Metabolomics strengthens -omics technologies at the JGI by identifying the actual molecules present in an environment that influence system behavior. Through this identification, metabolomics enables functional genome annotation, improves understanding of the role small molecules play in diverse biological systems, sheds light on nutrient and carbon cycling, and leads to the discovery of new molecules and pathways.
The JGI Metabolomics Platform delivers rich metabolite profiles from diverse biological and environmental samples using advanced liquid chromatography mass spectrometry (LC-MS) based methods in combination with advanced computational analysis.
Overview of metabolomics products
At JGI, in-depth molecular profiles are generated for metabolites extracted from a variety of experimental samples, including organisms (e.g. microbes, fungi, plant), media in which they grow, as well as different types of environments (e.g. soil, lake). A wide range of metabolites are identified using LC-MS/MS methods optimized for specific types of molecules.
Three standard types of mass spectrometry analytical products may be requested in a proposal:
- “Polar,” or primary metabolites. This is based on detection of metabolites using HILIC-Z chromatography. Here, small metabolites with polar functional groups, such as amino acids, nucleic acids, sugars, and small organic acids, are analyzed for semi-quantitative or quantitative analysis.
- “Nonpolar,” or secondary metabolites. This is based on detection of metabolites using a standard C18 chromatography. Here, metabolites with nonpolar functional groups, such as phenazines, polyketides, etc, can be analyzed.
- “Lipid,” or enhanced nonpolar metabolites. This is based on detection of lipid, or lipid-like molecules, using a C18 chromatography optimized for lipid detection. Here, metabolites with “lipid-like” chemistry can be analyzed, including common lipid species (triacylglycerols, phospholipids, cholesterols, sterols/steroids, etc), ubiquinones, carotenoids and other pigments.
Spectra from metabolomics datasets are analyzed to generate “comparative metabolomes” of identified metabolites using a variety of analytical workflows:
- Targeted analysis: Metabolite identification is based on comparison of m/z, RT and fragmentation spectra to the JGI’s internal database of metabolite standards run using the same LC-MS/MS methods. This analysis provides the most confident levels of identification.
- Untargeted analysis: In the absence of standards run in-house, a variety of software and algorithms are used to find and “putatively” identify features and relate them to known compounds. This workflow is currently based on feature-finding using open-source software mzmine3, with putative identifications made using the web-based GNPS2 platform that provides interactive interfaces for further data analysis, molecular networking, and data sharing.
- Stable Isotope Probing (SIP) analysis: For experimental samples with isotopic labeling (13C, 15N, 2H, etc), mass spectra are analyzed to provide information on the extent of stable isotope incorporation into metabolites for metabolic flux analysis or characterizing synthesis / turnover.
Additional capabilities are always in development, and custom analyses can be considered (LC-MS method, extraction, analysis, etc). Please contact us to discuss available metabolomics opportunities complementary to your research.
- Metabolomics datasets are publicly available at the MassIVE data repository, and can be easily explored using tools available at GNPS2.
- Reference MSMS spectra for the 1000s of compound standards run at the JGI have also been deposited in the GNPS Public Spectral Library, under the library name “BERKELEY-LAB”, as a community resource for aiding compound identification.
Documentation of methods, workflows and analyses developed and used by JGI Metabolomics is available at protocols.io in the workspace JGI/LBNL Metabolomics Repository.
Capabilities offered by the Metabolomics Platform are based on having developed:
- a strong core foundation of robust mass spectrometry workflows for polar, nonpolar and lipid metabolite analysis using 3 Thermo Orbitrap mass spectrometers (QE-HF, Exploris 120 and IQ-X) inline with Agilent 1290 UHPLC systems
- a continuously expanding metabolite database from running and annotating 1000s of metabolite standards (Berkeley Lab’s Environmental Metabolite Atlas)
- high-throughput targeted and untargeted analysis pipelines for metabolite identification
- numerous tools and research products including stable isotope probing (SIP) to assess metabolite turnover, DNA-SIP for helping identify active micro-organisms within complex communities, software tools for integrating metabolomics with genomic data (MAGI) and identifying unknown compounds (Pactolus), and most recently, ENVnet for analyzing complex organic matter in environmental samples.
Cutting-edge mass spectrometry capabilities are always in development including new LC-MS methods and analytical workflows, new research tools, and taking advantage of the Thermo Orbitrap Tribrid IQ-X, capable of up to 500k mass resolution for resolving molecular formula and fine isotope analysis and MSn (n=10) for deeper fragmentation and insight into molecular structure.
Find more details on the instrumentation we use and our methodology for metabolite analyses.
Read more about our submission guidelines, what you can expect from your results as well as our library standards.
