Summary of Ocean Metaproteome Datasets in the Ocean Protein Portal as of 2/23/19
| Dataset Name | Expedition | Submitting PI | Filter Type | # Samples | Publication Status |
|---|---|---|---|---|---|
| Metzyme 0.2 | KM1128 Central Pacific Ocean |
Mak Saito msaito@whoi.edu |
0.2-3.0 | 37 | Saito et al., 2014 |
| Metzyme 3.0 | KM1128 Central Pacific Ocean |
Mak Saito msaito@whoi.edu |
3.0-51 | 40 | In Preparation |
| Nunn Arctic-Bering Sea | HLY1301 Arctic Ocean and Bering Sea |
Brook Nunn brookh@uw.edu |
0.003-0.8 | 2 | May et al., 2016 |
| Morris CoFeMUG | KN192 South Atlantic Ocean |
Bob Morris morrisrm@uw.edu |
0.03-3 | 16 | Morris et al., 2010 |
| Walsh Canada Basin | JOIS 2015 Arctic Ocean |
David Walsh david.walsh@concordia.ca |
0.2-3.0 | 9 | In preparation |
| Walsh Baffin Bay | ArcticNet2013_CCSG_Amundsen Arctic Ocean |
David Walsh david.walsh@concordia.ca |
0.2-3.0 | 12 | In preparation |
| ProteOMZ | FK160115 Central Pacific Ocean |
Mak Saito msaito@whoi.edu |
0.2-3.0 | 103 | Saunders et al., 2022 |
| Ross Sea Net Tow (Bender) | NBP0601 Ross Sea, Southern Ocean/Coastal Antarctica |
Mak Saito msaito@whoi.edu |
> 20 | 2 | Bender et al., 2018 |
| Total | 221 |
If you are interested in data use from the Ocean Protein Portal, we strongly recommend reading the Data Use Policy) and also the Best Practices for data sharing workshop manuscript (https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.8b00761)
South Atlantic - CoFeMUG KN192 2007 (PI: Bob Morris)
Expedition KN192 R/V Knorr CoFeMUG expedition
BCO-DMO Project site: https://www.bco-dmo.org/project/2067
BCO-DMO Dataset site: https://www.bco-dmo.org/dataset/3444
Data type: LTQ Orbitrap Mass spectrometer
Publication: https://www.nature.com/articles/ismej20104
Bering Sea (PI: Brook Nunn)
Bering Strait (BSt) chlorophyll maximum layer (7 m depth, 65°43.44″ N, 168°57.42″ W)
Publication: https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.6b00239
DOI:10.1021/acs.jproteome.6b00239
TITLE: Bering Strait surface water and Chukchi Sea bottom water microbiome metaproteomics
PRIDE ACCESSION NUMBER: PXD006472
DATA TYPE: DDA
PUBLISHED MANUSCRIPT: May, D.H., Timmins-Schiffman, E., Mikan, M.P., Harvey, H.R., Borenstein, E., Nunn, B.L., Noble, W.S. (2016) An alignment-free "metapeptide" strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing. Journal of Proteome Research 15, 2697-2705.
Northern Chukchi Sea (CS) (PI: Brook Nunn)
bottom waters (55.5 m depth, 72°47.624″ N, 16°53.89″ W)
Publication: https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.6b00239
DOI:10.1021/acs.jproteome.6b00239
TITLE: Bering Strait surface water and Chukchi Sea bottom water microbiome metaproteomics
PRIDE ACCESSION NUMBER: PXD006472
DATA TYPE: DDA
PUBLISHED MANUSCRIPT: May, D.H., Timmins-Schiffman, E., Mikan, M.P., Harvey, H.R., Borenstein, E., Nunn, B.L., Noble, W.S. (2016) An alignment-free "metapeptide" strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing. Journal of Proteome Research 15, 2697-2705.
ProteOMZ Central Pacific OMZ (PI: Mak Saito)
Expedition: FK160115 Central Pacific Ocean R/V Falkor 2016;
https://schmidtocean.org/cruise/investigating-life-without-oxygen-in-the-tropical-pacific/
Chief Scientist: Mak Saito
PRIDE ACCESSION NUMBER: PXD030684
DATA TYPE: DDA
BCO-DMO: Project 685696
*Please note*: The default "ProteOMZ" dataset in the Ocean Protein Portal currently displays non-scaled unnormalized total spectral count units. Scaled normalized data similar to the units found in Saunders et al. (2022) will be provided as an additional dataset called "ProteOMZ normalized".
PUBLISHED MANUSCRIPT:Saunders, J. K., McIlvin, M. R., Dupont, C. L., Kaul, D., Moran, D. M., Horner, T., Laperriere, S. M., Webb, E. A., Bosak, T., Santoro, A. E., & Saito, M. A. (2022). Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean. Proceedings of the National Academy of Sciences, 119(37), e2200014119. doi.org/10.1073/pnas.2200014119
Metzyme 0.2 and 3.0 datasets (PI: Mak Saito)
Relevant publications for dataset:
Saito, M. A., McIlvin, M. R., Moran, D. M., Goepfert, T. J., DiTullio, G. R., Post, A. F., and Lamborg, C. H.: Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers, Science, 345, 1173-1177, 2014.
Saito, M. A., Dorsk, A., Post, A. F., McIlvin, M., Rappé, M. S., DiTullio, G., and Moran, D.: Needles in the Blue Sea: Sub‐Species Specificity in Targeted Protein Biomarker Analyses Within the Vast Oceanic Microbial Metaproteome, PROTEOMICS, 15, 3521-3531, 2015.
Canada Basin, Arctic Ocean
Expedition: JOIS 2015
Data Generator Laboratory: David Walsh
Chief Sci: William Williams
Data Type: Metaproteomics dataset collected by Thermo Orbitrap Elite Mass Sectrometer
Dataset and publication status: in preparation
North Water/Baffin Bay, Arctic Ocean
Expedition: ArcticNet2013_CCSG_Amundsen
Chief Sci: David Barber and Louis Fortier
Data Type: Metaproteomics dataset collected by Thermo Orbitrap Elite Mass Sectrometer
Data Generator Laboratory: David Walsh
Dataset and publication status: in preparation
Ross Sea Net Tow (Bender) - NBP0601 (PI: Saito)
CHIEF SCIENTIST: Jack DiTullio
DATA TYPE: DDA
PUBLISHED MANUSCRIPT: Biogeosciences, 15, 4923–4942, 2018 https://www.biogeosciences.net/15/4923/2018/
PROCESSED DATA: