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1
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Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC. Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation. Nat Biotechnol 2023; 41:1656. [PMID: 37853256 DOI: 10.1038/s41587-023-02025-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Affiliation(s)
- Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kiana A West
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Wout Bittremieux
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Candace L Williams
- Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Francesca Di Ottavio
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth Brown
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nicole C Sikora
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Cameron Martino
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Anupriya Tripathi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Roxana Coras
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Tara Schwartz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - MacKenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gregory Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Abigail J Johnson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Katharina Spengler
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Edgar Diaz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Emmanuel O Elijah
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kate E Sprecher
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
- Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniela Vargas-Robles
- Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, Puerto Ayacucho, Amazonas, Venezuela
| | - Dana Withrow
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lourdes Herrera
- Department of Pediatrics, Billings Clinic, Billings, MT, USA
| | - Barry J Bradford
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Lucas Maciel Mauriz Marques
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Juliano Geraldo Amaral
- Multidisciplinary Health Institute, Federal University of Bahia, Vitória da Conquista, Bahia, Brazil
| | - Rodrigo Moreira Silva
- NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Flavio Protasio Veras
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Thiago Mattar Cunha
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Rene Donizeti Ribeiro Oliveira
- Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Paulo Louzada-Junior
- Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Robert H Mills
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Paulina K Piotrowski
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Stephanie L Servetas
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Sandra M Da Silva
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Christina M Jones
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nancy J Lin
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Katrice A Lippa
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Scott A Jackson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Rima Kaddurah Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC, USA
| | - Douglas Galasko
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Parambir S Dulai
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Curt Wittenberg
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Robert Terkeltaub
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- San Diego VA Healthcare System, San Diego, CA, USA
| | - Megan M Doty
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Division of Neonatology, Department of Pediatrics, Kapi'olani Medical Center for Women and Children, John A. Burns School of Medicine, Honolulu, Hawaii, USA
| | - Jae H Kim
- Division of Neonatology, Perinatal Institute, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kyung E Rhee
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Julia Beauchamp-Walters
- Division of Pediatric Hospital Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kenneth P Wright
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Mark Manary
- Department of Pediatrics, Washington University, St. Louis, MO, USA
| | - Michelli F Oliveira
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Norberto Peporine Lopes
- NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Monica Guma
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
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Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC. Enhancing untargeted metabolomics using metadata-based source annotation. Nat Biotechnol 2022; 40:1774-1779. [PMID: 35798960 PMCID: PMC10277029 DOI: 10.1038/s41587-022-01368-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 05/20/2022] [Indexed: 01/30/2023]
Abstract
Human untargeted metabolomics studies annotate only ~10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS/MS reference library. Applying this approach to food source data, we show that it increases MS/MS spectral usage 5.1-fold over conventional structural MS/MS library matches and allows empirical assessment of dietary patterns from untargeted data.
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Affiliation(s)
- Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kiana A West
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Wout Bittremieux
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Candace L Williams
- Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Francesca Di Ottavio
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth Brown
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nicole C Sikora
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Cameron Martino
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Anupriya Tripathi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Roxana Coras
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Tara Schwartz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - MacKenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gregory Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Abigail J Johnson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Katharina Spengler
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Edgar Diaz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Emmanuel O Elijah
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kate E Sprecher
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
- Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniela Vargas-Robles
- Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, Puerto Ayacucho, Amazonas, Venezuela
| | - Dana Withrow
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lourdes Herrera
- Department of Pediatrics, Billings Clinic, Billings, MT, USA
| | - Barry J Bradford
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Lucas Maciel Mauriz Marques
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Juliano Geraldo Amaral
- Multidisciplinary Health Institute, Federal University of Bahia, Vitória da Conquista, Bahia, Brazil
| | - Rodrigo Moreira Silva
- NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Flavio Protasio Veras
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Thiago Mattar Cunha
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Rene Donizeti Ribeiro Oliveira
- Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Paulo Louzada-Junior
- Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Robert H Mills
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Paulina K Piotrowski
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Stephanie L Servetas
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Sandra M Da Silva
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Christina M Jones
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nancy J Lin
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Katrice A Lippa
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Scott A Jackson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Rima Kaddurah Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC, USA
| | - Douglas Galasko
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Parambir S Dulai
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Curt Wittenberg
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Robert Terkeltaub
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- San Diego VA Healthcare System, San Diego, CA, USA
| | - Megan M Doty
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Division of Neonatology, Department of Pediatrics, Kapi'olani Medical Center for Women and Children, John A. Burns School of Medicine, Honolulu, Hawaii, USA
| | - Jae H Kim
- Division of Neonatology, Perinatal Institute, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kyung E Rhee
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Julia Beauchamp-Walters
- Division of Pediatric Hospital Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kenneth P Wright
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Mark Manary
- Department of Pediatrics, Washington University, St. Louis, MO, USA
| | - Michelli F Oliveira
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Norberto Peporine Lopes
- NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Monica Guma
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
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3
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Lippa KA, Aristizabal-Henao JJ, Beger RD, Bowden JA, Broeckling C, Beecher C, Clay Davis W, Dunn WB, Flores R, Goodacre R, Gouveia GJ, Harms AC, Hartung T, Jones CM, Lewis MR, Ntai I, Percy AJ, Raftery D, Schock TB, Sun J, Theodoridis G, Tayyari F, Torta F, Ulmer CZ, Wilson I, Ubhi BK. Reference materials for MS-based untargeted metabolomics and lipidomics: a review by the metabolomics quality assurance and quality control consortium (mQACC). Metabolomics 2022; 18:24. [PMID: 35397018 PMCID: PMC8994740 DOI: 10.1007/s11306-021-01848-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/07/2021] [Indexed: 12/17/2022]
Abstract
INTRODUCTION The metabolomics quality assurance and quality control consortium (mQACC) is enabling the identification, development, prioritization, and promotion of suitable reference materials (RMs) to be used in quality assurance (QA) and quality control (QC) for untargeted metabolomics research. OBJECTIVES This review aims to highlight current RMs, and methodologies used within untargeted metabolomics and lipidomics communities to ensure standardization of results obtained from data analysis, interpretation and cross-study, and cross-laboratory comparisons. The essence of the aims is also applicable to other 'omics areas that generate high dimensional data. RESULTS The potential for game-changing biochemical discoveries through mass spectrometry-based (MS) untargeted metabolomics and lipidomics are predicated on the evolution of more confident qualitative (and eventually quantitative) results from research laboratories. RMs are thus critical QC tools to be able to assure standardization, comparability, repeatability and reproducibility for untargeted data analysis, interpretation, to compare data within and across studies and across multiple laboratories. Standard operating procedures (SOPs) that promote, describe and exemplify the use of RMs will also improve QC for the metabolomics and lipidomics communities. CONCLUSIONS The application of RMs described in this review may significantly improve data quality to support metabolomics and lipidomics research. The continued development and deployment of new RMs, together with interlaboratory studies and educational outreach and training, will further promote sound QA practices in the community.
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Affiliation(s)
- Katrice A Lippa
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD, 20899, USA
| | - Juan J Aristizabal-Henao
- Department of Physiological Sciences, Center for Environmental and Human Toxicology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
- BERG LLC, 500 Old Connecticut Path, Building B, 3rd Floor, Framingham, MA, 01710, USA
| | - Richard D Beger
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, AR, 72079, USA
| | - John A Bowden
- Department of Physiological Sciences, Center for Environmental and Human Toxicology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Corey Broeckling
- Analytical Resources Core: Bioanalysis and Omics Center, Colorado State University, Fort Collins, CO, 80523, USA
| | | | - W Clay Davis
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Charleston, SC, 29412, USA
| | - Warwick B Dunn
- School of Biosciences, Institute of Metabolism and Systems Research and Phenome Centre Birmingham, University of Birmingham, Birmingham, B15, 2TT, UK
| | - Roberto Flores
- Division of Program Coordination, Planning and Strategic Initiatives, Office of Nutrition Research, Office of the Director, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, BioSciences Building, Crown St., Liverpool, L69 7ZB, UK
| | - Gonçalo J Gouveia
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Amy C Harms
- Biomedical Metabolomics Facility Leiden, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Thomas Hartung
- Bloomberg School of Public Health, Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Christina M Jones
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD, 20899, USA
| | - Matthew R Lewis
- National Phenome Centre, Imperial College London, London, SW7 2AZ, UK
| | - Ioanna Ntai
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | - Andrew J Percy
- Cambridge Isotope Laboratories, Inc., Tewksbury, MA, 01876, USA
| | - Dan Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, 98109, USA
| | - Tracey B Schock
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Charleston, SC, 29412, USA
| | - Jinchun Sun
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, AR, 72079, USA
| | | | - Fariba Tayyari
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Federico Torta
- Centre for Life Sciences, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Candice Z Ulmer
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, 30341, USA
| | - Ian Wilson
- Computational & Systems Medicine, Imperial College, Exhibition Rd, London, SW7 2AZ, UK
| | - Baljit K Ubhi
- MOBILion Systems Inc., 4 Hillman Drive Suite 130, Chadds Ford, PA, 19317, USA.
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Mandal R, Cano R, Davis CD, Hayashi D, Jackson SA, Jones CM, Lampe JW, Latulippe ME, Lin NJ, Lippa KA, Piotrowski P, Da Silva SM, Swanson KS, Wishart DS. Workshop report: Toward the development of a human whole stool reference material for metabolomic and metagenomic gut microbiome measurements. Metabolomics 2020; 16:119. [PMID: 33164148 PMCID: PMC7649161 DOI: 10.1007/s11306-020-01744-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION To date, there has been little effort to develop standards for metabolome-based gut microbiome measurements despite the significant efforts toward standard development for DNA-based microbiome measurements. OBJECTIVES The National Institute of Standards and Technology (NIST), The BioCollective (TBC), and the North America Branch of the International Life Sciences Institute (ILSI North America) are collaborating to extend NIST's efforts to develop a Human Whole Stool Reference Material for the purpose of method harmonization and eventual quality control. METHODS The reference material will be rationally designed for adequate quality assurance and quality control (QA/QC) for underlying measurements in the study of the impact of diet and nutrition on functional aspects of the host gut microbiome and relationships of those functions to health. To identify which metabolites deserve priority in their value assignment, NIST, TBC, and ILSI North America jointly conducted a workshop on September 12, 2019 at the NIST campus in Gaithersburg, Maryland. The objective of the workshop was to identify metabolites for which evidence indicates relevance to health and disease and to decide on the appropriate course of action to develop a fit-for-purpose reference material. RESULTS This document represents the consensus opinions of workshop participants and co-authors of this manuscript, and provides additional supporting information. In addition to developing general criteria for metabolite selection and a preliminary list of proposed metabolites, this paper describes some of the strengths and limitations of this initiative given the current state of microbiome research. CONCLUSIONS Given the rapidly evolving nature of gut microbiome science and the current state of knowledge, an RM (as opposed to a CRM) measured for multiple metabolites is appropriate at this stage. As the science evolves, the RM can evolve to match the needs of the research community. Ultimately, the stool RM may exist in sequential versions. Beneficial to this evolution will be a clear line of communication between NIST and the stakeholder community to ensure alignment with current scientific understanding and community needs.
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Affiliation(s)
- Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Raul Cano
- The BioCollective, LLC, 5650 N Washington St, Denver, CO, 80216, USA
| | - Cindy D Davis
- Office of Dietary Supplements, National Institutes of Health, Bethesda, MD, 20852, USA
| | | | - Scott A Jackson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Christina M Jones
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Johanna W Lampe
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, M4-B802, PO Box 19024, Seattle, WA, 98109, USA
| | - Marie E Latulippe
- North American Branch of the International Life Sciences Institute (ILSI North America), 740 15th Street NW, Suite 600, Washington, DC, 20005, USA.
| | - Nancy J Lin
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Katrice A Lippa
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Paulina Piotrowski
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Sandra M Da Silva
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Kelly S Swanson
- University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
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Aristizabal-Henao JJ, Jones CM, Lippa KA, Bowden JA. Nontargeted lipidomics of novel human plasma reference materials: hypertriglyceridemic, diabetic, and African-American. Anal Bioanal Chem 2020; 412:7373-7380. [PMID: 32851459 DOI: 10.1007/s00216-020-02910-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/05/2020] [Accepted: 08/21/2020] [Indexed: 12/20/2022]
Abstract
The unavailability of appropriate quality assurance/quality control materials in many lipidomics applications poses a significant challenge for lipidomics research. It is recommended that samples with certified values and/or consensus estimates, such as NIST SRM 1950-Metabolites in Frozen Human Plasma, be implemented in routine analyses to enable community-wide comparisons of lipidomics results and analytical workflows. Herein, we applied a nontargeted lipidomics method for the analysis of a new human plasma reference material suite developed by NIST (hypertriglyceridemic, diabetic, and African-American plasma pools), in addition to SRM 1950. We identified specific lipidomics fingerprints associated with each sample type, including lauric acid-containing lipids and elevated triacylglycerol levels in hypertriglyceridemic plasma, palmitoleic acid-containing lipids in diabetic plasma, and oxidized fatty acid-containing phospholipids in African-American plasma. This work highlights the importance of developing and profiling application-specific reference materials, while establishing reference data that may be used for system suitability and/or quality control metrics.Graphical abstract.
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Affiliation(s)
- Juan J Aristizabal-Henao
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, 1333 Center Drive, Gainesville, FL, 32610, USA
| | - Christina M Jones
- Chemical Sciences Division, National Institutes of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Katrice A Lippa
- Chemical Sciences Division, National Institutes of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - John A Bowden
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, 1333 Center Drive, Gainesville, FL, 32610, USA.
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Phillips MM, Rimmer CA, Wood LJ, Lippa KA, Sharpless KE, Duewer DL, Sander LC, Betz JM. Dietary Supplement Laboratory Quality Assurance Program: The First Five Exercises. J AOAC Int 2019. [DOI: 10.1093/jaoac/94.3.803] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The National Institute of Standards and Technology (NIST) has established a Dietary Supplement Laboratory Quality Assurance Program (DSQAP) in collaboration with the National Institutes of Health Office of Dietary Supplements. Program participants measure concentrations of active and/or marker compounds as well as nutritional and toxic elements in food and dietary supplements distributed by NIST. Data are compiled at NIST, where they are analyzed for accuracy relative to reference values and concordance among the participants. Performance reports and certificates of completion are provided to participants, which can be used to demonstrate compliance with current Good Manufacturing Practices as promulgated by the U.S. Food and Drug Administration. The DSQAP has conducted five exercises to date, with total participation including more than 75 different laboratories and many more individual analysts.
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Affiliation(s)
- Melissa M Phillips
- National Institute of Standards and Technology, Analytical Chemistry Division, Material Measurement Laboratory, Gaithersburg, MD 20899-8392
| | - Catherine A Rimmer
- National Institute of Standards and Technology, Analytical Chemistry Division, Material Measurement Laboratory, Gaithersburg, MD 20899-8392
| | - Laura J Wood
- National Institute of Standards and Technology, Analytical Chemistry Division, Material Measurement Laboratory, Gaithersburg, MD 20899-8392
| | - Katrice A Lippa
- National Institute of Standards and Technology, Analytical Chemistry Division, Material Measurement Laboratory, Gaithersburg, MD 20899-8392
| | - Katherine E Sharpless
- National Institute of Standards and Technology, Analytical Chemistry Division, Material Measurement Laboratory, Gaithersburg, MD 20899-8392
| | - David L Duewer
- National Institute of Standards and Technology, Analytical Chemistry Division, Material Measurement Laboratory, Gaithersburg, MD 20899-8392
| | - Lane C Sander
- National Institute of Standards and Technology, Analytical Chemistry Division, Material Measurement Laboratory, Gaithersburg, MD 20899-8392
| | - Joseph M Betz
- National Institutes of Health, Office of Dietary Supplements, Bethesda, MD 20892-7517
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7
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Bearden DW, Sheen DA, Simón-Manso Y, Benner BA, Rocha WFC, Blonder N, Lippa KA, Beger RD, Schnackenberg LK, Sun J, Mehta KY, Cheema AK, Gu H, Marupaka R, Nagana Gowda GA, Raftery D. Metabolomics Test Materials for Quality Control: A Study of a Urine Materials Suite. Metabolites 2019; 9:metabo9110270. [PMID: 31703392 PMCID: PMC6918257 DOI: 10.3390/metabo9110270] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 12/20/2022] Open
Abstract
There is a lack of experimental reference materials and standards for metabolomics measurements, such as urine, plasma, and other human fluid samples. Reasons include difficulties with supply, distribution, and dissemination of information about the materials. Additionally, there is a long lead time because reference materials need their compositions to be fully characterized with uncertainty, a labor-intensive process for material containing thousands of relevant compounds. Furthermore, data analysis can be hampered by different methods using different software by different vendors. In this work, we propose an alternative implementation of reference materials. Instead of characterizing biological materials based on their composition, we propose using untargeted metabolomic data such as nuclear magnetic resonance (NMR) or gas and liquid chromatography-mass spectrometry (GC-MS and LC-MS) profiles. The profiles are then distributed with the material accompanying the certificate, so that researchers can compare their own metabolomic measurements with the reference profiles. To demonstrate this approach, we conducted an interlaboratory study (ILS) in which seven National Institute of Standards and Technology (NIST) urine Standard Reference Material®s (SRM®s) were distributed to participants, who then returned the metabolomic data to us. We then implemented chemometric methods to analyze the data together to estimate the uncertainties in the current measurement techniques. The participants identified similar patterns in the profiles that distinguished the seven samples. Even when the number of spectral features is substantially different between platforms, a collective analysis still shows significant overlap that allows reliable comparison between participants. Our results show that a urine suite such as that used in this ILS could be employed for testing and harmonization among different platforms. A limited quantity of test materials will be made available for researchers who are willing to repeat the protocols presented here and contribute their data.
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Affiliation(s)
- Daniel W. Bearden
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (D.W.B.); (W.F.C.R.); (N.B.); (K.A.L.)
| | - David A. Sheen
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (D.W.B.); (W.F.C.R.); (N.B.); (K.A.L.)
- Correspondence: ; Tel.: +1-301-975-2603
| | - Yamil Simón-Manso
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA;
| | - Bruce A. Benner
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (D.W.B.); (W.F.C.R.); (N.B.); (K.A.L.)
| | - Werickson F. C. Rocha
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (D.W.B.); (W.F.C.R.); (N.B.); (K.A.L.)
- National Institute of Metrology, Quality, and Technology—INMETRO, 25250-020 Duque de Caxias, RJ, Brazil
| | - Niksa Blonder
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (D.W.B.); (W.F.C.R.); (N.B.); (K.A.L.)
| | - Katrice A. Lippa
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (D.W.B.); (W.F.C.R.); (N.B.); (K.A.L.)
| | - Richard D. Beger
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (R.D.B.); (L.K.S.); (J.S.)
| | - Laura K. Schnackenberg
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (R.D.B.); (L.K.S.); (J.S.)
| | - Jinchun Sun
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (R.D.B.); (L.K.S.); (J.S.)
| | - Khyati Y. Mehta
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA; (K.Y.M.); (A.K.C.)
| | - Amrita K. Cheema
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA; (K.Y.M.); (A.K.C.)
- Departments of Oncology and Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA;
| | - Ramesh Marupaka
- Clinical Toxicology at CIAN Diagnostics, Frederick, MD 21703, USA;
| | - G. A. Nagana Gowda
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington, Seattle, WA 98109, USA; (G.A.N.G.); (D.R.)
| | - Daniel Raftery
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington, Seattle, WA 98109, USA; (G.A.N.G.); (D.R.)
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Lippa KA, Duewer DL, Nelson MA, Davies SR, Mackay LG. The role of the CCQM OAWG in providing SI traceable calibrators for organic chemical measurements. Accredit Qual Assur 2019; 24:10.1007/s00769-019-01407-6. [PMID: 38487299 PMCID: PMC10938631 DOI: 10.1007/s00769-019-01407-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/16/2019] [Indexed: 03/17/2024]
Abstract
Metrological traceability for organic chemical measurements is a documented unbroken chain of calibrations with stated uncertainties that ideally link the measurement result for a sample to a primary calibrator in appropriate SI units (e.g., mass fraction). A comprehensive chemical purity determination of the organic calibrator is required to ensure a true assessment of this result. We explore the evolution of chemical purity capabilities across metrology institute members of the Consultative Committee for Amount of Substance: Metrology in Chemistry and Biology's Organic Analysis Working Group (OAWG). The OAWG work program has promoted the development of robust measurement capabilities, using indirect "mass balance" determinations via rigorous assessment of impurities and direct determination using quantitative nuclear magnetic resonance spectroscopy methods. A combination of mass balance and qNMR has been shown to provide a best practice approach. Awareness of the importance of the traceability of organic calibrators continues to grow across stakeholder groups, particularly in key areas such as clinical chemistry where activities related to the Joint Committee for Traceability in Laboratory Medicine have raised the profile of traceable calibrators.
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Affiliation(s)
- Katrice A. Lippa
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899-8392, USA
| | - David L. Duewer
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899-8392, USA
| | - Michael A. Nelson
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899-8392, USA
| | - Stephen R. Davies
- National Measurement Institute, Australia, 105 Delhi Road, North Ryde, NSW 2113, Australia
| | - Lindsey G. Mackay
- National Measurement Institute, Australia, 105 Delhi Road, North Ryde, NSW 2113, Australia
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9
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Nelson MA, Waters JF, Toman B, Lang BE, Rück A, Breitruck K, Obkircher M, Windust A, Lippa KA. A New Realization of SI for Organic Chemical Measurement: NIST PS1 Primary Standard for Quantitative NMR (Benzoic Acid). Anal Chem 2018; 90:10510-10517. [PMID: 30058803 DOI: 10.1021/acs.analchem.8b02575] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metrological traceability to common references supports the comparability of chemical measurement results produced by different analysts, at various times, and at separate places. Ideally, these references are realizations of base units of the International System of Units (SI). ISO/IEC 17025 (Clause 6.5) states that traceability of measurement results is a necessary attribute of analytical laboratory competence, and as such, has become compulsory in many industries, especially clinical diagnostics and healthcare. Historically, claims of traceability for organic chemical measurements have relied on calibration chains anchored on unique reference materials with linkage to the SI that is tenuous at best. A first-of-its-kind National Institute of Standards and Technology (NIST) reference material, ultrapure and extensively characterized PS1 Benzoic Acid Primary Standard for quantitative NMR (qNMR), serves as a definitive, primary reference (calibrant) that assuredly links the qNMR spectroscopy technique to SI units. As qNMR itself is a favorable method for accurate, direct characterization of chemical reference materials, PS1 is a standard for developing other traceable standards and is intended to establish traceability for the measurement of thousands of organic chemical species. NIST PS1 will play a critical role in directly promoting accuracy and worldwide comparability of measurement results produced by the chemical measurement community, supporting the soundness of clinical diagnostics, food safety and labeling, forensic investigation, drug development, biomedical research, and chemical manufacturing. Confidence in this link to the SI was established through (i) unambiguous identification of chemical structure; (ii) determinations of isotopic composition and molecular weight; (iii) evaluation of the respective molecular amount by multiple primary measurement procedures, including qNMR and coulometry; and (iv) rigorous evaluation of measurement uncertainty using state-of-the-art statistical methods and measurement models.
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Affiliation(s)
- M A Nelson
- National Institute of Standards and Technology , US Department of Commerce, Gaithersburg , Maryland 20899 , United States
| | - J F Waters
- National Institute of Standards and Technology , US Department of Commerce, Gaithersburg , Maryland 20899 , United States
| | - B Toman
- National Institute of Standards and Technology , US Department of Commerce, Gaithersburg , Maryland 20899 , United States
| | - B E Lang
- National Institute of Standards and Technology , US Department of Commerce, Gaithersburg , Maryland 20899 , United States
| | - A Rück
- Sigma-Aldrich Production GmbH , 9471 Buchs , Switzerland
| | - K Breitruck
- Sigma-Aldrich Production GmbH , 9471 Buchs , Switzerland
| | - M Obkircher
- Sigma-Aldrich Production GmbH , 9471 Buchs , Switzerland
| | - A Windust
- Measurement Science and Standards , National Research Council Canada , Ottawa , ON K1A DR6 , Canada
| | - K A Lippa
- National Institute of Standards and Technology , US Department of Commerce, Gaithersburg , Maryland 20899 , United States
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10
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Josephs RD, Stoppacher N, Daireaux A, Choteau T, Lippa KA, Phinney KW, Westwood S, Wielgosz RI. State-of-the-art and trends for the SI traceable value assignment of the purity of peptides using the model compound angiotensin I. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2017.09.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Wise SA, Tai SSC, Burdette CQ, Camara JE, Bedner M, Lippa KA, Nelson MA, Nalin F, Phinney KW, Sander LC, Betz JM, Sempos CT, Coates PM. Role of the National Institute of Standards and Technology (NIST) in Support of the Vitamin D Initiative of the National Institutes of Health, Office of Dietary Supplements. J AOAC Int 2017; 100:1260-1276. [PMID: 28863788 DOI: 10.5740/jaoacint.17-0305] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Since 2005, the National Institute of Standards and Technology (NIST) has collaborated with the National Institutes of Health (NIH), Office of Dietary Supplements (ODS) to improve the quality of measurements related to human nutritional markers of vitamin D status. In support of the NIH-ODS Vitamin D Initiative, including the Vitamin D Standardization Program (VDSP), NIST efforts have focused on (1) development of validated analytical methods, including reference measurement procedures (RMPs); (2) development of Standard Reference Materials (SRMs); (3) value assignment of critical study samples using NIST RMPs; and (4) development and coordination of laboratory measurement QA programs. As a result of this collaboration, NIST has developed RMPs for 25-hydroxyvitamin D2 [25(OH)D2], 25(OH)D3, and 24R,25-dihydroxyvitamin D3 [24R,25(OH)2D3]; disseminated serum-based SRMs with values assigned for 25(OH)D2, 25(OH)D3, 3-epi-25(OH)D3, and 24R,25(OH)2D3; assigned values for critical samples for VDSP studies, including an extensive interlaboratory comparison and reference material commutability study; provided an accuracy basis for the Vitamin D External Quality Assurance Scheme; coordinated the first accuracy-based measurement QA program for the determination of 25(OH)D2, 25(OH)D3, and 3-epi-25(OH)D3 in human serum/plasma; and developed methods and SRMs for the determination of vitamin D and 25(OH)D in food and supplement matrix SRMs. The details of these activities and their benefit and impact to the NIH-ODS Vitamin D Initiative are described.
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Affiliation(s)
- Stephen A Wise
- National Institute of Standards and Technology, Chemical Sciences Division, Gaithersburg, MD 20899
| | - Susan S-C Tai
- National Institute of Standards and Technology, Chemical Sciences Division, Gaithersburg, MD 20899
| | - Carolyn Q Burdette
- National Institute of Standards and Technology, Chemical Sciences Division, Gaithersburg, MD 20899
| | - Johanna E Camara
- National Institute of Standards and Technology, Chemical Sciences Division, Gaithersburg, MD 20899
| | - Mary Bedner
- National Institute of Standards and Technology, Chemical Sciences Division, Gaithersburg, MD 20899
| | - Katrice A Lippa
- National Institute of Standards and Technology, Chemical Sciences Division, Gaithersburg, MD 20899
| | - Michael A Nelson
- National Institute of Standards and Technology, Chemical Sciences Division, Gaithersburg, MD 20899
| | - Federica Nalin
- National Institute of Standards and Technology, Chemical Sciences Division, Gaithersburg, MD 20899
| | - Karen W Phinney
- National Institute of Standards and Technology, Chemical Sciences Division, Gaithersburg, MD 20899
| | - Lane C Sander
- National Institute of Standards and Technology, Chemical Sciences Division, Gaithersburg, MD 20899
| | - Joseph M Betz
- National Institutes of Health, Office of Dietary Supplements, Bethesda, MD 20892
| | - Christopher T Sempos
- National Institutes of Health, Office of Dietary Supplements, Bethesda, MD 20892
| | - Paul M Coates
- National Institutes of Health, Office of Dietary Supplements, Bethesda, MD 20892
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de Carvalho Rocha WF, Schantz MM, Sheen DA, Chu PM, Lippa KA. Unsupervised classification of petroleum Certified Reference Materials and other fuels by chemometric analysis of gas chromatography-mass spectrometry data. Fuel (Lond) 2017; 197:248-258. [PMID: 28603295 PMCID: PMC5464420 DOI: 10.1016/j.fuel.2017.02.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
As feedstocks transition from conventional oil to unconventional petroleum sources and biomass, it will be necessary to determine whether a particular fuel or fuel blend is suitable for use in engines. Certifying a fuel as safe for use is time-consuming and expensive and must be performed for each new fuel. In principle, suitability of a fuel should be completely determined by its chemical composition. This composition can be probed through use of detailed analytical techniques such as gas chromatography-mass spectroscopy (GC-MS). In traditional analysis, chromatograms would be used to determine the details of the composition. In the approach taken in this paper, the chromatogram is assumed to be entirely representative of the composition of a fuel, and is used directly as the input to an algorithm in order to develop a model that is predictive of a fuel's suitability. When a new fuel is proposed for service, its suitability for any application could then be ascertained by using this model to compare its chromatogram with those of the fuels already known to be suitable for that application. In this paper, we lay the mathematical and informatics groundwork for a predictive model of hydrocarbon properties. The objective of this work was to develop a reliable model for unsupervised classification of the hydrocarbons as a prelude to developing a predictive model of their engine-relevant physical and chemical properties. A set of hydrocarbons including biodiesel fuels, gasoline, highway and marine diesel fuels, and crude oils was collected and GC-MS profiles obtained. These profiles were then analyzed using multi-way principal components analysis (MPCA), principal factors analysis (PARAFAC), and a self-organizing map (SOM), which is a kind of artificial neural network. It was found that, while MPCA and PARAFAC were able to recover descriptive models of the fuels, their linear nature obscured some of the finer physical details due to the widely varying composition of the fuels. The SOM was able to find a descriptive classification model which has the potential for practical recognition and perhaps prediction of fuel properties.
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Affiliation(s)
| | - Michele M Schantz
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
| | - David A Sheen
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
| | - Pamela M Chu
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
| | - Katrice A Lippa
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
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Sheen DA, de Carvalho Rocha WF, Lippa KA, Bearden DW. A scoring metric for multivariate data for reproducibility analysis using chemometric methods. Chemometr Intell Lab Syst 2017; 162:10-20. [PMID: 28694553 PMCID: PMC5500873 DOI: 10.1016/j.chemolab.2016.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Process quality control and reproducibility in emerging measurement fields such as metabolomics is normally assured by interlaboratory comparison testing. As a part of this testing process, spectral features from a spectroscopic method such as nuclear magnetic resonance (NMR) spectroscopy are attributed to particular analytes within a mixture, and it is the metabolite concentrations that are returned for comparison between laboratories. However, data quality may also be assessed directly by using binned spectral data before the time-consuming identification and quantification. Use of the binned spectra has some advantages, including preserving information about trace constituents and enabling identification of process difficulties. In this paper, we demonstrate the use of binned NMR spectra to conduct a detailed interlaboratory comparison and composition analysis. Spectra of synthetic and biologically-obtained metabolite mixtures, taken from a previous interlaboratory study, are compared with cluster analysis using a variety of distance and entropy metrics. The individual measurements are then evaluated based on where they fall within their clusters, and a laboratory-level scoring metric is developed, which provides an assessment of each laboratory's individual performance.
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Affiliation(s)
- David A Sheen
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | | | - Katrice A Lippa
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Daniel W Bearden
- Chemical Sciences Division, National Institute of Standards and Technology, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, USA
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14
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Toman B, Nelson MA, Lippa KA. Chemical purity using quantitative 1H-nuclear magnetic resonance: a hierarchical Bayesian approach for traceable calibrations. Metrologia 2016; 53:1193-1203. [PMID: 28670006 PMCID: PMC5486237 DOI: 10.1088/0026-1394/53/5/1193] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Chemical purity assessment using quantitative 1H-nuclear magnetic resonance spectroscopy is a method based on ratio references of mass and signal intensity of the analyte species to that of chemical standards of known purity. As such, it is an example of a calculation using a known measurement equation with multiple inputs. Though multiple samples are often analyzed during purity evaluations in order to assess measurement repeatability, the uncertainty evaluation must also account for contributions from inputs to the measurement equation. Furthermore, there may be other uncertainty components inherent in the experimental design, such as independent implementation of multiple calibration standards. As such, the uncertainty evaluation is not purely bottom up (based on the measurement equation) or top down (based on the experimental design), but inherently contains elements of both. This hybrid form of uncertainty analysis is readily implemented with Bayesian statistical analysis. In this article we describe this type of analysis in detail and illustrate it using data from an evaluation of chemical purity and its uncertainty for a folic acid material.
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Affiliation(s)
- Blaza Toman
- National Institute of Standards and Technology, US Department of Commerce, Gaithersburg, MD, USA
| | - Michael A Nelson
- National Institute of Standards and Technology, US Department of Commerce, Gaithersburg, MD, USA
| | - Katrice A Lippa
- National Institute of Standards and Technology, US Department of Commerce, Gaithersburg, MD, USA
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15
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Affiliation(s)
- Joseph P. Klems
- Chemical Sciences Division, National Institute of Standards and Technology, 100 Bureau Drive Stop 8320, Gaithersburg, Maryland 20899, United States
| | - Katrice A. Lippa
- Chemical Sciences Division, National Institute of Standards and Technology, 100 Bureau Drive Stop 8320, Gaithersburg, Maryland 20899, United States
| | - W. Sean McGivern
- Chemical Sciences Division, National Institute of Standards and Technology, 100 Bureau Drive Stop 8320, Gaithersburg, Maryland 20899, United States
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16
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Rhieu SY, Urbas AA, Bearden DW, Marino JP, Lippa KA, Reipa V. Berichtigung: Probing the Intracellular Glutathione Redox Potential by In-Cell NMR Spectroscopy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Rhieu SY, Urbas AA, Bearden DW, Marino JP, Lippa KA, Reipa V. Corrigendum: Probing the Intracellular Glutathione Redox Potential by In-Cell NMR Spectroscopy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/anie.201401007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Bisceglia KJ, Lippa KA. Stability of cocaine and its metabolites in municipal wastewater--the case for using metabolite consolidation to monitor cocaine utilization. Environ Sci Pollut Res Int 2014; 21:4453-4460. [PMID: 24337995 DOI: 10.1007/s11356-013-2403-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 11/25/2013] [Indexed: 06/03/2023]
Abstract
Transformations of cocaine and eleven of its metabolites were investigated in untreated municipal sewage at pH ≈ 7 and 9, 23, and 31 °C. Results indicated that hydrolysis-possibly bacterially mediated-was the principal transformation pathway. Residues possessing alkyl esters were particularly susceptible to hydrolysis, with pseudo-first-order rate constants varying from 0.54 to 1.7 day(-1) at 23 °C. Metabolites lacking esters or possessing only a benzoyl ester appeared stable. Residues lacking alkyl esters did accumulate through hydrolysis of precursors, however. As noted previously, this may positively bias cocaine utilization estimates based on benzoylecgonine alone. Reported variability in metabolic excretion was used in conjunction with transformation data to evaluate different approaches for estimating cocaine loading. Results indicate that estimates derived from measurands that capture all major cocaine metabolites, such as COCtot (the sum of all measurable metabolites) and EChyd (the sum of all metabolites that can be hydrolyzed to ecgonine), may reduce uncertainty arising from variability in metabolite transformation and excretion, possibly to ≈ 10 % RSD. This is more than a two-fold reduction relative to estimates derived from benzoylecgonine (>26 % RSD), and roughly equivalent to reported uncertainties from sources that are not metabolite-specific (e.g., sampling frequency, flow variability). They and other composite measurands merit consideration from the sewage epidemiology community, beginning with efforts to evaluate the stability of the total cocaine load under realistic sewer conditions.
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Affiliation(s)
- Kevin J Bisceglia
- Department of Geography and Environmental Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA,
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Rhieu SY, Urbas AA, Bearden DW, Marino JP, Lippa KA, Reipa V. Probing the Intracellular Glutathione Redox Potential by In-Cell NMR Spectroscopy. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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20
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Rhieu SY, Urbas AA, Bearden DW, Marino JP, Lippa KA, Reipa V. Probing the Intracellular Glutathione Redox Potential by In-Cell NMR Spectroscopy. Angew Chem Int Ed Engl 2013; 53:447-50. [DOI: 10.1002/anie.201308004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Indexed: 11/09/2022]
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21
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Bedner M, Lippa KA, Tai SSC. An assessment of 25-hydroxyvitamin D measurements in comparability studies conducted by the Vitamin D Metabolites Quality Assurance Program. Clin Chim Acta 2013; 426:6-11. [PMID: 23978484 DOI: 10.1016/j.cca.2013.08.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/20/2013] [Accepted: 08/12/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND The National Institute of Standards and Technology (NIST), in collaboration with the National Institutes of Health Office of Dietary Supplements, established the first accuracy-based program for improving the comparability of vitamin D metabolite measurements, the Vitamin D Metabolites Quality Assurance Program. METHODS The study samples were human serum or plasma Standard Reference Materials (SRMs) with 25-hydroxyvitamin D values that were determined at NIST. Participants evaluated the materials using immunoassay (IA), liquid chromatography (LC) with mass spectrometric detection, and LC with ultraviolet absorbance detection. NIST evaluated the results for concordance within the participant community as well as trueness relative to the NIST value. RESULTS For the study materials that contain mostly 25-hydroxyvitamin D3 (25(OH)D3),the coefficient of variation (CV) for the participant results was consistently in the range from 7% to 19%, and the median values were biased high relative to the NIST values. However, for materials that contain significant concentrations of both 25-hydroxyvitamin D2 (25(OH)D2) and 25(OH)D3, the median IA results were biased lower than both the LC and the NIST values, and the CV was as high as 28%. The first interlaboratory comparison results for SRM 972a Vitamin D Metabolites in Human Serum are also reported. CONCLUSIONS Relatively large within-lab and between-lab variability hinders conclusive assessments of bias and accuracy.
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Affiliation(s)
- Mary Bedner
- National Institute of Standards and Technology, Material Measurement Laboratory, Chemical Sciences Division, United States.
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22
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Sander LC, Bedner M, Duewer DL, Lippa KA, Phillips MM, Phinney KW, Rimmer CA, Schantz MM, Sharpless KE, Tai SSC, Thomas JB, Wise SA, Wood LJ, Betz JM, Coates PM. The development and implementation of quality assurance programs to support nutritional measurements. Anal Bioanal Chem 2013; 405:4437-41. [PMID: 23552970 DOI: 10.1007/s00216-013-6864-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/14/2013] [Accepted: 02/21/2013] [Indexed: 01/12/2023]
Abstract
The National Institute of Standards and Technology administers quality assurance programs devoted to improving measurements of nutrients and related metabolites in foods, dietary supplements, and serum and plasma samples. These programs have been developed in collaboration with the National Institutes of Health to assist measurement communities in their efforts to achieve accurate results that are comparable among different laboratories and over time. Targeted analytes include micronutrients, botanical markers, nutritional elements, contaminants, fatty acids, and vitamin D metabolites.
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Affiliation(s)
- L C Sander
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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23
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Rhieu SY, Urbas AA, Lippa KA, Reipa V. Quantitative measurements of glutathione in yeast cell lysate using 1H NMR. Anal Bioanal Chem 2013; 405:4963-8. [PMID: 23471371 DOI: 10.1007/s00216-013-6858-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/19/2013] [Accepted: 02/20/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Steve Y Rhieu
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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24
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Wood LJ, Lippa KA, Phillips MM, Rimmer CA, Heckert NA, Leigh SD, Moors AJ, Pugh RS, Rust LB. Breakfast cereal sampling study for nutritional elements. Anal Bioanal Chem 2013; 405:4569-78. [PMID: 23380950 DOI: 10.1007/s00216-013-6727-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/17/2012] [Accepted: 01/11/2013] [Indexed: 11/29/2022]
Abstract
The National Institute of Standards and Technology (NIST) has established a Dietary Supplement Laboratory Quality Assurance Program (DSQAP) in collaboration with the National Institutes of Health Office of Dietary Supplements (NIH-ODS). The DSQAP invites laboratories twice annually to participate in interlaboratory studies where participants elect to measure concentrations of nutritional and/or toxic elements as well as active and/or marker compounds. One of these studies was designed to determine the effects of material granularity and sample processing techniques on measurement variability (precision) as well as to provide participating laboratories information on their performance relative to the NIST assigned values (bias) and to the other participants (concordance). Participants were asked to determine the mass fractions of Ca, Fe, and Zn, in mg/kg, in six breakfast cereal samples. Cereal samples consisted of three ground materials (homogenized wheat, wheat, and rice), two flake materials (wheat and rice) and a partially crushed material (a wheat/rice mixture). In general, approximately 25% of the laboratories processed and analyzed the suite of six cereal materials with adequate to exemplary measurement precision. Over half of the laboratories (60%) experienced measurement issues related to only a particular type of cereal matrix or for only a single element. A small number (15%) of laboratories experienced significant sample processing or measurement problems. Future studies planned by the DSQAP may be designed to use commercial products to aid laboratories with their sampling and analytical techniques.
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Affiliation(s)
- Laura J Wood
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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25
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Kraigsley AM, Tang K, Lippa KA, Howarter JA, Lin-Gibson S, Lin NJ. Effect of Polymer Degree of Conversion onStreptococcus mutansBiofilms. Macromol Biosci 2012; 12:1706-13. [DOI: 10.1002/mabi.201200214] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 08/16/2012] [Indexed: 01/22/2023]
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26
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Camara JE, Lippa KA, Duewer DL, Gasca-Aragon H, Toman B. An international assessment of the metrological equivalence of higher-order measurement services for creatinine in serum. Anal Bioanal Chem 2012; 403:527-35. [DOI: 10.1007/s00216-012-5869-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/10/2012] [Accepted: 02/12/2012] [Indexed: 10/28/2022]
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27
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Phillips MM, Rimmer CA, Wood LJ, Lippa KA, Sharpless KE, Duewer DL, Sander LC, Betz JM. Dietary supplement laboratory quality assurance program: the first five exercises. J AOAC Int 2011; 94:803-14. [PMID: 21797008 PMCID: PMC3173719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The National Institute of Standards and Technology (NIST) has established a Dietary Supplement Laboratory Quality Assurance Program (DSQAP) in collaboration with the National Institutes of Health Office of Dietary Supplements. Program participants measure concentrations of active and/or marker compounds as well as nutritional and toxic elements in food and dietary supplements distributed by NIST. Data are compiled at NIST, where they are analyzed for accuracy relative to reference values and concordance among the participants. Performance reports and certificates of completion are provided to participants, which can be used to demonstrate compliance with current Good Manufacturing Practices as promulgated by the U.S. Food and Drug Administration. The DSQAP has conducted five exercises to date, with total participation including more than 75 different laboratories and many more individual analysts.
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Affiliation(s)
- Melissa M Phillips
- National Institute of Standards and Technology, Analytical Chemistry Division, Material Measurement Laboratory, Gaithersburg, MD 20899-8392, USA.
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Lippa KA, Duewer DL, Salit ML, Game L, Causton HC. Exploring the use of internal and externalcontrols for assessing microarray technical performance. BMC Res Notes 2010; 3:349. [PMID: 21189145 PMCID: PMC3020182 DOI: 10.1186/1756-0500-3-349] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 12/28/2010] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscript presents a retrospective study characterizing several approaches to assess technical performance of microarray data measured on the Affymetrix GeneChip platform, including whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. Spike-in controls were found to carry the same information about technical performance as whole-array metrics and endogenous "housekeeping" genes. These results support the use of spike-in controls as general tools for performance assessment across time, experimenters and array batches, suggesting that they have potential for comparison of microarray data generated across species using different technologies. RESULTS A layered PCA modeling methodology that uses data from a number of classes of controls (spike-in hybridization, spike-in polyA+, internal RNA degradation, endogenous or "housekeeping genes") was used for the assessment of microarray data quality. The controls provide information on multiple stages of the experimental protocol (e.g., hybridization, RNA amplification). External spike-in, hybridization and RNA labeling controls provide information related to both assay and hybridization performance whereas internal endogenous controls provide quality information on the biological sample. We find that the variance of the data generated from the external and internal controls carries critical information about technical performance; the PCA dissection of this variance is consistent with whole-array quality assessment based on a number of quality assurance/quality control (QA/QC) metrics. CONCLUSIONS These results provide support for the use of both external and internal RNA control data to assess the technical quality of microarray experiments. The observed consistency amongst the information carried by internal and external controls and whole-array quality measures offers promise for rationally-designed control standards for routine performance monitoring of multiplexed measurement platforms.
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Affiliation(s)
- Katrice A Lippa
- Chemical Science and Technology Laboratory.National Institute of Standards and Technology (NIST) Gaithersburg, Maryland 20899 USA
| | - David L Duewer
- Chemical Science and Technology Laboratory.National Institute of Standards and Technology (NIST) Gaithersburg, Maryland 20899 USA
| | - Marc L Salit
- Chemical Science and Technology Laboratory.National Institute of Standards and Technology (NIST) Gaithersburg, Maryland 20899 USA
| | - Laurence Game
- MRC Clinical Sciences Centre (CSC) Imperial College Microarray Centre Hammersmith Hospital Campus London W12 0NN, UK
| | - Helen C Causton
- MRC Clinical Sciences Centre (CSC) Imperial College Microarray Centre Hammersmith Hospital Campus London W12 0NN, UK
- Department of Biological Sciences Columbia University New York, NY 10027 USA
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Bisceglia KJ, Roberts AL, Schantz MM, Lippa KA. Quantification of drugs of abuse in municipal wastewater via SPE and direct injection liquid chromatography mass spectrometry. Anal Bioanal Chem 2010; 398:2701-12. [PMID: 20865408 DOI: 10.1007/s00216-010-4191-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 08/30/2010] [Accepted: 09/02/2010] [Indexed: 11/26/2022]
Abstract
We present an isotopic-dilution direct injection reversed-phase liquid chromatography-tandem mass spectrometry method for the simultaneous determination of 23 drugs of abuse, drug metabolites, and human-use markers in municipal wastewater. The method places particular emphasis on cocaine; it includes 11 of its metabolites to facilitate assessment of routes of administration and to enhance the accuracy of estimates of cocaine consumption. Four opioids (6-acetylmorphine, morphine, hydrocodone, and oxycodone) are also included, along with five phenylamine drugs (amphetamine, methamphetamine, 3,4-methylenedioxy-methamphetamine, methylbenzodioxolyl-butanamine, and 3,4-methylenedioxy-N-ethylamphetamine) and two human-use markers (cotinine and creatinine). The method is sufficiently sensitive to directly quantify (without preconcentration) 18 analytes in wastewater at concentrations less than 50 ng/L. We also present a modified version of this method that incorporates solid-phase extraction to further enhance sensitivity. The method includes a confirmatory LC separation (selected by evaluating 13 unique chromatographic phases) that has been evaluated using National Institute of Standards and Technology Standard Reference Material 1511 Multi-Drugs of Abuse in Freeze-Dried Urine. Seven analytes (ecgonine methyl ester, ecgonine ethyl ester, anhydroecgonine methyl ester, m-hydroxybenzoylecgonine, p-hydroxybenzoyl-ecgonine, ecgonine, and anhydroecgonine) were detected for the first time in a wastewater sample.
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Affiliation(s)
- Kevin J Bisceglia
- Department of Geography and Environmental Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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30
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Kühnle M, Friebolin V, Albert K, Rimmer CA, Lippa KA, Sander LC. Architecture and Dynamics of C18 Bonded Interphases with Small Molecule Spacers. Anal Chem 2009; 81:10136-42. [DOI: 10.1021/ac901911w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Duewer DL, Lippa KA, Long SE, Murphy KE, Sharpless KE, Sniegoski LT, Welch MJ, Tani W, Umemoto M. Demonstrating the comparability of certified reference materials. Anal Bioanal Chem 2009; 395:155-69. [DOI: 10.1007/s00216-009-2949-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Revised: 06/15/2009] [Accepted: 07/01/2009] [Indexed: 11/24/2022]
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Mountain RD, Lippa KA. Solvation of Perfluorooctane and Octane in Water, Methanol, Acetonitrile, and Aqueous Mixtures of Methanol and Acetonitrile. J Phys Chem B 2008; 112:7785-93. [DOI: 10.1021/jp0774802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Raymond D. Mountain
- Physical and Chemical Properties Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8380, and Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8392
| | - Katrice A. Lippa
- Physical and Chemical Properties Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8380, and Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8392
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Lippa KA, Sander LC. Identification of isolated cavity features within molecular dynamics simulated chromatographic surfaces. J Chromatogr A 2006; 1128:79-89. [PMID: 16846606 DOI: 10.1016/j.chroma.2006.06.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Revised: 06/06/2006] [Accepted: 06/13/2006] [Indexed: 10/24/2022]
Abstract
Highly ordered morphological features were characterized for molecular dynamics simulated alkyl-modified silica models that represent chromatographic materials with enhanced shape recognition capability. Deep cavities (8-10A wide) within the alkyl chains were identified for C18 polymeric models corresponding to shape-selective RPLC stationary phases. The all-trans conformational distal-end segments of these isolated cavities averaged over a 100 ps simulation time interval were observed to increase (up to 15 A) in models with an increase in both surface coverage and corresponding shape selectivity. Similar-structure cavities with significant alkyl chain ordered regions (>11A) were isolated from two independent C18 models (differing in bonding chemistry, density and temperature) that represent highly shape-selective materials. The size and depth of these ordered regions increased (up to 28 A) for the extended-length C30 alkyl phase models. These initial results offer a physical representation of alkyl-modified surfaces that may facilitate the identification of potential molecular features that may be involved in the shape-selective retentive processes, as well as illustrating the potential for such computational techniques to predict the molecular recognition capabilities of novel analyte-specific sorbents.
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Affiliation(s)
- Katrice A Lippa
- Analytical Chemistry Division, Chemical Science and Technology Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
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Lippa KA, Schantz MM. Microheterogeneity evaluation of polycyclic aromatic hydrocarbons in particulate standard reference materials. Anal Bioanal Chem 2006; 387:2389-99. [PMID: 16896630 DOI: 10.1007/s00216-006-0583-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Revised: 05/24/2006] [Accepted: 05/31/2006] [Indexed: 10/24/2022]
Abstract
With the emergence of highly sensitive analytical techniques, the microanalysis of natural-matrix materials employing smaller sample sizes is increasingly more common, which subsequently warrants a homogeneity assessment for the individual components at the appropriate sampling level. Pressurized liquid extraction (PLE) in combination with gas chromatography/mass spectrometry (GC/MS) has been used to determine the sampling constants and evaluate the relative homogeneity of trace levels of polycyclic aromatic hydrocarbons (PAHs) for two previously certified particulate standard reference materials, SRM 1649a Urban Dust and SRM 1650b Diesel Particulate Matter, in the milligram sampling range. Fluoranthene, pyrene, benz[a]anthracene and benzo[e]pyrene within SRM 1650b Diesel Particulate Matter were deemed to be homogeneous, based on relatively small sampling constants (K (S)<100 mg), whereas the larger sampling constants (K (S)>100 mg) obtained for all PAHs in SRM 1649a Urban Dust suggest more material heterogeneity. The material heterogeneity of ten individual PAHs (phenanthrene, anthracene, fluoranthene, pyrene, benz[a]anthracene, benzo[k]fluoranthene, benzo[e]pyrene, benzo[a]pyrene, indeno[1,2,3-cd]pyrene and benzo[ghi]perylene) was also described via nonlinear relationships (i.e., power law) between subsampling error S (s) (%) and sample mass, which are used to predict analyte-specific minimum sample masses that result in a specific level of analytical uncertainty.
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Affiliation(s)
- Katrice A Lippa
- Analytical Chemistry Division, Chemical Science and Technology Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
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Lippa KA, Sander LC, Mountain RD. Molecular Dynamics Simulations of Alkylsilane Stationary-Phase Order and Disorder. 1. Effects of Surface Coverage and Bonding Chemistry. Anal Chem 2005; 77:7852-61. [PMID: 16351130 DOI: 10.1021/ac0510843] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
"Shape-selective" polymeric alkylsilane stationary phases are routinely employed over the more common monomeric phases in reversed-phase liquid chromatography (RPLC) to improve the separation of geometric isomers of shape-constrained solutes. We have investigated the molecular dynamics of chromatographic models that represent both monomeric and polymeric stationary phases with alkylsilane surface coverages and bonding chemistries typical of actual materials in an effort to elucidate the molecular-level structural features that control shape-selective separations. The structural characterization of these models is consistent with previous experimental observations of alkyl chain order and disorder: (1) alkyl chain order increases with increased surface coverage; and (2) monomeric and polymeric phases with similar surface coverages yield similar alkyl chain order (although subtle differences exist). In addition, a significant portion of the alkyl chain proximal to the silica surface is disordered (primarily gauche conformations) and the distal end is most ordered. Models that represent shape-selective RPLC phases possess a significant region of distal end chain order with primarily trans dihedral angle conformations. This is consistent with the view that the alkyl chains comprising polymeric stationary phases contain a series of well-defined and rigid voids in which shape-constrained solutes can penetrate and hence be selectively retained.
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Affiliation(s)
- Katrice A Lippa
- Analytical Chemistry Division and Physical and Chemical Properties Division, Chemical Sciences and Technology Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA.
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Lippa KA, Sander LC, Mountain RD. Molecular Dynamics Simulations of Alkylsilane Stationary-Phase Order and Disorder. 2. Effects of Temperature and Chain Length. Anal Chem 2005; 77:7862-71. [PMID: 16351131 DOI: 10.1021/ac051085v] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In an effort to elucidate the molecular-level structural features that control shape-selective separations, we have investigated the molecular dynamics of chromatographic models that represent both monomeric and polymeric stationary phases with alkylsilane length and temperature conditions analogous to actual materials of low to high shape selectivity. The structural characterization of these models is consistent with previous experimental observations of alkyl chain order and disorder: alkyl chain order increases both with alkyl chain length and with reduced temperature. Models that represent shape-selective reversed-phase liquid chromatography (RPLC) phases possess a significant region of distal end chain order with primarily trans dihedral angle conformations; the extension of these ordered regions into the phase increases with an increase in chain length. Models with extended chain length (C30) possess a higher degree of conformational order and are relatively insensitive to changes in surface coverage, bonding chemistry, and temperature. Chromatography models of various chain lengths and over a temperature range that represents highly shape-selective RPLC stationary phases all contain a series of well-defined and rigid cavities; the size and depth of these "slots" increase for the C30 models, which may promote the enhanced separations of larger size shape-constrained solutes, such as carotenoids.
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Affiliation(s)
- Katrice A Lippa
- Analytical Chemistry Division and Physical and Chemical Properties Division, Chemical Sciences and Technology Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA.
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Lippa KA, Roberts AL. Correlation analyses for bimolecular nucleophilic substitution reactions of chloroacetanilide herbicides and their structural analogs with environmentally relevant nucleophiles. Environ Toxicol Chem 2005; 24:2401-9. [PMID: 16268142 DOI: 10.1897/04-450r.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Second-order rate constants (kNuc) for aqueous-phase bimolecular nucleophilic substitution (SN2) reactions of a range of anionic nucleophiles with alachlor, propachlor, and two analogs of propachlor (a thioacetanilide and a beta-anilide) were fit to the Swain-Scott and Edwards models. Correlations of literature kNuc values for analogous reactions of methyl chloride and methyl benzenesulfonate were included for comparison. The Swain-Scott correlation yielded poor to fair results for chloroacetanilides and their analogs, with adjusted (adj) r2 values ranging from 0.67 to 0.89, which are comparable to correlations for CH3Cl and CH3OSO2Ph (r2 (adj) = 0.80 and 0.85, respectively). Both the one- and two-parameter Edwards models yielded improved correlations for the majority of substrates. A pronounced dependence on the substrate polarizability (alpha) factor generally was observed for the Edwards model, with a negligible dependence on the substrate basicity (beta) factor. Substrate polarizability factors for the one-parameter Edwards model were significantly larger for alachlor, propachlor, and the beta-anilide analog of propachlor than for methyl chloride and methyl benzenesulfonate. This indicates that the chloroacetanilides are activated toward SN2 reactions with highly reactive nucleophiles (e.g., HS-, PhS-, and Sn(2-)) relative to other saturated carbon substrates. At best, the Swain-Scott and Edwards models only furnish order-of-magnitude predictions of kNuc for the substrates investigated.
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Affiliation(s)
- Katrice A Lippa
- Department of Geography and Environmental Engineering, 313 Ames Hall, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218-2686, USA
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Sander LC, Lippa KA, Wise SA. Order and disorder in alkyl stationary phases. Anal Bioanal Chem 2005; 382:646-68. [PMID: 15827723 DOI: 10.1007/s00216-005-3127-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Revised: 01/21/2005] [Accepted: 01/24/2005] [Indexed: 11/28/2022]
Abstract
Covalently modified surfaces represent a unique state of matter that is not well described by liquid or solid phase models. The chemical bond in tethered alkanes imparts order to the surface in the form of anisotropic properties that are evident in chromatographic and spectroscopic studies. An understanding of the structure, conformation, and organization of alkyl-modified surfaces is requisite to the design of improved materials and the optimal utilization of existing materials. In recent years, the study of alkyl-modified surfaces has benefited from advances in modern analytical instrumentation. Aspects of alkyl chain conformation and motion have been investigated through the use of nuclear magnetic resonance spectroscopy, Fourier transform infrared spectroscopy, Raman spectroscopy, fluorescence spectroscopy, and neutron scattering studies. Chromatography provides complementary evidence of alkyl chain organization through interactions with solute probes. Computational simulations offer insights into the structure of covalently modified surfaces that may not be apparent through empirical observation. This manuscript reviews progress achieved in the study of the architecture of alkyl-modified surfaces.
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Affiliation(s)
- Lane C Sander
- Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899-8392, USA.
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Lippa KA, Demel S, Lau IH, Roberts AL. Kinetics and mechanism of the nucleophilic displacement reactions of chloroacetanilide herbicides: investigation of alpha-substituent effects. J Agric Food Chem 2004; 52:3010-3021. [PMID: 15137847 DOI: 10.1021/jf030290d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The ease with which alpha-chloroacetanilide herbicides undergo displacement reactions with strong nucleophiles, and their recalcitrance toward weak ones, is intimately related to their herbicidal properties and environmental chemistry. In this study, we investigate the kinetics and mechanisms of nucleophilic substitution reactions of propachlor and alachlor in aqueous solution. The role played by the alpha-amide group was examined by including several structurally related analogs of propachlor possessing modified alpha substituents. The overall second-order nature of the reaction, the negative DeltaS(double dagger) values, the weak influence of ionic strength on reactivity, and structure-reactivity trends together support an intermolecular S(N)2 mechanism rather than an intramolecular reaction for alpha-chloroacetanilides as well as the alpha-chlorothioacetanilide analog of propachlor. In contrast, the alpha-methylene analog exhibits kinetics and a salt effect consistent with anchimeric assistance by the aniline nitrogen. Electronic interactions with the alpha-anilide substituent, rather than neighboring group participation, can be inferred to govern the reactivity of alpha-chloroacetanilides toward nucleophiles.
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Affiliation(s)
- Katrice A Lippa
- Department of Geography and Environmental Engineering, 313 Ames Hall, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218-2686, USA
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Lippa KA, Sander LC, Wise SA. Chemometric studies of polycyclic aromatic hydrocarbon shape selectivity in reversed-phase liquid chromatography. Anal Bioanal Chem 2004; 378:365-77. [PMID: 14647936 DOI: 10.1007/s00216-003-2419-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2003] [Revised: 11/09/2003] [Accepted: 11/12/2003] [Indexed: 10/26/2022]
Abstract
The molecular shape recognition differences between monomeric and polymeric C18 stationary phases in the reversed-phase liquid chromatography (RPLC) separation of unsubstituted polycyclic aromatic hydrocarbons (PAHs) and methyl-substituted polycyclic aromatic hydrocarbons (MPAHs) are examined through the use of partial least squares (PLS) analysis techniques. The resulting PLS models are able to describe the enhanced shape selectivity of the polymeric phase for recognizing subtle structural differences among planar and nonplanar isomers. PLS component analyses of these models reveal that spatial and topological descriptors are primarily used to rank structural differences among the PAHs (i.e., fused-ring patterns, molecular length and breadth) that control such shape-selective chromatographic processes. This is consistent with the view that polymeric alkyl chain stationary phases contain size- and shape-specific "slots" that promote the separation of structurally-related solutes. In contrast, the monomeric phase model is limited in resolving both the isomer classes and the nonplanarity shape differences among the PAHs. However, an improvement of shape recognition on the monomeric phase was elucidated by the PLS model for two PAHs (phenanthro[3,4-c]phenanthrene and dibenzo[g,p]chrysene) exhibiting the most extreme nonplanarity. These results suggest that a limited amount of space between alkyl chains may exist within the higher-density polymeric phase to recognize shape differences among the bulkier and nonplanar solutes.
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Affiliation(s)
- Katrice A Lippa
- Analytical Chemistry Division, Chemical Sciences and Technology Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8392, Gaithersburg, MD 20899-8392, USA.
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Loch AR, Lippa KA, Carlson DL, Chin YP, Traina SJ, Roberts AL. Nucleophilic aliphatic substitution reactions of propachlor, alachlor, and metolachlor with bisulfide (HS-) and polysulfides (Sn2-). Environ Sci Technol 2002; 36:4065-4073. [PMID: 12380076 DOI: 10.1021/es0206285] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Reactions of bisulfide and polysulfides with alachlor, propachlor, and metolachlor were examined in aqueous solution to investigate the role reduced sulfur species could play in effecting abiotic transformations of chloroacetanilide herbicides. Experiments at 25 degrees C demonstrated that reactions were approximately first-order in HS- concentration and revealed that polysulfides are considerably more reactive than HS-. delta H not equal to values for reactions of the three chloroacetanilides with HS- are statistically indistinguishable at the 95% confidence level, as are delta S not equal to values, despite significant differences in second-order rate constants (kHS-). Transformation products were characterized by GC/MS (in some cases following methylation) and were found to be consistent with substitution of chlorine by the sulfur nucleophile. Products containing multiple sulfur atoms were observed for the reactions of chloroacetanilides with polysulfides, while products resulting from reaction with HS- only possessed a single sulfur atom. When second-order rate constants at 25 degrees C are multiplied by HS- and polysulfide concentrations reported in salt marsh porewaters, predicted half-lives range from minutes to hours. HS- and especially polysulfides could thus exert a substantial influence on the fate of chloroacetanilide herbicides in aquatic environments. Oxidation of the resulting sulfur-substituted products could generate ethane sulfonic acid derivatives, previously reported as prevalent chloroacetanilide degradates.
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Affiliation(s)
- A R Loch
- School of Natural Resources, Ohio State University, Columbus, Ohio, USA
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Lippa KA, Roberts AL. Nucleophilic aromatic substitution reactions of chloroazines with bisulfide (HS-) and polysulfides (Sn2-). Environ Sci Technol 2002; 36:2008-18. [PMID: 12026986 DOI: 10.1021/es011255v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Reactions of bisulfide and polysulfides with chloroazines (important constituents of agrochemicals and textile dyes) were examined in aqueous solution at 25 degrees C. For atrazine, rates are first-order in polysulfide concentration, and polysulfide dianions are the principal reactive nucleophiles; no measurable reaction occurs with HS-. Second-order rate constants for reactions of an array of chloroazines with polysulfides are several orders of magnitude greater than for reactions with HS-. Transformation products indicate the substitution of halogen(s) by sulfur. Ring aza nitrogens substantially enhance reactivity through a combination of inductive and mesomeric effects, and electron-withdrawing or electron-donating substituents markedly enhance or diminish reactivity, respectively. The overall second-order nature of the reaction, the products observed, and reactivity trends are all consistent with a nucleophilic aromatic substitution (S(N)Ar) mechanism. Rate constants for reactions with HS- and Sn2- (n = 2-5) correlate only weakly with lowest unoccupied molecular orbital energies, suggesting that the electrophilicity of a chloroazine is not the sole determinant of its reactivity. When second-order rate constants are extrapolated to HS- and Sn2- concentrations reported in salt marsh pore waters, half-lives of minutes to years are obtained. Polysulfides in particular could play an important role in effecting abiotic transformations of chloroazines in hypoxic marine waters.
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Affiliation(s)
- K A Lippa
- Department of Geography and Environmental Engineering, The Johns Hopkins University, Baltimore, Maryland 21218-2686, USA
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Godfrey JT, Foster GD, Lippa KA. Estimated Annual Loads of Selected Organic Contaminants to Chesapeake Bay via a Major Tributary. Environ Sci Technol 1995; 29:2059-2064. [PMID: 22191356 DOI: 10.1021/es00008a027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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