013

Dengue virus infection perturbs lipid homeostasis in infected mosquito cells.

PLoS Pathog 2012 22;8(3):e1002584. Epub 2012 Mar 22.

Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1002584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310792PMC
July 2012

Metabolomic response of human skin tissue to low dose ionizing radiation.

Mol Biosyst 2012 Jul 18;8(7):1979-86. Epub 2012 May 18.

Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, PO BOX 999, MSIN K8-98, Richland, WA 99352, USA.

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http://dx.doi.org/10.1039/c2mb25061fDOI Listing
July 2012

Technologies and approaches to elucidate and model the virulence program of salmonella.

Front Microbiol 2011 2;2:121. Epub 2011 Jun 2.

Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory Richland, WA, USA.

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http://dx.doi.org/10.3389/fmicb.2011.00121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108385PMC
July 2011

Separation and classification of lipids using differential ion mobility spectrometry.

J Am Soc Mass Spectrom 2011 Jul 12;22(7):1146-55. Epub 2011 Apr 12.

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.

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http://dx.doi.org/10.1007/s13361-011-0114-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187568PMC
July 2011

Performing comparative peptidomics analyses of Salmonella from different growth conditions.

Methods Mol Biol 2010 ;615:13-27

Pacific Northwest National Laboratory, Fundamental and Computational Sciences Directorate, Richland, WA, USA.

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http://dx.doi.org/10.1007/978-1-60761-535-4_2DOI Listing
February 2010

Improved methods for the enrichment and analysis of glycated peptides.

Anal Chem 2008 Dec;80(24):9822-9

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.

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http://dx.doi.org/10.1021/ac801704jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752342PMC
December 2008

Application of the accurate mass and time tag approach in studies of the human blood lipidome.

J Chromatogr B Analyt Technol Biomed Life Sci 2008 Aug 7;871(2):243-52. Epub 2008 May 7.

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.

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http://dx.doi.org/10.1016/j.jchromb.2008.04.040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2598838PMC
August 2008

Proteomic profiling of nonenzymatically glycated proteins in human plasma and erythrocyte membranes.

J Proteome Res 2008 May 9;7(5):2025-32. Epub 2008 Apr 9.

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.

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http://dx.doi.org/10.1021/pr700763rDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2731429PMC
May 2008

High Resolution Separations and Improved Ion Production and Transmission in Metabolomics.

Trends Analyt Chem 2008 Mar;27(3):205-214

Biological Sciences Division Pacific Northwest National Laboratory Richland, WA.

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http://dx.doi.org/10.1016/j.trac.2007.11.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2625305PMC
March 2008

Capillary LC coupled with high-mass measurement accuracy mass spectrometry for metabolic profiling.

Anal Chem 2007 Aug 18;79(16):6081-93. Epub 2007 Jul 18.

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.

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http://dx.doi.org/10.1021/ac070080qDOI Listing
August 2007

Enrichment and analysis of nonenzymatically glycated peptides: boronate affinity chromatography coupled with electron-transfer dissociation mass spectrometry.

J Proteome Res 2007 Jun 9;6(6):2323-30. Epub 2007 May 9.

Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.

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http://dx.doi.org/10.1021/pr070112qDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2587408PMC
June 2007

The future of liquid chromatography-mass spectrometry (LC-MS) in metabolic profiling and metabolomic studies for biomarker discovery.

Biomark Med 2007 Jun;1(1):159-185

Biological Science Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA.

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http://dx.doi.org/10.2217/17520363.1.1.159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631423PMC
June 2007