Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures

Saito, Mak A.; Saunders, Jaclyn K.; McIlvin, Matthew R.; Bertrand, Erin M.; Breier, John A.; Brisbin, Margaret Mars; Colston, Sophie M.; Compton, Jaimee R.; Griffin, Tim J.; Hervey, W. Judson; Hettich, Robert L.; Jagtap, Pratik D.; Janech, Michael; Johnson, Rod; Keil, Rick; Kleikamp, Hugo; Leary, Dagmar; Martens, Lennart; McCain, J. Scott P.; Moore, Eli; Mehta, Subina; Moran, Dawn M.; Neibauer, Jaqui; Neely, Benjamin A.; Jakuba, Michael V.; Johnson, Jim; Duffy, Megan; Herndl, Gerhard J.; Giannone, Richard; Mueller, Ryan; Nunn, Brook L.; Pabst, Martin; Peters, Samantha; Rajczewski, Andrew; Rowland, Elden; Searle, Brian; Van Den Bossche, Tim; Vora, Gary J.; Waldbauer, Jacob R.; Zheng, Haiyan; Zhao, Zihao

Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-Series Study in the North Atlantic Ocean collected by in situ pumps and the AUV Clio were distributed with a paired metagenome, and one-dimensional liquid chromatographic data dependent acquisition mass spectrometry analyses was stipulated. Analysis of mass spectra from seven laboratories through a common informatic pipeline identified a shared set of 1056 proteins from 1395 shared peptides constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R 2 values ranging from 0.43 to 0.83, and a Sørensen similarity analysis of the top 1,000 proteins revealed 70–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. An informatic intercomparison study, involving 10 laboratories using 8 software packages successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research including integration into global scale ocean surveys and ocean biogeochemical models.

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Saito, Mak A. / Saunders, Jaclyn K. / McIlvin, Matthew R. / et al: Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures. 2024. Copernicus Publications.

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