DOE Joint Genome Institute

  • COVID-19
  • About
  • Phones
  • Contacts
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Products
    • Science Highlights
    • Scientists
    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

    More

    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

    More

    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

    More:

    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

    Read more

    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

    Read more

  • Data & Tools
    • IMG
    • Genome Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

    More

    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

    More

    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

    Read more

  • User Programs
    • Calls for User Proposals
    • Special Initiatives & Programs
    • User Support
    • Submit a Proposal
    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

    Read more

    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

    Read more

    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

    Read more

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Publications
    • Scientific Posters
    • Newsletter
    • Logos and Templates
    • Photos
    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

    More

    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

    More

    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

    Read more

Our Science
Home › Our Science › Science Programs › Metabolomics Program › Metabolite Analyses

Metabolite Analyses

At JGI we analyze metabolite profiles from a wide range of samples including microbes, plants and fungi, as well as the media in which they grow and environment in which they are found, including soil, bodies of water (e.g. ocean, lake), etc.  Metabolites are extracted from each type of sample using a variety of methods and solvent systems optimized for specific metabolites of interest. Metabolites from extracts are then detected using our liquid-chromatography tandem mass spectrometry (LC-MS/MS) system, and analyzed using a “targeted” approach, in which standards are used for identification, or an “untargeted” approach, in which software and algorithms are used to help identify compounds, or both depending on the experiment hypotheses.

Currently, the following types of metabolite analyses can be requested in a CSP proposal:

  1. Polar Metabolite Analysis – small, hydrophilic polar metabolites such as amino acids, nucleic acids, sugars and small organic acids, often involved in primary metabolism.  Limit 200 samples.
  2. Non-polar Metabolite Analysis – generally non-polar metabolites not directly involved in primary metabolism, such as antibiotics, polyketides, phenolics.  Limit 500 samples.
  3. “Targeted” stable isotope labeling of either polar or non-polar metabolites.  Limit 200 (if polar) or 500 (if non-polar) samples.

Additional Capabilities – JGI also has limited capacity for samples that include (a) stable isotopic labeling or (b) lipidomics. Please contact Metabolomics group lead Trent Northen or Katherine Louie to discuss available metabolomics analyses complementary to your research.

Polar Metabolite Analysis

Polar metabolite analysis consists of small, polar metabolites such as amino acids, nucleic acids, sugars and small organic acids that are typically part of primary metabolism, often playing a role in normal growth and development and part of fundamental metabolic pathways essential for survival.  Characterizing primary metabolites is important for examining interspecies interactions and cross-feeding, and can be used to determine what substrates are synthesized, taken up or released by different organisms under various environmental conditions.

Extraction is performed on a sample (e.g. media, microbial pellet) that has been lyophilized dry, then 100% methanol added to extract the primary metabolites while precipitating most proteins and salts.  Each sample extract is run on the JGI LC-MS/MS system with HILIC chromatography, with acquisition of UV as well as MS and MS/MS fragmentation spectra. (~1 hr/sample)

Non-polar Metabolite Analysis

Non-polar metabolite analysis consists of metabolites that have non-polar or hydrophobic chemical properties, and often encompasses secondary metabolites such as polyketides and phenolics.  Although not usually essential, secondary metabolites can provide evolutionary advantages important for survival. As more and more organisms are sequenced, more and more new, unique biosynthetic clusters are revealed each day, with the associated secondary metabolites yet to be discovered and functionally characterized.

Analyzing the non-polar or secondary metabolite profile of organisms under various conditions provides the opportunity to identify new compounds, and to gain insight and create linkages between sequence and function, especially in combination with transcriptomics performed on replicate samples.  In synthetic biology, this information can be used to determine relative synthesis levels between constructs, discover new compounds as they relate to organism genomics, as well as identify pathway intermediate, shunt products and precursors to better understand pathway dynamics.

Since secondary metabolites are typically non-polar or hydrophobic in nature, either chloroform, methanol or ethyl acetate is used for extraction of a sample.  Each sample extract is run on the JGI LC-MS/MS system with C18 chromatography, with acquisition of UV as well as MS and MS/MS fragmentation spectra. (~35 min/sample)

Stable isotope labeling

Stable isotope labeling analysis consists of profiling the relative amount of incorporation of a heavy isotope (e.g. 13C, 2H, 15N) into synthesized metabolites. Mass spectrometry is an ideal analysis tool for stable isotope labeling, since the isotope of each compound is detected in a typical mass spectrum.  Here, by comparing ion intensities of isotopes for a metabolite in unlabeled vs. labeled (treated with 13C or deuterium source, for instance) samples, active metabolic pathways can be traced through an organism, fate of a carbon source can be identified, and newly synthesized compounds can be identified.

The heavy isotope can be introduced, for example, as a labeled metabolite serving as a carbon source (e.g. 13C-acetate) to a microbial culture, and then using mass spectrometry to track to what degree (and potentially where) 13C is incorporated into metabolites in various metabolic pathways.  For these types of experiments, unlabeled control samples must also be prepared for analysis.

This type of analysis can be performed on any ion feature (unique m/z, RT pair) detected by mass spectrometry; however, currently JGI Metabolomics is restricting analysis to “targeted” metabolites only.  Here, the metabolites of interest need to be specified and have a standard available.

“Targeted” Approach

To identify metabolites using a “targeted” approach, we have already run a large library of metabolite standards (currently >500 and growing) to which we are able to compare retention time, m/z (detected mass/charge ratio) and fragmentation spectra to definitively identify metabolites in a sample.  Here is a representative sampling of metabolite standards in our library.  This approach can be used for any metabolite in which a standard is available, including secondary metabolites (e.g. violacein, prodigiosin).

“Untargeted” Approach

Often, a metabolite standard is not available and no database contains MS/MS fragmentation spectra, especially in the case of many secondary metabolites, or when little is known about the sample submitted for analysis and many unknown or novel compounds are expected.  Here, metabolites are putatively identified using an “untargeted approach” with a variety of developed software and algorithms.

Pactolus, a new version of MIDAS (Metabolite Identification via Database Searching), is one solution for “untargeted” analysis developed by LBL researchers.  This is essentially an open-source software tool that is able to predict MS/MS fragments from any chemical structure, real or theoretical, available in a database.  A metabolite in a sample can then be putatively identified, with a percent probability, by comparing predicted fragments to actual measured fragments from a sample. In the absence of MS/MS fragmentation data from a standard, this is a powerful tool for metabolite identification and dereplication for discovery.  Our current database has over 180,000 compounds for untargeted analysis. Additional software tools are in development for identification of unknowns and linkage to genomics.

Lipidomics

A diversity of lipids are found across organisms and environments, each playing critical roles in membrane organization, structure, and signaling, responding to environmental conditions such as desiccation or light, sporulation, as well as being important precursors for production of biofuels or involved in secondary metabolite biosynthesis.  Often, species of lipids (e.g. phosphatidylcholine, or PC lipid) are distinguished by a common headgroup attached to fatty acid chains of various carbon length and degree of saturation. Although several hundred forms of each species may exist, fragmentation during mass spectrometry analysis often leads to a characteristic fragmentation ion (e.g. 184 for PC) or neutral loss (e.g. -179 for MGDG) allowing for identification.

Here, we are able to identify common lipid species that have characteristic fragmentation spectra, and are often able to purchase a standard of each species.  Some lipid species we have recently annotated include TG, DG, PC, PE, SQDG, SM, MGDG, DGDG, PG and respective lyso-lipids. Please contact Trent Northen or Katherine Louie to discuss available lipidomics analyses.

  • Plant Program
  • Fungal & Algal Program
  • Metagenome Program
  • Microbial Program
  • DNA Synthesis Science Program
  • Metabolomics Program
    • Metabolite Analyses
    • Metabolite Standards in JGI Library
    • Metabolomics Results - Basic
    • Metabolomics Instrumentation
    • Sample Submission and Guidelines
    • Metabolomics Select Publications
    • Metabolomics Data Analysis - Tips From Users

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Podcasts
  • CSP Plans
  • Featured Profiles
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Emergency Info
  • Accessibility / Section 508 Statement
  • RSS feed
  • Flickr
  • LinkedIn
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2021 The Regents of the University of California