PML | AspenDB

Plant Metabolomics Laboratory

Welcome to the Plant Metabolomics Laboratory (PML)

PML houses a state-of-the-art ultra-performance liquid chromatography (Agilent 1290 Infinity II UPLC) coupled to a quadrupole time-of-flight (Agilent 6546 QTOF) tandem mass spectrometer. Funded by an USDA-NIFA equipment grant, the LC-MS/MS supports metabolic approaches and their integration into crop and tree genetics and genomics research at the University of Georgia (UGA) and beyond.

Since May 2022, PML has performed 35+ metabolite profiling projects for UGA graduate students, research scientists, and faculty that span multiple colleges and departments, including the Warnell School of Forestry and Natural Resources, the College of Agricultural and Environmental Sciences (Center for Applied Genetic Technologies, Department of Entomology, Department of Food Science and Technology, Department of Plant Pathology), and the Franklin College of Arts and Sciences (Department of Genetics and Department of Plant Biology), for researchers from the Oak Ridge National Laboratory. These projects ranged from non-targeted profiling of phenolics and flavonoids in Arabidopsis, poplar, soybean, and sugarberry leaves, to lettuce leaf exudate profiling, to quantification of acidic hormones in Arabidopsis, cotton, and poplars.

Please contact us to discuss your project needs.

Contact: pml@uga.edu, Davison Life Sciences C310
PML advisory committee: CJ Tsai (chair), Scott Harding, Melissa Mitchum, Caterina Villari

Funding for the Agilent UPLC-QTOF was provided by the U.S. Department of Agriculture, National Institute of Food and Agriculture, Equipment Grant Program award no. 2021-70410-35297, with matching support from the Office of Research, the College of Agricultural and Environmental Sciences, the Warnell School of Forestry and Natural Resources, the Department of Genetics and the Department of Plant Biology.

Non-targeted LC-MS profiling

Metabolite samples are resolved using UPLC with a C18 reverse-phase column and detected by MS with high mass resolution using electrospray ionization (ESI) in either negative or positive mode. Both tissue extracts and exudates can be used (see Sample Preparation below). This is the most popular and mature LC-MS profiling method. The standard protocol primarily resolves non-volatile phenolics, flavonoids, terpenoids and alkaloids. Metabolite data are processed by Agilent software suite and aligned peaks outputted in a spreadsheet format. The spreadsheet data include peak abundance and metabolite attributes (retention time, m/z, putative identity, and chemical formula based on NIST or inhouse library search) aligned for all sample in a batch. Quantification of specified metabolites can be performed for an additional fee. Authentic standards not available at PML may need to be supplied by the user.
Acidic plant hormone profiling

Plant tissues are prepared via homogenization, liquid-liquid extraction and/or solid phase extraction to enrich for low-abundance hormone species. The analytes are separated by reverse phase UPLC and detected by MS in negative mode. Calibration curves for ABA, IAA, JA, and SA will be provided. Additional fees apply for quantification using stable isotope-labeled standards or for additional hormone analogs and/or conjugates (their authentic standards may need to be supplied by the user). Detection limits: coming soon.
LC-MS/MS Profiling

Selected samples from the standard, non-targeted LC-MS profiling can be used for tandem MS analysis either in negative or positive mode for high-resolution identification of unknown metabolites of interest. In LC-MS/MS analysis, precursor ions are further fragmented to aid compound identification against the NIST MS/MS library. Authentic standards supplied by the user may be necessary for unequivocal compound identification. This analysis is recommended for advanced users.
Additional Methods

HILIC (hydrophilic interaction liquid chromatography) methods will be developed for profiling of polar metabolites such as amino acids and lipids. Please contact pml@uga.edu to discuss other method development projects.
In-house metabolite library

Below is a list of metabolites in our small but growing in-house library. User-provided authentic standards will be run without charge to aid compound identification.
Samples accepted

User-collected exudates: Xylem, phloem or petiole exudates must be stored at -80C until delivery. Root exudates must be freeze-dried after consultation. Pre-weighed freeze-dried tissue powders: >1 mg for standard non-targeted profiling or >10 mg for acidic hormone profiling. Tissues should be ball-milled (if freeze-dried) or ground under liquid N to a fine powder. Pre-weighed flash-frozen tissues can be accommodated but must be snap-frozen in liquid nitrogen and stored at -80C prior to delivery in liquid nitrogen or on dry ice (>5 mg for standard non-targeted profiling or >50 mg for acidic hormone profiling). User-prepared metabolite extracts from fresh-frozen or freeze-dried tissues may be accepted after consultation.
Sample processing services provided

Standard, non-targeted LC-MS or LC-MS/MS profiling: External loading standards addition and two-phase solvent (chloroform-methanol) extraction of pre-weighed frozen or freeze-dried tissues. Solvent extraction protocol can be modified upon user request with consultation. Exudate profiling: Small volumes (<100 ul) of frozen phloem, xylem or petiole exudates are dried in a Centrivap and resuspended in solvent containing external loading standards. Freeze-dried root (or other bulk) exudates will be resuspended in solvent containing external loading standards. Sample clean-up via 0.2 um PTFE filtering is included in all samples prior to LC-MS analysis. Sample extraction and purification is included in acidic hormone profiling.
Sample submission

Please fill out the sample submission form. Submit an e-copy to pml@uga.edu and arrange for sample drop-off at PML (Davison Life Sciences C310).
UGA users

Standard metabolite extraction: $100 per batch of up to 24 pre-weighed samples. Small volume (<100 ul) exudate preparation: $60 per batch of up to 24 samples. Bulk (freeze-dried) exudate preparation: $50 per batch of up to 24 samples. Freeze-drying: $3 per microtube, $5 per foil packet, or $80 per liter of sample. LC-MS profiling: $30 per sample per run (either negative or positive mode). LC-MS/MS profiling: $100 per sample per run (either negative or positive mode). Acidic plant hormone profiling: $70 per sample for up to 12 samples per batch. Quantification of selected metabolites: $100 for up to four standard curves. Additional sample processing or data analysis: $50 per hour. New method development: please contact pml@uga.edu. All prices are subject to change without notice.
Non-UGA and commercial users

Please contract pml@uga.edu for pricing.

Plant Center Plant Metabolomics Mini-Grant (PC-PMMG) Competition

FY23 competition winners: Ben Long (Genetics), Summer Blanco (PBIO), and Brandon Mangum (Plant Pathology).
FY24 competition winners: Hallie Wright (PBGG)

Goal: PC-PMMGs support Plant Center graduate students or postdocs conducting feasibility studies for incorporation of UPLC-QTOF (ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry) metabolomics into their research.

Proposal format: One-page description of the research, the feasibility study design, and how the pilot scale data can lead to further research that utilizes the Plant Metabolomics Lab (PML) services.

PI endorsement is required upon recipient of the proposal, via separate email confirmation.

Eligibility: Graduate students and postdocs in Plant Center-affiliated laboratories. Current and past PML users are not eligible.

Grants: Each grant is in the form of (1) up to 8 staff-assisted sample extraction and standard, non-targeted phenolic profiling, or (2) up to 4 staff-assisted acidic hormone (ABA, IAA, JA, SA) profiling. Other feasibility studies may be possible after consultation (contact pml@uga.edu before submission).

Project duration: All users must submit their samples as a single batch before May 31. Unused service credit will not be carried through the next FY.

PML committee: CJ Tsai (chair), Scott Harding, Melissa Mitchum, Hasti Mozaffari, Caterina Villari

No experience in metabolomics? Fear no more!
PML aims to remove the barrier of unfamiliarity and make the technology accessible to all researchers.
Just send us your precious tissue powders or exudates and we will do the rest!
Users receive data in a spreadsheet format (e.g., metabolite attributes and abundance)
which can be further analyzed similar to other large-scale omics/quantitative data.

Don’t want to wait until spring? We are ready to accept work requests!
Take advantage of the introductory rates: $30 per LC-MS run for standard non-targeted profiling; $100 per LC-MS/MS run for compound identification (advanced users); $50 per hour for sample milling/processing, metabolite extraction, or additional data analysis; $70 per sample (up to 12 samples/batch) for acidic hormone profiling. Additional methods under development.

Publications

Yao T, Zhang J, Yates T, Shrestha H, Engle N, Ployet R, John C, Feng K, Bewg WP, Chen MSS, Lu H, Harding SA, Qiao Z, Jawdy S, Shu M, Yuan W, Mozaffari K, Harman-Ware A, Happs R, York L, Binder B, Yoshinaga Y, Daum C, Tschaplinski T, Abraham P, Tsai C-J, Barry K, Lipzen A, Schmutz J, Tuskan G, Chen I-G, Muchero W (2023) eQTL mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus. New Phytologist 239: 2248-2264.

Tran S, Ison M, Dias NCF, Ortega MA, Peper A, Hu L, Xu D, Mozaffari K, Chen YFS, Severns PM, Yao Y, Tsai C-J, Teixeira PJPL, Yang L (2023) Endogenous salicylic acid suppresses de novo root regeneration from leaf explants. PLOS Genetics 19(3): e1010636.

Hu L, Qi P, Peper A, Kong F, Yao Y, Yang L (2023) Distinct function of SPL genes in age-related resistance in Arabidopsis. PLoS Pathogens 19(3): e1011218.