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Prediction and eval...
Prediction and evaluation of the effect of pre-centrifugation sample management on the measurable untargeted LC-MS plasma metabolome
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- Zheng, Rui, 1990 (author)
- Uppsala universitet,Medicinsk epidemiologi,Chalmers Univ Technol, Dept Biol & Biol Engn, Div Food & Nutr Sci, Gothenburg, Sweden.,Chalmers tekniska högskola,Chalmers University of Technology,Uppsala University,Department of Surgical Sciences, Uppsala University, Uppsala, Sweden; Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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- Brunius, Carl, 1974 (author)
- Uppsala universitet,Medicinsk epidemiologi,Chalmers Univ Technol, Dept Biol & Biol Engn, Div Food & Nutr Sci, Gothenburg, Sweden.;Chalmers Univ Technol, Chalmers Mass Spectrometry Infrastruct, Gothenburg, Sweden.,Chalmers tekniska högskola,Chalmers University of Technology,Uppsala University,Department of Surgical Sciences, Uppsala University, Uppsala, Sweden; Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Chalmers Mass Spectrometry Infrastructure, Chalmers University of Technology, Gothenburg, Sweden
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- Shi, Lin, 1988 (author)
- Shaanxi Normal University,Chalmers tekniska högskola,Chalmers University of Technology,Chalmers Univ Technol, Dept Biol & Biol Engn, Div Food & Nutr Sci, Gothenburg, Sweden.;Shaanxi Normal Univ, Sch Food Engn & Nutr Sci, Xian, Peoples R China.,Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi’ an, China
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- Zafar, Huma (author)
- Sahlgrenska universitetssjukhuset,Sahlgrenska University Hospital,Sahlgrens Univ Hosp, Biobank West, Gothenburg, Vastra Gotaland, Sweden.,Biobank West, Sahlgrenska University Hospital, Region Västra Götaland, Sweden
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- Paulson, Linda (author)
- Sahlgrenska universitetssjukhuset,Sahlgrenska University Hospital,Sahlgrens Univ Hosp, Biobank West, Gothenburg, Vastra Gotaland, Sweden.,Biobank West, Sahlgrenska University Hospital, Region Västra Götaland, Sweden
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- Landberg, Rikard, 1981 (author)
- Umeå universitet,Avdelningen för medicin,Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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- Torinsson Naluai, Åsa, 1968 (author)
- Gothenburg University,Göteborgs universitet,Core Facilities, Genomics,Institutionen för biomedicin,Core Facilities, Genomics,Institute of Biomedicine,University of Gothenburg,Sahlgrenska universitetssjukhuset,Sahlgrenska University Hospital,Biobank West, Sahlgrenska University Hospital, Region Västra Götaland, Sweden; Institute of Biomedicine, Biobank Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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(creator_code:org_t)
- Elsevier BV, 2021
- 2021
- English.
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In: Analytica Chimica Acta. - : Elsevier BV. - 0003-2670 .- 1873-4324. ; 1182
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Abstract
Subject headings
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- Optimal handling is the most important means to ensure adequate sample quality. We aimed to investigate whether pre-centrifugation delay time and temperature could be accurately predicted and to what extent variability induced by pre-centrifugation management can be adjusted for. We used untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics to predict and evaluate the influence of pre-centrifugation temperature and delayed time on plasma samples. Pre-centrifugation temperature (4, 25 and 37 °C; classification rate 87%) and time (5–210 min; Q2 = 0.82) were accurately predicted using Random Forest (RF). Metabolites uniquely reflecting temperature and temperature-time interactions were discovered using a combination of RF and generalized linear models. Time-related metabolite profiles suggested a perturbed stability of the metabolome at all temperatures in the investigated time period (5–210 min), and the variation at 4 °C was observed in particular before 90 min. Fourteen and eight metabolites were selected and validated for accurate prediction of pre-centrifugation temperature (classification rate 94%) and delay time (Q2 = 0.90), respectively. In summary, the metabolite profile was rapidly affected by pre-centrifugation delay at all temperatures and thus the pre-centrifugation delay should be as short as possible for metabolomics analysis. The metabolite panels provided accurate predictions of pre-centrifugation delay time and temperature in healthy individuals in a separate validation sample. Such predictions could potentially be useful for assessing legacy samples where relevant metadata is lacking. However, validation in larger populations and different phenotypes, including disease states, is needed.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Farmaceutiska vetenskaper (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Pharmaceutical Sciences (hsv//eng)
- NATURVETENSKAP -- Kemi -- Analytisk kemi (hsv//swe)
- NATURAL SCIENCES -- Chemical Sciences -- Analytical Chemistry (hsv//eng)
- NATURVETENSKAP -- Geovetenskap och miljövetenskap -- Miljövetenskap (hsv//swe)
- NATURAL SCIENCES -- Earth and Related Environmental Sciences -- Environmental Sciences (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Keyword
- Plasma
- Untargeted metabolomics
- Machine learning
- Biobank
- Pre-centrifugation management
- Sample quality
- Biobank
- Machine learning
- Plasma
- Pre-centrifugation management
- Sample quality
- Untargeted metabolomics
Publication and Content Type
- art (subject category)
- ref (subject category)
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