Dataset: Scaffold-derived metaproteomic exclusive and total spectral counts associated with proteins from samples taken during R/V Atlantic Explorer cruise AE1913 from the Sargasso Sea to Northeast US shelf waters in June of 2019

Final no updates expectedDOI: 10.26008/1912/bco-dmo.934706.1Version 1 (2024-08-01)Dataset Type:Cruise Results

Principal Investigator: Mak A. Saito (Woods Hole Oceanographic Institution)

Scientist: Natalie Cohen (Woods Hole Oceanographic Institution)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

Project: Collaborative Research: Direct Characterization of Adaptive Nutrient Stress Responses in the Sargasso Sea using Protein Biomarkers and a Biogeochemical AUV (Nutrient Stress Responses and AUV Clio)

Abstract

These are the Scaffold-derived metaproteomic exclusive and total spectral counts associated with proteins. Samples were taken during R/V Atlantic Explorer cruise AE1913 in Subtropical North Atlantic, beginning at the Bermuda Atlantic Time-series Station (BATS) of the Sargasso Sea and ending in coastal Northeast US shelf waters in June of 2019.

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Related data table and dataset descriptions:

The primary data table for this dataset is provided under the "Data Files" section and contains total protein spectral counts while the table under "Supplemental Files" provides the exclusive protein spectral counts. 

Total spectral counts refer to the total number of spectra with peptide to spectrum matches (PSMs) that matches to each entry within the FASTA sequence database. This approach allows each peptide to map to multiple closely related sequences. In contrast, with exclusive spectral counts each peptide is only allowed to map to one sequence within the FASTA database, and when a peptide is found in multiple database sequences the one with the most peptides mapping (parsimony) to it is selected. There are pros and cons to each approach, where total spectral counts will double count peptides when two similar proteins are compared, and exclusive spectral counts will underrepresent less abundant proteins with shared peptides, favoring the most homolog with the most shared peptides. Considering protein groups with shared peptides or focusing on peptide-level analyses are alternative approaches that could be constructed from these results.  

See "Related Datasets" section for:
*  "AE1913 Peptide Spectral Counts" which includes the individual peptides associated with these proteins (includes total spectral counts for each peptide).
* "AE1913 Protein Identification FASTA"

CTD and other data from the same cruise are listed on deployment page AE1913: https://www.bco-dmo.org/deployment/916412

These data will become part of the Ocean Protein Portal (https://proteinportal.whoi.edu/; Saito et al., 2020).

The assembly, annotations, metatranscriptomic assembly products, the same exclusive protein spectral counts, and other useful information associated with this multi-omic analysis was published as a package at Zenodo (doi: 10.5281/zenodo.8287779). 

Related Datasets

IsRelatedTo
Dataset: https://doi.org/10.5281/zenodo.8287779
Cohen, N., Krinos, A., Alexander, H., & Saito, M. (2022). Protistan metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling (Version 2) [Data set]. Zenodo. https://doi.org/10.5281/ZENODO.8287779
IsRelatedTo
Dataset: AE1913 Peptide Spectral Counts
Relationship Description: These datasets are from the same collection and study and will be included in the Ocean Protein Portal (https://proteinportal.whoi.edu).
Saito, M. A., Cohen, N. (2024) Peptides associated with scaffold-derived metaproteomic proteins from samples taken during R/V Atlantic Explorer cruise AE1913 from the Sargasso Sea to Northeast US shelf waters in June of 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-08-01 doi:10.26008/1912/bco-dmo.934718.1
IsRelatedTo
Dataset: AE1913 Protein Identification FASTA
Relationship Description: These datasets are from the same collection and study and will be included in the Ocean Protein Portal (https://proteinportal.whoi.edu).
Saito, M. A., Cohen, N. (2024) Protein identification FASTA file (scaffold-derived metaproteomic proteins) from samples taken during R/V Atlantic Explorer cruise AE1913 from the Sargasso Sea to Northeast US shelf waters in June of 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-08-01 doi:10.26008/1912/bco-dmo.934727.1

Related Publications

Related Research
Saito, M. A., Saunders, J. K., Chagnon, M., Gaylord, D. A., Shepherd, A., Held, N. A., Dupont, C., Symmonds, N., York, A., Charron, M., & Kinkade, D. B. (2020). Development of an Ocean Protein Portal for Interactive Discovery and Education. Journal of Proteome Research, 20(1), 326–336. https://doi.org/10.1021/acs.jproteome.0c00382

Saito, M. A., Cohen, N. (2024) Scaffold-derived metaproteomic exclusive and total spectral counts associated with proteins from samples taken during R/V Atlantic Explorer cruise AE1913 from the Sargasso Sea to Northeast US shelf waters in June of 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-08-01 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.934706.1 [access date]

Terms of Use

This dataset is licensed under Creative Commons Attribution 4.0.


If you wish to use this dataset, it is highly recommended that you contact the original principal investigators (PI). Should the relevant PI be unavailable, please contact BCO-DMO (info@bco-dmo.org) for additional guidance. For general guidance please see the BCO-DMO Terms of Use document.

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Funded by the U.S. National Science Foundation