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Bertić M, Zimmer I, Andrés-Montaner D, Rosenkranz M, Kangasjärvi J, Schnitzler JP, Ghirardo A. Automatization of metabolite extraction for high-throughput metabolomics: case study on transgenic isoprene-emitting birch. TREE PHYSIOLOGY 2023; 43:1855-1869. [PMID: 37418159 DOI: 10.1093/treephys/tpad087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/28/2023] [Accepted: 07/02/2023] [Indexed: 07/08/2023]
Abstract
Metabolomics studies are becoming increasingly common for understanding how plant metabolism responds to changes in environmental conditions, genetic manipulations and treatments. Despite the recent advances in metabolomics workflow, the sample preparation process still limits the high-throughput analysis in large-scale studies. Here, we present a highly flexible robotic system that integrates liquid handling, sonication, centrifugation, solvent evaporation and sample transfer processed in 96-well plates to automatize the metabolite extraction from leaf samples. We transferred an established manual extraction protocol performed to a robotic system, and with this, we show the optimization steps required to improve reproducibility and obtain comparable results in terms of extraction efficiency and accuracy. We then tested the robotic system to analyze the metabolomes of wild-type and four transgenic silver birch (Betula pendula Roth) lines under unstressed conditions. Birch trees were engineered to overexpress the poplar (Populus × canescens) isoprene synthase and to emit various amounts of isoprene. By fitting the different isoprene emission capacities of the transgenic trees with their leaf metabolomes, we observed an isoprene-dependent upregulation of some flavonoids and other secondary metabolites as well as carbohydrates, amino acid and lipid metabolites. By contrast, the disaccharide sucrose was found to be strongly negatively correlated to isoprene emission. The presented study illustrates the power of integrating robotics to increase the sample throughput, reduce human errors and labor time, and to ensure a fully controlled, monitored and standardized sample preparation procedure. Due to its modular and flexible structure, the robotic system can be easily adapted to other extraction protocols for the analysis of various tissues or plant species to achieve high-throughput metabolomics in plant research.
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Affiliation(s)
- Marko Bertić
- Research Unit Environmental Simulation (EUS), Environmental Health Center (EHC), Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Ina Zimmer
- Research Unit Environmental Simulation (EUS), Environmental Health Center (EHC), Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - David Andrés-Montaner
- Atmospheric Environmental Research, Institute of Meteorology and Climate Research, Karlsruhe Institute of Technology, Kreuzeckbahnstr. 19, Garmisch-Partenkirchen 82467, Germany
- Corteva Agriscience Spain S.L.U, Carreño, Spain
| | - Maaria Rosenkranz
- Research Unit Environmental Simulation (EUS), Environmental Health Center (EHC), Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
- Institute of Plant Sciences, Ecology and Conservation Biology, University of Regensburg, Regensburg 93053, Germany
| | - Jaakko Kangasjärvi
- Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1, P.O Box 65, FI-00014, Finland
| | - Jörg-Peter Schnitzler
- Research Unit Environmental Simulation (EUS), Environmental Health Center (EHC), Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Andrea Ghirardo
- Research Unit Environmental Simulation (EUS), Environmental Health Center (EHC), Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
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Loroch S, Kopczynski D, Schneider AC, Schumbrutzki C, Feldmann I, Panagiotidis E, Reinders Y, Sakson R, Solari FA, Vening A, Swieringa F, Heemskerk JWM, Grandoch M, Dandekar T, Sickmann A. Toward Zero Variance in Proteomics Sample Preparation: Positive-Pressure FASP in 96-Well Format (PF96) Enables Highly Reproducible, Time- and Cost-Efficient Analysis of Sample Cohorts. J Proteome Res 2022; 21:1181-1188. [PMID: 35316605 PMCID: PMC8981309 DOI: 10.1021/acs.jproteome.1c00706] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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As novel liquid chromatography–mass
spectrometry (LC-MS)
technologies for proteomics offer a substantial increase in LC-MS
runs per day, robust and reproducible sample preparation emerges as
a new bottleneck for throughput. We introduce a novel strategy for
positive-pressure 96-well filter-aided sample preparation (PF96) on
a commercial positive-pressure solid-phase extraction device. PF96
allows for a five-fold increase in throughput in conjunction with
extraordinary reproducibility with Pearson product-moment correlations
on the protein level of r = 0.9993, as demonstrated
for mouse heart tissue lysate in 40 technical replicates. The targeted
quantification of 16 peptides in the presence of stable-isotope-labeled
reference peptides confirms that PF96 variance is barely assessable
against technical variation from nanoLC-MS instrumentation. We further
demonstrate that protein loads of 36–60 μg result in
optimal peptide recovery, but lower amounts ≥3 μg can
also be processed reproducibly. In summary, the reproducibility, simplicity,
and economy of time provide PF96 a promising future in biomedical
and clinical research.
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Affiliation(s)
- Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - Dominik Kopczynski
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - Adriana C Schneider
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany.,Faculty of Biochemical and Chemical Engineering, Technical University of Dortmund, 44227 Dortmund, Germany
| | - Cornelia Schumbrutzki
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - Ingo Feldmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | | | - Yvonne Reinders
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - Roman Sakson
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - Fiorella A Solari
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - Alicia Vening
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Frauke Swieringa
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Johan W M Heemskerk
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Maria Grandoch
- Institut für Pharmakologie und Klinische Pharmakologie, Universitätsklinikum der Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany.,Medizinisches Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany.,Department of Chemistry, College of Physical Sciences, University of Aberdeen, AB24 3FX Aberdeen, United Kingdom
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