Saito, M. A., Saunders, J. K., McIlvin, M. R., Bertrand, E. M., Breier, J. A., Brisbin, M. M., Colston, S. M., Compton, J. R., Griffin, T. J., Hervey, W. J., Hettich, R. L., Jagtap, P. D., Janech, M., Johnson, R., Keil, R., Kleikamp, H., Leary, D., Martens, L., McCain, J. S. P., Moore, E., Mehta, S., Moran, D. M., Neibauer, J., Neely, B. A., Jakuba, M. V., Johnson, J., Duffy, M., Herndl, G. J., Giannone, R., Mueller, R., Nunn, B. L., Pabst, M., Peters, S., Rajczewski, A., Rowland, E., Searle, B., Van Den Bossche, T., Vora, G. J., Waldbauer, J. R., Zheng, H., and Zhao, Z.: Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures, Biogeosciences, 21, 4889–4908, https://doi.org/10.5194/bg-21-4889-2024, 2024.
Objective: Ocean metaproteomics is an exciting new datatype that has the potential to provide valuable new insights into the metabolic functions of marine microbes and their impact on ecological and biogeochemical processes. However, as for most new measurement types there are uncertainties associated with the accuracy and precision of measurements due to the limited extent of the application of analyses thus far, and hence there is a need to generate community confidence in metaproteomics. We propose to initiate an intercomparison effort whereby an ocean metaproteome sample from the Bermuda Atlantic Time Series is collected, divided and shared among multiple laboratories for global and targeted metaproteomic analyses. The results will be collated and discussed at a workshop of intercomparison participants. In addition, an informatic intercomparison will be conducted using a representative mass spectra data file. This effort is a follow up of the 2010 OCB scoping workshop “ The Molecular Biology of Biogeochemistry: Using molecular methods to link ocean chemistry with biological activity" and NSF EarthCube workshop that assembled US and Canadian scientists involved in metaproteomic research in May of 2017: Ocean Proteomics Data Sharing and Best Practices Workshop (Report).
Saito et al. (2019). Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. J. Proteome Res. 18(4), 1461-1476.
PIs: Mak Saito and Matthew McIlvin (Woods Hole Oceanographic Institution)
Activities Timeline
Summer 2018: Protein sample collection and dissecting at BATS
BATS 348 Metaproteome intercalibration standards (Document Version October 4, 2018)
2019 Paired metagenomic extraction, sequencing, and annotation for peptide database searching
2019 Isotope labeled standard production
Samples were shipped to laboratories in early 2020. Due to the COVID-19 pandemic during the spring, efforts to follow through on the original timeline were delayed due to laboratory shutdowns and an inability to conduct an in-person workshop. With most laboratories resuming activities at this point in autumn of 2020, we are re-starting the intercalibration effort.
Revised data submission dates are:
1. Global Metaproteome laboratory datasets by December 1, 2020
2. Targeted Metaproteome laboratory dataset to be determined (contact us if interested in participating and if we have sufficient participation we will plan a date)
3. Informatic component of the shared RAW file by January 8, 2021. Prepared raw files for the informatic study will be distributed for informatic analyses on December 2, 2020 to allow submission of global metaproteome datasets prior to that.
Results were anonymized, tabulated, re-analyzed by a common informatic pipeline and shared with participants at this virtual meeting. The participants elected to proceed to a peer-reviewed manuscript based on the successful intercomparison.
A draft Version 1 of the manuscript was shared with study participants in May 2022 and comments received in the subsequent months.
A draft Version 2 of the manuscript was shared with study participants in January 2023.
September 16-17, 2021: Ocean Metaproteomics Intercomparison Workshop (virtual, Zoom)
Two McLane pump samplers with two Mini-MULVS sampler heads clamped together and deployed on BATS expedition 348 on June 16th 2018 aboard the R/V Atlantic Explorer.
The four 142 mm filter 0.2 μm filters used for this intercomparison study collected by McLane pump (X-Acto knife for scale). Each filter was sliced into 8 fractions (inset) and frozen at -80C in a cryovial. Samples were labeled by pump and pump head (Table 1; pump-2A upper left; pump-1A upper right; pump-2B lower left; pump-1B lower right).
Acknowledgements
Funds for distributing intercomparison samples and a future workshop to discuss results is being supported by Ocean Carbon and Biogeochemistry (OCB). Funds for the research expedition where samples were collected were supported by the US National Science Foundation Biological Oceanography and Chemical Oceanography and the Gordon and Betty Moore Foundation. We thank Sophie Colston, Judson Harvey, and Gary Vora (Naval Research Laboratory) for metagenomic sequencing and Jaci Saunders (WHOI) for assembly and annotation of the paired sample.
