About Datasets

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 In preparation
Total 219

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)

Additional Dataset Information:

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
Publication: Saunders et al., In preparation
Pride submission: In preparation
BCO-DMO: In preparation

Metzyme 0.2 and 3.0 datasets (PI: Mak Saito)

  • Expedition: METZYME KM1128 R/V Kilo Moana Hawaii - Tahiti 2011
  • Data type: Global proteomics 1D dataset collected by Thermo Fusion Mass Spectrometer
  • Units deposited: unnormalized spectral counts. Note that datasets in use for publication for the 3.0 dataset have been converted to relative spectral counts.
  • Chief Scientists Carl Lamborg and Mak Saito
  • Data Generator Laboratory: Mak Saito
  • Region: Central Pacific Ocean
  • Number of samples: 37
  • Number of stations: 7
  • Filter fractions: 0.2-3.0 micron fraction and 3.0-51 micron fractions
  • Repository for 0.2-3.0 micron Raw Files: PRIDE
    • Project Name: Pacific Ocean metaproteomics, METZYME KM1128
    • Project accession: PXD009712
    • Project DOI: 10.6019/PXD009712
  • BCO-DMO Environmental Data Repository: https://www.bco-dmo.org/project/2236
  • Status targeted data published, global proteomic datasets in preparation (Cohen et al., in prep)
  • Matching Metagenomic dataset 0.2-3.0 fraction: https://genome.jgi.doe.gov/portal/FungenequPacific/FungenequPacific.info.html
  • Matching metatrascriptomic dataset for 3.0-51 micron fraction: in prep for submission

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