Comparative Evaluation of Plasma Metabolomic Data from Multiple Laboratories
Shin Nishiumi,
Yoshihiro Izumi,
Akiyoshi Hirayama,
Masatomo Takahashi,
Motonao Nakao,
Kosuke Hata,
Daisuke Saigusa,
Eiji Hishinuma,
Naomi Matsukawa,
Suzumi M. Tokuoka,
Yoshihiro Kita,
Fumie Hamano,
Nobuyuki Okahashi,
Kazutaka Ikeda,
Hiroki Nakanishi,
Kosuke Saito,
Masami Yokota Hirai,
Masaru Yoshida,
Yoshiya Oda,
Fumio Matsuda,
Takeshi Bamba
Affiliations
Shin Nishiumi
Department of Omics Medicine, Hyogo College of Medicine, 1-1 Mukogawa-cho, Nishinomiya-city, Hyogo 663-8501, Japan
Yoshihiro Izumi
Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-city, Fukuoka 812-8582, Japan
Akiyoshi Hirayama
Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka-city, Yamagata 997-0052, Japan
Masatomo Takahashi
Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-city, Fukuoka 812-8582, Japan
Motonao Nakao
Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-city, Fukuoka 812-8582, Japan
Kosuke Hata
Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-city, Fukuoka 812-8582, Japan
Daisuke Saigusa
Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo 173-8605, Japan
Eiji Hishinuma
Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai-city, Miyagi 980-8573, Japan
Naomi Matsukawa
Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai-city, Miyagi 980-8573, Japan
Suzumi M. Tokuoka
Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
Yoshihiro Kita
Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
Fumie Hamano
Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
Nobuyuki Okahashi
Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita-city, Osaka 565-0871, Japan
Kazutaka Ikeda
Laboratory of Biomolecule Analysis, Department of Applied Genomics, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu-city, Chiba 292-0818, Japan
Division of Medical Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi Kawasaki-ku, Kawasaki-city, Kanagawa 210-9501, Japan
Masami Yokota Hirai
RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama-city, Kanagawa 230-0045, Japan
Masaru Yoshida
Department of Food Science & Nutrition, Research Institute of Food and Nutritional Sciences, Graduate School of Human Science & Environment, University of Hyogo, 1-1-12 Shinzaikehon-cho, Himeji-city, Hyogo 670-0092, Japan
Yoshiya Oda
Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
Fumio Matsuda
Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita-city, Osaka 565-0871, Japan
Takeshi Bamba
Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-city, Fukuoka 812-8582, Japan
In mass spectrometry-based metabolomics, the differences in the analytical results from different laboratories/machines are an issue to be considered because various types of machines are used in each laboratory. Moreover, the analytical methods are unique to each laboratory. It is important to understand the reality of inter-laboratory differences in metabolomics. Therefore, we have evaluated whether the differences in analytical methods, with the exception sample pretreatment and including metabolite extraction, are involved in the inter-laboratory differences or not. In this study, nine facilities are evaluated for inter-laboratory comparisons of metabolomic analysis. Identical dried samples prepared from human and mouse plasma are distributed to each laboratory, and the metabolites are measured without the pretreatment that is unique to each laboratory. In these measurements, hydrophilic and hydrophobic metabolites are analyzed using 11 and 7 analytical methods, respectively. The metabolomic data acquired at each laboratory are integrated, and the differences in the metabolomic data from the laboratories are evaluated. No substantial difference in the relative quantitative data (human/mouse) for a little less than 50% of the detected metabolites is observed, and the hydrophilic metabolites have fewer differences between the laboratories compared with hydrophobic metabolites. From evaluating selected quantitatively guaranteed metabolites, the proportion of metabolites without the inter-laboratory differences is observed to be slightly high. It is difficult to resolve the inter-laboratory differences in metabolomics because all laboratories cannot prepare the same analytical environments. However, the results from this study indicate that the inter-laboratory differences in metabolomic data are due to measurement and data analysis rather than sample preparation, which will facilitate the understanding of the problems in metabolomics studies involving multiple laboratories.
