Standardization and Intercalibration
There is currently no single gold standard practice for the collection, preservation, or processing of metagenomics, metatranscriptomics, metaproteomics, metabarcoding, and eDNA samples—nor is there a sense of how variable these measures might be among labs or research cruise endeavors. Intercomparison and intercalibration of ‘omic studies is a critical component of BioGeoSCAPES.
An effort supported by the Ocean Carbon & Biogeochemistry (OCB) Project Office has been underway since 2018 to develop intercomparable metaproteomic datasets.
Check out the latest metaproteomic intercomparison exercise results recently available as a preprint in EGUsphere: Saito et al.: Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2023-3148, 2024.
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The workshop on Ocean nucleic acids 'omics intercalibration and standardization was convened by the US Ocean Carbon Biogeochemistry (OCB) program, January 8-11, 2020. The goal of this workshop was to develop a focused marine microbial nucleic acid (na) 'omics intercomparison and intercalibration effort to enhance future field programs that integrate methods such as molecular barcoding, metagenomics and transcriptomics to understand the functioning of prokaryotic and eukaryotic microbes in the ocean. Initial efforts are guided, in part, by the success of the marine geochemistry community in implementing programs like GEOTRACES.
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Meta-eukomic: Intercomparison of metatranscriptomic methods for characterizing microbial eukaryote contributions to the biological carbon pump. This Working Group is supported by the Ocean Carbon & Biogeochemistry (OCB) Project Office.
August 27, 2024
Sarah Smith (Moss Landing Marine Laboratories) - Metatranscriptomics of Monterey Bay Phytoplankton During Experimental Upwelling Mesocosm Experiments
Mora Groussman (Univ. Washington) - Using the MarFERReT eukaryotic sequence library for dynamic, custom and reproducible reference libraries
May 1, 2024: theme: Omics intercomparisons and proteomic/transcriptomic applications in the field
Mak Saito (WHOI) - Intercomparison of ocean metaproteomics analysis: Initial results of global data-dependent acquisition analyses
Erin Bertrand (Dalhousie University) - Toward understanding rates of eukaryotic microbial processes through metaproteomics
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