International Lipidomics Society
Published July 31, 2024 | Version v1
Dataset Open

Lab_06_OTHER - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards

Authors/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

Lab_06_OTHER - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files

This dataset is part of the ILS Ceramide Ring Trial. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.

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. The archived version of the lab reports, workflow source code and manuscript visualizations are also available here.

Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.

The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.

Files

Lab_06_OTHER.zip

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Additional details

Related works

Is part of
Dataset: 10.5281/zenodo.12632989 (DOI)
Is supplement to
Dataset: 10.5281/zenodo.10081970 (DOI)