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).
- Intercomparison Plan (PDF)
- Saito et al. (2019). Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. J. Proteome Res. 18(4), 1461-1476.
- Activity Proposal (PDF)
PIs: Mak Saito and Matthew McIlvin (Woods Hole Oceanographic Institution)
- 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
- Beginning January 2020 Intercomparison sample distribution to participating laboratories (until samples run out)
- Winter/Spring 2020 Intercomparison sample analyses
- April 1, 2020 Proposed Deadline for submission of global metaproteomic results
- May 1, 2020 Proposed Deadline for submission of targeted metaproteomic results and informatic search results
- POSTPONED May 13-15, 2020 Planned Workshop to discuss intercomparison results (Woods Hole, MA)
- Summer/Fall 2020 Write-up and submit results to peer reviewed journal
3/10/20: Due to concerns about the COVID-19 public health situation, we have discussed this among the steering committee and decided to delay our May meeting to a later to be determined date, perhaps during the summer months. Our apologies about this, but with numerous travel advisories and institutional travel restrictions this seems prudent at this time. With this, and since some of our colleagues have limited laboratory access with shutdowns, we will also push back the upcoming data submission dates as well, with new dates to be determined as the travel situation becomes clearer.
Also as an operational note, we will be sharing a metagenomic database for the intercomparison in a future email, and have been working on a new batch of the isotope labeled standard for those interested in participating in the targeted component of the study.