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Untargeted plant metabolomics: Evaluation of lyophilization as sample preparation technique

ABSTRACT: Data for publication "Untargeted plant metabolomics: Evaluation of lyophilization as sample preparation technique" of Christina Maisl, Maria Doppler, Bernhard Seidl, Christoph Bueschl and Rainer Schuhmacher.

INSTRUMENT(S): Orbitrap Q Exactive HF (Thermo scientific instrument model)

ORGANISM(S): Wheat Cultivar Remus

SUBMITTER: Rainer Schuhmacher

PROVIDER: MSV000091769 | MassIVE | Fri Apr 21 09:58:00 BST 2023

REPOSITORIES: MassIVE

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GNPS - Untargeted plant metabolomics: Evaluation of lyophilization as sample preparation technique

Project description:Data for publication "Untargeted plant metabolomics: Evaluation of lyophilization as sample preparation technique" of Christina Maisl, Maria Doppler, Bernhard Seidl, Christoph Bueschl and Rainer Schuhmacher.

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Untargeted Plant Metabolomics: Evaluation of Lyophilization as a Sample Preparation Technique.

Project description:Lyophilization is a common method used for stabilizing biological samples prior to storage or to concentrate extracts. However, it is possible that this process may alter the metabolic composition or lead to the loss of metabolites. In this study, the performance of lyophilization is investigated in the example of wheat roots. To this end, native and 13C-labelled, fresh or already lyophilized root samples, and (diluted) extracts with dilution factors up to 32 and authentic reference standards were investigated. All samples were analyzed using RP-LC-HRMS. Results show that using lyophilization for the stabilization of plant material altered the metabolic sample composition. Overall, 7% of all wheat metabolites detected in non-lyophilized samples were not detected in dried samples anymore, and up to 43% of the remaining metabolites exhibited significantly increased or decreased abundances. With respect to extract concentration, less than 5% of the expected metabolites were completely lost by lyophilization and the recovery rates of the remaining metabolites were slightly reduced with increasing concentration factors to an average of 85% at an enrichment factor of 32. Compound annotation did not indicate specific classes of wheat metabolites to be affected.

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Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes

Project description:We tested four gene enrichment and complexity reduction target preparation methods for scoring SFPs on the Affymetrix GeneChip 18k Maize Genome Array (Maize GeneChip). Methylation filtration (MF), Cot filtration (CF), mRNA-derived cRNA, and amplified fragment length polymorphism (AFLP) methods were applied to three diverse maize inbred lines (B73, Mo17, and CML69) with three replications per line (36 Maize GeneChips). Due to large amounts of repetitive, mobile DNA, the maize genome requires a target preparation method that offers both a high level of gene enrichment and accurate scoring of SFPs. The objectives of this research are (i) to determine which target preparation method (CF, MF, mRNA, or AFLP) optimally enriches for gene sequences complementary to probe sequences on the Affymetrix GeneChip Maize Genome Array and (ii) to estimate SFP detection power for each target method. The AFLP technology is covered by patents, and patent applications owned by Keygene N.V. AFLP is a registered trademark of Keygene N.V. GeneChip. This work was supported in part by U.S. National Science Foundation grant DBI-0321467 and USDA-ARS. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Michael Gore. The equivalent experiment is ZM10 at PLEXdb.]

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