DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Science Programs
    • Science Highlights
    • Scientists
    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

    More

    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

    More

    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

    Listen

    A light green shrub with spiny leaves, up close.
    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

    Listen

    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

    More

    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

    More

    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

    More

    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

    More

    croppe image of the JGI helix sculpture
    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

    Listen

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

    More

    image from gif that shows where in the globe JGI fungal collaborators are located.
    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

    More

    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

    More

Our Science
Home › Our Science › Science Programs › Metabolomics Program › Sample Submission and Guidelines

Sample Submission and Guidelines

The first step to submitting samples is a discussion with the JGI Metabolomics group and program manager regarding experimental design and sample preparation for metabolomics analysis.  All samples are different, and it is important to make sure that the correct controls are prepared, enough sample provided, experimental design and samples are compatible for MS analysis, and that extraction method and solvents are suitable to detect metabolites of interest and compatible with the sample and sample container.  Measurements for normalization, if necessary, are also discussed (TOC analysis,  dry weight, OD, etc).

Pilot Project

Prior to submitting all experimental samples, a small subset of samples for a pilot project are determined.  This is typically 3-20 samples in size, depending on the experiment.  According to the methods and procedures discussed, these will be extracted, run on LC-MS and undergo a preliminary analysis.

Here we will test / determine / decide:

  • Amount of sample, sample preparation
    • Can we detect the metabolites of interest?  Is there anything contaminating the MS signal?
  • Sample container
    • Is this compatible with extraction solvents, etc?
  • Extraction method
  • Additional measurements (e.g. dry weight, OD)
  • Number of replicates
    • How variable are replicates?
  • Controls
    • Extraction blanks, conditioned media
  • LC-MS method (w/ chromatography)
    • HILIC, C18, etc

Once the pilot experiment has been completed and everything “goes well,” the final samples can be submitted.  More than 1 pilot may be necessary based on results.

Sample Submission Form

Before shipping samples, a “Sample Submission Form” must be filled out and approved.  This provides the relevant metadata necessary to catalog and appropriately analyze the submitted samples.  Review of this sheet also ensures all the appropriate controls and samples are being included.

An example form can be viewed here (March 2017 version).

The form has 3 sheets:

  • Sheet 1 – Sample information
  • Sheet 2 – Media recipes
  • Sheet 3 – Metabolites of interest

Sample information. The requested metadata is important for identifying each sample and the components of each sample.  Much of this information is needed for generating high quality LC-MS data for subsequent analysis.

Media recipes. Submit detailed media recipes used in the experiment including a list of specific compounds and concentrations.  When appropriate, include media preparation steps.  For complex media or “environmental” media, include the source or catalog information.

Metabolites of interest. This information is used to ensure that if specific metabolites of interest are important to an experiment, especially in a “targeted” analysis, these will be considered in the analysis.  Metabolic pathways or classes of metabolites may also be listed (e.g. amino acids) but please provide as much detail as possible and hyperlinks.

Considerations in Experimental Design

Sample amount. Usually >1 mg C for soil, media, plant exudates.  Other typical amounts – soil (0.5-2 g), media (1 mL), wet biomass (~20 mg, 3 mm pellet – often pellet from 1 mL media), dry biomass (2-10 mg).

Number of replicates. Usually 4 replicates (up to 8 if highly variable between sample replicates).  Note: For each type of MS analysis, a separate replicate sample needs to be prepared (different extractions used for each).

Sample processing / things to avoid. Some chemical are not compatible with sample extraction (e.g. glycerol, DMSO), or have strong signals that suppress and interfere with detecting metabolites of interest.  This includes surfactants, PEG, dirty glass with soap residue, some buffers.  Other sources of contamination include polymers leaching from plastic, especially if they contact organic solvent (e.g. filters, acrylate, pipette tips with low adhesive polymer coating).

Media. Defined and minimal media are preferred since competitive ionization and signal suppression is minimized.  Also, since metabolites in these can be fully characterized, this makes it easier to detect new peaks / metabolites and to track increases or decreases in metabolites versus control media.  Complex media is OK but analysis may also be more complex.

Salt. In general, high salt is not mass spectrometry friendly when using chromatography for primary metabolite analysis (HILIC).  For these samples (e.g. ocean), a large amount of salt is removed during extraction but sometimes the remaining salt may still suppress signal during portions of the LC-MS run.  For C18 analysis (secondary metabolites, non-polar), salt is not an issue.

Controls – Do not forget!!

Conditioned media control. Incubate media but do not inoculate.  This media should be subject to the same processing conditions and environments as the inoculated samples (e.g. filtering, temperature, light, time, etc).  This control is necessary to determine what is being made by the organism, or consumed, when compared to the control.  Fresh media is not comparable because metabolite degradation or other changes may occur during incubation, especially in the case of high temperature samples.

Extraction blanks (just the containers). Please send the same containers that samples were shipped in but with no sample.  This control is necessary to determine sample signal from “background” signal that arises from the container itself, extraction solvents, or somewhere else during LC-MS sample preparation or system itself.

Fresh media. This control is used to evaluate how much the experimental procedures have changed the media, and to determine the initial metabolite composition.

Positive / Negative. When possible, please include a positive and negative control.  For instance, if you expect to see synthesis of a metabolite of interest in one sample and not in another.

Unlabeled controls. When performing an experiment with stable isotopic labeling, include replicate samples that do not have any labeling.  This control is used to determine the relative isotopic levels of a specific metabolite when unlabeled, and necessary to calculate how much labeling has occurred.

Other. Additional controls may be necessary depending on your experimental design.

  • 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
  • Secondary Metabolites

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • 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

© 1997-2023 The Regents of the University of California