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    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.

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

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    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.

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    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.

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    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.

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    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.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
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    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.

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    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.

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    Tips for a Winning Community Science Program Proposal
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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
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    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.

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    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.

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Our Science
Home › Our Science › Science Programs › Metabolomics Program › Metabolomics Instrumentation

Metabolomics Instrumentation

Mass Spectrometry

LC-MS system with a Thermo Q-Exactive Orbitrap mass spectrometer coupled to an Agilent 1290 UHPLC enabling analysis of complex samples for semi-quantitative and quantitative measurements and detection of novel secondary metabolites.  Coupled with chromatographic separation, UV as well as MS and MS/MS fragmentation spectra are acquired during the same run from each sample extract, with each detected m/z having a mass resolution of 70,000 for MS (accuracy of ~3 ppm) and 17,500 for MS/MS.  With this information, metabolites can be identified by comparison to standards using a “targeted” approach, and with an “untargeted” approach, putative chemical formulas can be generated (from accurate mass) for unknowns and fragmentation spectra used for further insight into chemical structure and potential identification.

Thermo Q-Exactive Orbitrap mass spectrometer coupled to an Agilent 1290 UHPLC

Thermo LTQXL Maldi Orbitrap enabling high-throughput MS analysis of hundreds to thousands of samples.

Thermo LTQXL Maldi Orbitrap

Sample Preparation

Hamilton Vantage robotic liquid handler for automated sample extraction.

Hamilton Vantage

Additional equipment routinely used in sample extraction at the JGI includes a SpeedVac for drying solvent extracts, lyophilizer to freeze-dry aqueous samples as well as a bead-beater and probe sonicator for lysing cells and other biomass.

 

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  • Secondary Metabolites

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