Table of Contents

• Coverage
• Dataset Description
  • Data Processing Description
  • BCO-DMO Processing Description
• Data Files
• Related Datasets
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

These data are part of the Ocean Protein Portal "ProteOMZ" dataset (https://proteinportal.whoi.edu/; Saito et al., 2019).

The raw mass spectra files were searched against SEQUEST within Proteome Discoverer v2.2 software. Processed files were then loaded into Proteome Software and protein and peptide reports as well as and fasta files were exported. The files were modified slightly to map to the Protein Portal data model for submission to BCO-DMO.

Preprocessing:
-Date, time, filter min, filter max, lat, lon, and cruise columns were added based on information from the Falkor 160115 Event log and CTD log.
-Column names reformatted to comply with BCO-DMO standards.

Dataset version 3 revision (2019-02-24): replaces the earlier data version from date (2018-05-25)
* Values "#N/A" changed to "Unknown" which has a different meaning than blank values. Unknown = "Protein functional and taxonomic annotations are marked as "Unknown" for protein sequences which did not have any significant hits to known reference sequences or motifs in the metagenome annotation database. "
* Event log and McLane pump log were updated to fix lat/lon, date/time issues. Since these were sources of information in this dataset, this dataset is also being updated. See respective "processing notes" sections for these two logs for detailed information about changes to those data sources. event log: https://www.bco-dmo.org/dataset/708384 pump log: https://www.bco-dmo.org/dataset/708495
* ISO_DateTime_UTC timestamp added from Date and time columns in the McLane log dataset. Date and time columns were HST time zone so 10 hours were added to make the time in UTC.
* columns for max and min pump filter size added (min 0.2 max 3.0).
* some station and target depths for station and target depth combinations did not exist in the Mclane pump log so the missing values were added to the mclane pump log. The following columns in this dataset come from the pump log: cruise, cast, date, time, lat, lon, depth (ISO_DateTime_UTC is derived from local date and time). Where there were two matched casts in the pump log for a station and target depth, the first cast for the station was used. The only differences between the two possible casts were the date/time columns.

Dataset Version 3: This file revision (2022-06-06) replaces a previous revision of dataset version 1 from 2019-02-24. This is still dataset version 3 because previous revisions of version 3 were not made public.

* Data from source file "ProteOMZ_proteins_for_OPP.csv" was imported into the BCO-DMO data system for this dataset. This file "ProteOMZ_proteins_for_OPP.csv" is from Ocean Protein Portal "ProteOMZ" dataset v3 (file version 2022-06-06)
** In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values.

* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores.  Can not start with a number] e.g. date_y-m-d changed to date_ymd

* ISO DateTime with timezone (UTC) column added in ISO 8601 format from local date and times in HST.

* ".0" removed from ncbi_id values to correspond to the integer identifier at NCBI.

* Data table attached to dataset as Data File:"737620_v3_proteomz-proteins.csv"

From Schmidt Ocean Institute's ProteOMZ Project page:

Rising temperatures, ocean acidification, and overfishing have now gained widespread notoriety as human-caused phenomena that are changing our seas. In recent years, scientists have increasingly recognized that there is yet another ingredient in that deleterious mix: a process called deoxygenation that results in less oxygen available in our seas.

Large-scale ocean circulation naturally results in low-oxygen areas of the ocean called oxygen deficient zones (ODZs). The cycling of carbon and nutrients – the foundation of marine life, called biogeochemistry – is fundamentally different in ODZs than in oxygen-rich areas. Because researchers think deoxygenation will greatly expand the total area of ODZs over the next 100 years, studying how these areas function now is important in predicting and understanding the oceans of the future. This first expedition of 2016 led by Dr. Mak Saito from the Woods Hole Oceanographic Institution (WHOI) along with scientists from University of Maryland Center for Environmental Science, University of California Santa Cruz, and University of Washington aimed to do just that, investigate ODZs.

During the 28 day voyage named “ProteOMZ,” researchers aboard R/V Falkor traveled from Honolulu, Hawaii to Tahiti to describe the biogeochemical processes that occur within this particular swath of the ocean’s ODZs. By doing so, they contributed to our greater understanding of ODZs, gathered a database of baseline measurements to which future measurements can be compared, and established a new methodology that could be used in future research on these expanding ODZs.