Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures
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 comparabilit...
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ftcopernicus:oai:publications.copernicus.org:egusphere117286 2024-09-15T18:23:50+00:00 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 Bossche, Tim Vora, Gary J. Waldbauer, Jacob R. Zheng, Haiyan Zhao, Zihao 2024-01-16 application/pdf https://doi.org/10.5194/egusphere-2023-3148 https://egusphere.copernicus.org/preprints/2024/egusphere-2023-3148/ eng eng doi:10.5194/egusphere-2023-3148 https://egusphere.copernicus.org/preprints/2024/egusphere-2023-3148/ eISSN: Text 2024 ftcopernicus https://doi.org/10.5194/egusphere-2023-3148 2024-08-28T05:24:15Z 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. Text North Atlantic Copernicus Publications: E-Journals |
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Copernicus Publications: E-Journals |
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English |
description |
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. 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 Bossche, Tim Vora, Gary J. Waldbauer, Jacob R. Zheng, Haiyan Zhao, Zihao |
spellingShingle |
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 Bossche, Tim Vora, Gary J. Waldbauer, Jacob R. Zheng, Haiyan Zhao, Zihao Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures |
author_facet |
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 Bossche, Tim Vora, Gary J. Waldbauer, Jacob R. Zheng, Haiyan Zhao, Zihao |
author_sort |
Saito, Mak A. |
title |
Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures |
title_short |
Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures |
title_full |
Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures |
title_fullStr |
Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures |
title_full_unstemmed |
Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures |
title_sort |
results from a multi-laboratory ocean metaproteomic intercomparison: effects of lc-ms acquisition and data analysis procedures |
publishDate |
2024 |
url |
https://doi.org/10.5194/egusphere-2023-3148 https://egusphere.copernicus.org/preprints/2024/egusphere-2023-3148/ |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_source |
eISSN: |
op_relation |
doi:10.5194/egusphere-2023-3148 https://egusphere.copernicus.org/preprints/2024/egusphere-2023-3148/ |
op_doi |
https://doi.org/10.5194/egusphere-2023-3148 |
_version_ |
1810464108724617216 |