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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2024
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ftnonlinearchiv:oai:noa.gwlb.de:cop_mods_00071058 2024-02-11T10:06:35+01:00 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 Van Den Bossche, Tim Vora, Gary J. Waldbauer, Jacob R. Zheng, Haiyan Zhao, Zihao 2024-01 electronic https://doi.org/10.5194/egusphere-2023-3148 https://noa.gwlb.de/receive/cop_mods_00071058 https://noa.gwlb.de/servlets/MCRFileNodeServlet/cop_derivate_00069370/egusphere-2023-3148.pdf https://egusphere.copernicus.org/preprints/2024/egusphere-2023-3148/egusphere-2023-3148.pdf eng eng Copernicus Publications https://doi.org/10.5194/egusphere-2023-3148 https://noa.gwlb.de/receive/cop_mods_00071058 https://noa.gwlb.de/servlets/MCRFileNodeServlet/cop_derivate_00069370/egusphere-2023-3148.pdf https://egusphere.copernicus.org/preprints/2024/egusphere-2023-3148/egusphere-2023-3148.pdf https://creativecommons.org/licenses/by/4.0/ uneingeschränkt info:eu-repo/semantics/openAccess article Verlagsveröffentlichung article Text doc-type:article 2024 ftnonlinearchiv https://doi.org/10.5194/egusphere-2023-3148 2024-01-22T00:22:46Z 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 R2 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. Article in Journal/Newspaper North Atlantic Niedersächsisches Online-Archiv NOA |
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English |
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article Verlagsveröffentlichung |
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article Verlagsveröffentlichung 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 Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures |
topic_facet |
article Verlagsveröffentlichung |
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 R2 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. |
format |
Article in Journal/Newspaper |
author |
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 |
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 Van Den 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 |
publisher |
Copernicus Publications |
publishDate |
2024 |
url |
https://doi.org/10.5194/egusphere-2023-3148 https://noa.gwlb.de/receive/cop_mods_00071058 https://noa.gwlb.de/servlets/MCRFileNodeServlet/cop_derivate_00069370/egusphere-2023-3148.pdf https://egusphere.copernicus.org/preprints/2024/egusphere-2023-3148/egusphere-2023-3148.pdf |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_relation |
https://doi.org/10.5194/egusphere-2023-3148 https://noa.gwlb.de/receive/cop_mods_00071058 https://noa.gwlb.de/servlets/MCRFileNodeServlet/cop_derivate_00069370/egusphere-2023-3148.pdf https://egusphere.copernicus.org/preprints/2024/egusphere-2023-3148/egusphere-2023-3148.pdf |
op_rights |
https://creativecommons.org/licenses/by/4.0/ uneingeschränkt info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.5194/egusphere-2023-3148 |
_version_ |
1790604395586519040 |