International Lipidomics Society
Published August 1, 2024 | Version v1
Dataset Open

Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards

Creators

  • 1. Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore.;Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore.;Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore 169857, Singapore.
  • 2. Institute for Bio- and Geosciences (IBG-5), Forschungszentrum Juelich GmbH, 52428 Juelich, Germany.;Department of Analytical Chemistry, University of Vienna, Vienna, Austria.
  • 3. Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore.

Contributors

Researchers:

  • 1. Neural Regeneration Laboratory, Ottawa Institute of Systems Biology, Ottawa Brain and Mind Research Institute, Department of Biochemistry, Microbiology, and Immunology, and Department of Chemistry, Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, K1H 8M5, Canada.
  • 2. RIKEN Center for Sustainable Resource Science, Yokohama, Japan.;RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
  • 3. Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3‑1‑1, Maidashi, Higashi‑ku, Fukuoka 812‑8582, Japan.
  • 4. MetaboHUBMetaToul Facility, I2MC U1297 Inserm, Toulouse, France.
  • 5. Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
  • 6. Metabolomics Core Facility-MetCore, Universidad de los Andes, Bogotá 111711, Colombia.
  • 7. Laboratory for Lipidomics and Lipid Biology, Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9NT, United Kingdom.
  • 8. Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
  • 9. Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
  • 10. Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic.
  • 11. Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.;Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Bundoora, VIC, 3086, Australia.
  • 12. Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191, Gif sur Yvette, France.
  • 13. Department of Analytical Chemistry, University of Vienna, Vienna, Austria.
  • 14. Avanti Polar Lipids.
  • 15. Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom.
  • 16. Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland.;Department of Chemistry, University of Turku, Turku, Finland.
  • 17. Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, 04013 Leipzig, Germany.;Center for Biotechnology and Biomedicine, University of Leipzig, 04013 Leipzig, Germany.;Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, 01307 Dresden, Germany.
  • 18. Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavik, Iceland.;ArcticMass, Reykjavik, Iceland.
  • 19. Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
  • 20. Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands.
  • 21. Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore.
  • 22. Metabolomics and Proteomics Core, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, 85764, Germany.
  • 23. Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands.
  • 24. University Hospital of Regensburg, Institute of Clinical Chemistry and Laboratory Medicine, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany.
  • 25. Institute of Clinical Chemistry, University Hospital Zurich, 8952 Zuerich, Switzerland.
  • 26. CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
  • 27. Chemical Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899, USA.
  • 28. Laboratory for Lipidomics and Lipid Biology, Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9NT, United Kingdom.
  • 29. Core Facility Mass Spectrometry, Medical University of Graz, 8010 Graz, Austria.
  • 30. LipidALL Technologies, Changzhou 213000, Jiangshu, China.;State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
  • 31. Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, 04013 Leipzig, Germany.;Center for Biotechnology and Biomedicine, University of Leipzig, 04013 Leipzig, Germany.
  • 32. Department of Chemistry, Yonsei University, Seoul, 03722, Korea.
  • 33. Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad de Buenos Aires, Argentina.;Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Gueiraldes, 2160 C1428EGA Buenos Aires, Argentina.;Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Departamento de Desarrollo Analítico y Control de Procesos, Instituto Nacional de Tecnología Industrial, Av. General Paz 5445, B1650WAB Buenos Aires, Argentina.
  • 34. Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad de Buenos Aires, Argentina.;Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Buenos Aires, Junin 954, C1113AAD, CABA, Argentina.
  • 35. National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India.
  • 36. Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad de Buenos Aires, Argentina.
  • 37. Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore.;National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India.
  • 38. Laboratory for Lipidomics and Lipid Biology, Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9NT, United Kingdom.;Lydia Becker Institute of Immunology and Inflammation; Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9NT, United Kingdom.
  • 39. Systems Immunity Research Institute, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
  • 40. Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland.;School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden.
  • 41. Institute for Stem Cell Science and Regenerative Medicine, 560065 Bangalore, India.
  • 42. Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan.;Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
  • 43. Chemical Science Division, National Institute of Standards and Technology, Charleston, South Carolina, 29412, USA.
  • 44. Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFATulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria.
  • 45. State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
  • 46. RIKEN Center for Sustainable Resource Science, Yokohama, Japan.;RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.;Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.;Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.
  • 47. St. Paul's Hospital, Department of Pathology and Laboratory Medicine, Vancouver, British Columbia, Canada.
  • 48. Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.;Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm, Sweden.
  • 49. Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32610, United States.
  • 50. Lipidomics Consulting Ltd., Espoo, Finland.
  • 51. Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore.;Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore.;College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.

Description

Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards

In this community effort, we compared measurements between 34 laboratories from 19 countries, utilizing mixtures of labelled authentic synthetic standards, to quantify by mass spectrometry four clinically used ceramide species in the NIST (National Institute of Standards and Technology) human blood plasma Standard Reference Material (SRM) 1950, as well as new suite of candidate plasma reference materials (RM 8231). Participants either utilized a provided validated method (SOP) and/or their method of choice (OTHER). Mean concentration values, and intra- and inter-laboratory coefficients of variation (CV) were calculated using single-point and multi-point calibrations, respectively.

The attached file "ILS-Ceramide-Ring-Trial-Datasets.csv"  and the table below map the lab number (LabNum) used in the manuscript in all plots to the originally assigned submission Id (LabId) used in the anonymized reports containing the peak areas submitted by each lab for their SOP (Standard) and / or OTHER (Preferred) workflow. The table below provides further information on the separation used (LC), the mass analyzer type (QQQ=Triple Quads and Traps, Orbitrap, TOF) and the associated mass analyzer resolution (LowRes, HighRes), and links each LabNum to the corresponding dataset name and Zenodo DOI, if available. In order to retain the anonymity of all participating labs w.r.t. the submitted datasets, only the converted mzML files are provided in the linked submissions. Please note that labs were free to choose whether they wanted to disclose their MS data or not. Thus, missing datasets indicate that the corresponding lab did not provide their raw / mzML data. 

All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: https://zenodo.org/doi/10.5281/zenodo.10081970. This links to releases of the following GitHub repository: https://github.com/lifs-tools/ils-ceramide-ring-trial. 

Ring Trial mzML Datasets

LabNum LabId Protocol LC MassAnalyzerType MassAnalyzerResolution DatasetName DOI
1 02b SOP RP QQQ LowRes Lab_01_SOP 10.5281/zenodo.13134264
2 3 OTHER RP QQQ LowRes Lab_02_OTHER 10.5281/zenodo.13145059
3 4 SOP RP QQQ LowRes Lab_03_SOP 10.5281/zenodo.13134437
4 5 OTHER RP QQQ LowRes Lab_04_OTHER  
5 7 OTHER RP Orbitrap HighRes Lab_05_OTHER 10.5281/zenodo.13134439
6 9 OTHER FIA QQQ LowRes Lab_06_OTHER 10.5281/zenodo.13134441
7 10a SOP RP QQQ LowRes Lab_07_SOP 10.5281/zenodo.13134445
7 10b OTHER RP QQQ LowRes Lab_07_OTHER 10.5281/zenodo.13134443
8 12 SOP RP QQQ LowRes Lab_08_SOP 10.5281/zenodo.13134447
9 13 OTHER RP QQQ LowRes Lab_09_OTHER  
10 14 SOP RP QQQ LowRes Lab_10_SOP  
11 15 SOP RP QQQ LowRes Lab_11_SOP 10.5281/zenodo.13134449
12 16 OTHER RP Orbitrap HighRes Lab_12_OTHER 10.5281/zenodo.13134451
13 17a OTHER RP TOF HighRes Lab_13_OTHER  
14 18a SOP RP QQQ LowRes Lab_14_SOP 10.5281/zenodo.13135617
14 18b SOP RP QQQ LowRes Lab_14_SOP 10.5281/zenodo.13135617
15 19 SOP RP QQQ LowRes Lab_15_SOP 10.5281/zenodo.13135625
16 20a SOP RP QQQ LowRes Lab_16_SOP  
16 20b OTHER RP QQQ LowRes Lab_16_OTHER  
17 21 SOP RP QQQ LowRes Lab_17_SOP  
18 22 SOP RP QQQ LowRes Lab_18_SOP 10.5281/zenodo.13135627
19 23 SOP RP QQQ LowRes Lab_19_SOP 10.5281/zenodo.13135629
20 24 SOP RP QQQ LowRes Lab_20_SOP  
21 25 SOP RP QQQ LowRes Lab_21_SOP 10.5281/zenodo.13244007
22 26a OTHER FIA Orbitrap HighRes Lab_22_OTHER  
22 26b OTHER FIA QQQ LowRes Lab_22_OTHER  
23 27 SOP RP QQQ LowRes Lab_23_SOP 10.5281/zenodo.13135632
24 28 SOP RP QQQ LowRes Lab_24_SOP 10.5281/zenodo.13135634
25 29a SOP RP TOF HighRes Lab_25_SOP 10.5281/zenodo.13136167
25 29b OTHER SFC QQQ LowRes Lab_25_OTHER 10.5281/zenodo.13135638
26 30 SOP RP QQQ LowRes Lab_26_SOP 10.5281/zenodo.13136171
27 31 SOP RP QQQ LowRes Lab_27_SOP 10.5281/zenodo.13136176
28 32 OTHER RP TOF HighRes Lab_28_OTHER  
29 33 OTHER RP QQQ LowRes Lab_29_OTHER  
30 34 SOP RP QQQ LowRes Lab_30_SOP  
31 35 OTHER RP QQQ LowRes Lab_31_OTHER  
32 36 SOP RP QQQ LowRes Lab_32_SOP 10.5281/zenodo.13166454
33 37 OTHER RP QQQ LowRes Lab_33_OTHER 10.5281/zenodo.13732469
34 38 SOP RP QQQ LowRes Lab_34_SOP 10.5281/zenodo.13324807

Files

ILS-Ceramide-Ring-Trial-Datasets.csv

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Additional details

Is part of
Dataset: 10.5281/zenodo.12632989 (DOI)
Is supplement to
Dataset: 10.5281/zenodo.10081970 (DOI)
Is supplemented by
Dataset: 10.5281/zenodo.13134264 (DOI)
Dataset: 10.5281/zenodo.13134437 (DOI)
Dataset: 10.5281/zenodo.13134439 (DOI)
Dataset: 10.5281/zenodo.13134441 (DOI)
Dataset: 10.5281/zenodo.13134443 (DOI)
Dataset: 10.5281/zenodo.13134445 (DOI)
Dataset: 10.5281/zenodo.13134447 (DOI)
Dataset: 10.5281/zenodo.13134449 (DOI)
Dataset: 10.5281/zenodo.13134451 (DOI)
Dataset: 10.5281/zenodo.13134453 (DOI)
Dataset: 10.5281/zenodo.13134580 (DOI)
Dataset: 10.5281/zenodo.13135617 (DOI)
Dataset: 10.5281/zenodo.13135625 (DOI)
Dataset: 10.5281/zenodo.13135627 (DOI)
Dataset: 10.5281/zenodo.13135629 (DOI)
Dataset: 10.5281/zenodo.13135632 (DOI)
Dataset: 10.5281/zenodo.13135634 (DOI)
Dataset: 10.5281/zenodo.13135638 (DOI)
Dataset: 10.5281/zenodo.13136167 (DOI)
Dataset: 10.5281/zenodo.13136171 (DOI)
Dataset: 10.5281/zenodo.13136176 (DOI)
Dataset: 10.5281/zenodo.13136178 (DOI)
Dataset: 10.5281/zenodo.13145059 (DOI)
Dataset: 10.5281/zenodo.13166454 (DOI)
Dataset: 10.5281/zenodo.13244007 (DOI)
Dataset: 10.5281/zenodo.13324807 (DOI)
Dataset: 10.5281/zenodo.13732469 (DOI)