• New software to help discover valuable c

    From ScienceDaily@1:317/3 to All on Tuesday, March 29, 2022 22:30:40
    New software to help discover valuable compounds

    Date:
    March 29, 2022
    Source:
    Boyce Thompson Institute
    Summary:
    Because the comparative metabolomics field lacks sophisticated
    data analysis tools that are available to genomics and proteomics
    researchers, metabolomics researchers spend a lot of time hunting
    for candidate compounds that could be useful as leads for the
    development of new pharmaceuticals or agrochemicals. To solve
    this problem, scientists have developed Metaboseek, a free,
    easy-to-use app that integrates multiple data analysis features
    for the metabolomics community.



    FULL STORY ========================================================================== Because the comparative metabolomics field lacks sophisticated data
    analysis tools that are available to genomics and proteomics researchers, metabolomics researchers spend a lot of time hunting for candidate
    compounds that could be useful as leads for the development of new pharmaceuticals or agrochemicals. To solve this problem, scientists have developed Metaboseek, a free, easy-to-use app that integrates multiple
    data analysis features for the metabolomics community.


    ==========================================================================
    As a postdoctoral research associate in the lab of BTI faculty member
    Frank Schroeder, Max Helf saw his labmates continually struggle when
    they were analyzing data. So, he decided to do something about it
    and developed a free, open-source app called Metaboseek, which is now
    essential to the lab's work.

    The Schroeder lab studies the roundworm Caenorhabditis elegans, one of
    the most successful model systems for human biology, to discover new metabolites that govern evolutionarily conserved signaling pathways and
    could be useful as leads for the development of new pharmaceuticals or agrochemicals. The researchers accomplish this task by comparing the metabolites between two different worm populations -- a process called comparative metabolomics.

    Given that samples routinely have more than 100,000 compounds in them, computational approaches are essential to perform the analysis.

    The team had been relying on software packages that did not offer
    the required level of flexibility to easily customize analysis
    parameters. That limitation, and the lack of a suitable graphical user interface, meant Helf's colleagues faced the cumbersome task of visually inspecting mounds of data -- for example, to spot possible false positives
    -- and jumping between several other software tools to confirm and filter
    out those meaningless results.

    "It just seemed very inefficient to me, and I couldn't get over the shortcomings of other software solutions for this problem," Helf said. "I thought there had to be an easier way, so I started to write code for
    my own software." Helf developed the initial version of his software
    in 2017, and continued to improve it over the next two years. "Besides addressing the problems my labmates were already facing, I talked to them
    about what else held them back - - what they wanted to do but weren't
    even trying -- and built those features in the app," said Helf, who is
    now a bioinformatics product manager at proteomics company Biognosys
    AG. "I wanted this new tool to be user-friendly and accessible to anyone
    who does chemical biology."


    ==========================================================================
    The result was Metaboseek, an app with a graphical interface that
    incorporates multiple data analysis tools that non-coding researchers
    would otherwise not have. The app streamlines the analysis of comparative metabolomics data by helping the researcher determine which data features
    are real and letting them dig deeper into those features -- all within
    the same tool.

    "Max did this without me even requesting it," Schroeder said. "Before I
    knew that this was happening, there was Metaboseek. We started using it,
    and now our lab and many collaborators couldn't exist without it." In a
    study published in Nature Communications on February 10, Schroeder's team provided proof-of-concept for Metaboseek by applying it to an important
    fat metabolism pathway that hadn't yet been studied: the a-oxidation
    pathway in C.

    elegans that helps break down a class of fatty acids.

    Using Metaboseek, the team found that roundworms lacking a key gene in
    the a- oxidation pathway accumulated hundreds of previously unreported metabolites.

    The findings are important because a-oxidation is a basic biochemical
    pathway in worms that is conserved in humans, Schroeder said.

    "Bennett Fox did the chemistry work, so this study was a nice
    collaboration between the two postdocs," added Schroeder, who is also
    professor in Cornell University's Department of Chemistry and Chemical
    Biology.



    ========================================================================== According to Schroeder and Helf, there are a few reasons why there aren't
    a lot of good analytic tools for comparing metabolomics data. First, comparative metabolomics is a relatively young field compared with
    other data-heavy fields of biology like genomics (which focuses on DNA)
    and proteomics (which focuses on proteins), so there hasn't been enough
    time to develop software tools and database infrastructure.

    Additionally, over the last decade, the advent of affordable, ultra-high- resolution mass spectrometers for collecting metabolomics data has
    increased by perhaps more than tenfold the amount of data one sample can generate - - creating an even greater need for sophisticated tools that
    can keep up with the flood of data.

    Metaboseek meets these needs with an array of features for analyzing
    various types of data to aid compound identification, structure
    determination, assignment of metabolites to families based on structural similarities, tracking radiolabeled compounds, and more.

    The study was supported in part by grants from the National Institutes
    of Health (R35GM131877 and U01GM110714) and a research fellowship
    Helf received from the Deutsche Forschungsgemeinschaft (Project Number 386228702).


    ========================================================================== Story Source: Materials provided by Boyce_Thompson_Institute. Note:
    Content may be edited for style and length.


    ========================================================================== Journal Reference:
    1. Maximilian J. Helf, Bennett W. Fox, Alexander B. Artyukhin, Ying K.

    Zhang, Frank C. Schroeder. Comparative metabolomics with Metaboseek
    reveals functions of a conserved fat metabolism pathway in
    C. elegans.

    Nature Communications, 2022; 13 (1) DOI: 10.1038/s41467-022-28391-9 ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2022/03/220329142528.htm

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