Dataset - Proteomics, Computed Analysis SoDA-PAL Protein Profiling Proteomics of Sorgoleone Catabolizing Microbial Isolate Acinetobacter pittii SO1

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https://doi.org/10.25584/PerConSFA/2338181
Chemical & Biological Signatures Science
Scientific Discovery
Biology
Microbiome Science
PerCon SFA
Mass spectrometry data
Proteomics
Photoaffinity Probe Labeling
AlphaFold2 Analysis
Sorgoleone Catabolism
A. pittii SO1

Last updated on 2024-09-17T15:49:08+00:00 by LN Anderson

PerCon SFA: Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders in Acinetobacter pitti

Mass spectrometry-based global proteome analysis and SoDA-PAL photoaffinity probe labeled protein analysis of microbial isolate Acinetobacter pittii SO1 sorgoleone interactome. DataHub download includes processed MaxQuant proteomics anlaysis (global and probe-labeled), sample naming key, updated GenBank protein locus tags (OH685), protein annotation file (.fasta), and computationally derived protein modeling (.pdb) outputs supporting data transparency and reuse.

    Accessible Digital Data Downloads

    Proteomics, Computed Analysis

    1. Protein quantification by liquid chromatography mass spectrometry (LC-MS)
    2. AlphaFold2 protein structure predictions

    Linked Primary Data Accessions

    • MassIVE: MSV000091986 (global and probe-labeled datasets)

    Related Sequence Collections

       

      Data Download Reference Citations

      1. Anderson, Lindsey N, Van Fossen, Elise, Mcnaughton, Andrew D, Egbert, Robert G. SoDA-PAL Protein Profiling Proteomics of Sorgoleone Catabolizing Microbial Isolate Acinetobacter pittii SO1. United States. 2024. PNNL DataHub (Web). DOI: 10.25584/PerConSFA/2338181
      2. Van Fossen EM, Kroll JO, Anderson LN, McNaughton AD, Herrera D, Oda Y, Wilson AJ, Nelson WC, Kumar N, Frank AR, Elmore JR, Handakumbura P, Lin VS, Egbert RG. 0. Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders in Acinetobacter pittii. Appl Environ Microbiol 0:e01026-24. DOI: 10.1128/aem.01026-24

       

        Funding Acknowledgments

        The provided material is based upon work supported by the  U.S. Department of Energy, Office of Biological and Environmental Research, Genomic Science Program and is a contribution of the Pacific Northwest National Laboratory Persistence Control of Engineered Functions in Complex Soil Microbiomes project. A portion of this research is supported under the EMSL user project award 10.46936/cpcy.proj.2022.60649/60008751, for leveraging instrument capabilities operating at the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility, sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830. 

        Citation Policy

        When referencing and reusing linked PerCon SFA project digital data assets listed at the PNNL DataHub institutional repository, we ask that users please cite the dataset digital object identifier provided at the download page and any corresponding journal article publications. Reference citations, where applicable, should provide the necessary metadata information required to support, corroborate, verify, and otherwise determine the legitimacy of the research findings provided (data and code) from scholarly publications and corresponding project data releases.

        Data Licensing

        CC BY 4.0 (dataset DOI downloads), CC0 1.0 (PNNL DataHub policy default)

        English
        Projects (1)
        Persistence Control of Engineered Functions in Complex Soil Microbiomes (PerCon SFA), Secure Biosystems Design Project
        Datasets (1)
        Whole Genome Sequencing of Sorgoleone Promoting Rhizobacteria Isolates
        People (5)
        Lindsey N. Anderson

        Lindsey Anderson’s research has been dedicated to the identification and characterization of novel, targeted and non-targeted, functional metabolic interactions using a high-throughput systems biology and computational biology approach. Her expertise in functional metabolism and multidisciplinary...

        Elise Van Fossen

        Elise Van Fossen is a Post-Doctorate Research Associate in the Biological Sciences Division. Her research focuses on developing synthetic and chemical biology techniques for microorganism engineering.

        Vivian Lin

        PerCon SFA, Co-Investigator Vivian Lin earned her PhD in organic chemistry from the University of California, Berkeley with Professor Chris Chang, developing fluorescent probes for imaging redox active small molecules. Afterward, she traveled to Switzerland for a postdoctoral fellowship in the...

        Andrew McNaughton

        Andrew McNaughton is a computational scientist currently working in the areas of modeling metabolic networks, multi-omics data analysis and integration, and computational chemistry. His areas of interest include high performance computing (HPC), artificial intelligence, and machine learning (ML) to...

        Robert Egbert

        Biography I am a biological engineer working to advance high-throughput biological engineering for rapid optimization of complex gene clusters and dynamical systems in microbes through pooled genomic library assembly, high-throughput sequencing and variant scoring. I utilize machine learning...

        Data Sources (1)
        Q Exactive Plus Mass Spectrometer
        Institutions (1)
        Environmental Molecular Sciences Laboratory