Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma

John A Bowden¹, Alan Heckert², Candice Z Ulmer³, Christina M Jones³, Jeremy P Koelmel⁴, Laila Abdullah⁵, Linda Ahonen⁶, Yazen Alnouti⁷, Aaron M Armando⁸, John M Asara^{9

10}, Takeshi Bamba¹¹, John R Barr¹², Jonas Bergquist¹³, Christoph H Borchers^{14

15

16

17}, Joost Brandsma¹⁸, Susanne B Breitkopf⁹, Tomas Cajka¹⁹, Amaury Cazenave-Gassiot²⁰, Antonio Checa²¹, Michelle A Cinel²², Romain A Colas²³, Serge Cremers²⁴, Edward A Dennis⁸, James E Evans⁵, Alexander Fauland²¹, Oliver Fiehn^{19

25}, Michael S Gardner¹², Timothy J Garrett⁴, Katherine H Gotlinger²⁶, Jun Han¹⁴, Yingying Huang²⁷, Aveline Huipeng Neo²⁰, Tuulia Hyötyläinen²⁸, Yoshihiro Izumi¹¹, Hongfeng Jiang²⁴, Houli Jiang²⁶, Jiang Jiang⁸, Maureen Kachman²⁹, Reiko Kiyonami²⁷, Kristaps Klavins³⁰, Christian Klose³¹, Harald C Köfeler³², Johan Kolmert²¹, Therese Koal³⁰, Grielof Koster¹⁸, Zsuzsanna Kuklenyik¹², Irwin J Kurland³³, Michael Leadley³⁴, Karen Lin¹⁴, Krishna Rao Maddipati³⁵, Danielle McDougall⁴, Peter J Meikle²², Natalie A Mellett²², Cian Monnin³⁶, M Arthur Moseley³⁷, Renu Nandakumar²⁴, Matej Oresic³⁸, Rainey Patterson⁴, David Peake²⁷, Jason S Pierce³⁹, Martin Post³⁴, Anthony D Postle¹⁸, Rebecca Pugh⁴⁰, Yunping Qiu³³, Oswald Quehenberger⁴¹, Parsram Ramrup³⁶, Jon Rees¹², Barbara Rembiesa³⁹, Denis Reynaud³⁴, Mary R Roth⁴², Susanne Sales⁴³, Kai Schuhmann⁴³, Michal Laniado Schwartzman²⁶, Charles N Serhan²³, Andrej Shevchenko⁴³, Stephen E Somerville⁴⁴, Lisa St John-Williams³⁷, Michal A Surma³¹, Hiroaki Takeda¹¹, Rhishikesh Thakare⁷, J Will Thompson³⁷, Federico Torta²⁰, Alexander Triebl³², Martin Trötzmüller³², S J Kumari Ubhayasekera¹³, Dajana Vuckovic³⁶, Jacquelyn M Weir²², Ruth Welti⁴², Markus R Wenk²⁰, Craig E Wheelock²¹, Libin Yao⁴², Min Yuan⁹, Xueqing Heather Zhao³³, Senlin Zhou³⁵

Affiliations

¹ Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC john.bowden@nist.gov.
² Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD.
³ Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC.
⁴ Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL.
⁵ The Roskamp Institute, Sarasota, FL.
⁶ Steno Diabetes Center Copenhagen, Gentofte, Denmark.
⁷ Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE.
⁸ Departments of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA.
⁹ Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA.
¹⁰ Department of Medicine, Harvard Medical School, Boston, MA.
¹¹ Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan.
¹² Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA.
¹³ Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden.
¹⁴ University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada.
¹⁵ Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
¹⁶ Gerald Bronfman Department of Oncology McGill University, Montreal, Quebec, Canada.
¹⁷ Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.
¹⁸ Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton General Hospital, University of Southampton, Southampton, United Kingdom.
¹⁹ National Institutes of Health West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA.
²⁰ Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore.
²¹ Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
²² Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
²³ Department of Anesthesiology, Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital and Harvard Medical School, Boston, MA.
²⁴ Biomarker Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY.
²⁵ Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia.
²⁶ Department of Pharmacology, New York Medical College School of Medicine, Valhalla, NY.
²⁷ Thermo Fisher Scientific, San Jose, CA.
²⁸ Department of Chemistry, Örebro University, Örebro, Sweden.
²⁹ Metabolomics Core, BRCF, University of Michigan, Ann Arbor, MI.
³⁰ Biocrates Life Sciences AG, Innsbruck, Austria.
³¹ Lipotype GmbH, Dresden, Germany.
³² Core Facility for Mass Spectrometry, Medical University of Graz, Graz, Austria.
³³ Stable Isotope and Metabolomics Core Facility, Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY.
³⁴ Analytical Facility of Bioactive Molecules, The Hospital for Sick Children Research Institute, Toronto, ON, Canada.
³⁵ Lipidomics Core Facility and Department of Pathology, Wayne State University, Detroit, MI.
³⁶ Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada.
³⁷ Proteomics and Metabolomics Shared Resource, Levine Science Research Center, Duke University School of Medicine, Durham, NC.
³⁸ Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
³⁹ Department of Biochemistry and Molecular Biology Medical University of South Carolina, Charleston, SC.
⁴⁰ Chemical Sciences Division, Environmental Specimen Bank Group, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC.
⁴¹ Departments of Medicine and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA.
⁴² Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Manhattan, KS.
⁴³ Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
⁴⁴ Hollings Marine Laboratory, Medical University of South Carolina, Charleston, SC.

PMID: 28986437
PMCID: PMC5711491
DOI: 10.1194/jlr.M079012

Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma

John A Bowden et al. J Lipid Res. 2017 Dec.

. 2017 Dec;58(12):2275-2288.

doi: 10.1194/jlr.M079012. Epub 2017 Oct 6.

Authors

Affiliations

¹ Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC john.bowden@nist.gov.
² Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD.
³ Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC.
⁴ Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL.
⁵ The Roskamp Institute, Sarasota, FL.
⁶ Steno Diabetes Center Copenhagen, Gentofte, Denmark.
⁷ Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE.
⁸ Departments of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA.
⁹ Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA.
¹⁰ Department of Medicine, Harvard Medical School, Boston, MA.
¹¹ Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan.
¹² Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA.
¹³ Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden.
¹⁴ University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada.
¹⁵ Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
¹⁶ Gerald Bronfman Department of Oncology McGill University, Montreal, Quebec, Canada.
¹⁷ Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.
¹⁸ Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton General Hospital, University of Southampton, Southampton, United Kingdom.
¹⁹ National Institutes of Health West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA.
²⁰ Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore.
²¹ Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
²² Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
²³ Department of Anesthesiology, Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital and Harvard Medical School, Boston, MA.
²⁴ Biomarker Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY.
²⁵ Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia.
²⁶ Department of Pharmacology, New York Medical College School of Medicine, Valhalla, NY.
²⁷ Thermo Fisher Scientific, San Jose, CA.
²⁸ Department of Chemistry, Örebro University, Örebro, Sweden.
²⁹ Metabolomics Core, BRCF, University of Michigan, Ann Arbor, MI.
³⁰ Biocrates Life Sciences AG, Innsbruck, Austria.
³¹ Lipotype GmbH, Dresden, Germany.
³² Core Facility for Mass Spectrometry, Medical University of Graz, Graz, Austria.
³³ Stable Isotope and Metabolomics Core Facility, Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY.
³⁴ Analytical Facility of Bioactive Molecules, The Hospital for Sick Children Research Institute, Toronto, ON, Canada.
³⁵ Lipidomics Core Facility and Department of Pathology, Wayne State University, Detroit, MI.
³⁶ Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada.
³⁷ Proteomics and Metabolomics Shared Resource, Levine Science Research Center, Duke University School of Medicine, Durham, NC.
³⁸ Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
³⁹ Department of Biochemistry and Molecular Biology Medical University of South Carolina, Charleston, SC.
⁴⁰ Chemical Sciences Division, Environmental Specimen Bank Group, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC.
⁴¹ Departments of Medicine and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA.
⁴² Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Manhattan, KS.
⁴³ Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
⁴⁴ Hollings Marine Laboratory, Medical University of South Carolina, Charleston, SC.

PMID: 28986437
PMCID: PMC5711491
DOI: 10.1194/jlr.M079012

Abstract

As the lipidomics field continues to advance, self-evaluation within the community is critical. Here, we performed an interlaboratory comparison exercise for lipidomics using Standard Reference Material (SRM) 1950-Metabolites in Frozen Human Plasma, a commercially available reference material. The interlaboratory study comprised 31 diverse laboratories, with each laboratory using a different lipidomics workflow. A total of 1,527 unique lipids were measured across all laboratories and consensus location estimates and associated uncertainties were determined for 339 of these lipids measured at the sum composition level by five or more participating laboratories. These evaluated lipids detected in SRM 1950 serve as community-wide benchmarks for intra- and interlaboratory quality control and method validation. These analyses were performed using nonstandardized laboratory-independent workflows. The consensus locations were also compared with a previous examination of SRM 1950 by the LIPID MAPS consortium. While the central theme of the interlaboratory study was to provide values to help harmonize lipids, lipid mediators, and precursor measurements across the community, it was also initiated to stimulate a discussion regarding areas in need of improvement.

Keywords: National Institute of Standards and Technology; Standard Reference Material 1950; fatty acyls; glycerolipids; lipids; phospholipids; quality control; quantitation; sphingolipids; sterols.

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Figures

**Fig. 1.**
Lipid class composition of SRM 1950, according to number of lipid species (A) and concentration (B). Only lipid species that were measured by at least five participating laboratories are included in this figure (n = 339).

**Fig. 2.**
COD (in percent) for the MEDM lipids (n ≥ 5 laboratories reporting) organized by lipid class. Each point on the figure represents a single sum lipid composition. The COD was calculated by dividing the standard uncertainty by the final MEDM. CODs not shown in the figure are FC, eicosanoids, PGs, and PSs.

**Fig. 3.**
Sum of MEDM values for the most (in micromoles per milliliter plasma) (A) and least (in nanomoles per milliliter plasma) (B) concentrated lipid classes (EICO* in pmol/ml plasma) compared with the sum of concentrations provided by the LIPID MAPS consortium. The comparisons entail summing only the lipids measured in common between the compared data sets, with the total number of lipids fitting this criterion (per class and total) provided above each bar graph. Other PL represents the sum of PG and PS species. The error bars associated with the values standard uncertainties on the location estimates. Further information on this comparison, including total lipid concentrations, is included in the supplemental material (supplemental Table S17).

See this image and copyright information in PMC

References

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Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma

Affiliations

Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma

Authors

Affiliations

Abstract

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References

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LinkOut - more resources

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