Dataset: ProteOMZ Protein Level Spectral Counts

Name: Total spectral count of proteins from R/V Falkor cruise 160115 for the ProteOMZ expedition in the Central Pacific in 2016
Published: 2024-10-21
Keywords: oceans

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Spatial Extent: N:17.4465 E:-139.1089 S:-0.4708 W:-157.3022

Central Pacific

Temporal Extent: 2016-01-19 - 2016-01-28

Project:

The ProteOMZ Expedition: Investigating Life Without Oxygen in the Pacific Ocean (ProteOMZ (Proteomics in an Oxygen Minimum Zone))

Principal Investigator:

Mak A. Saito (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Hannah Ake (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-10-21

Restricted:

Release Date:

2019-02-24

Validated:

Current State:

Under revision

Total spectral count of proteins from R/V Falkor cruise 160115 for the ProteOMZ expedition in the Central Pacific in 2016

Abstract:

Relative protein abundance data of the upper 1000m water column from the ProteOMZ R/V Falkor expedition. There are 56,577 protein identifications over 103 samples, for ~6 million data points.

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Description

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

Data Processing Description

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.

BCO-DMO Processing

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 (2024-10-21) 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"

More Information about this dataset

Funding Sources

Funding Source	Award Number
Gordon and Betty Moore Foundation: Marine Microbiology Initiative	GBMF3782
Schmidt Ocean Institute	R/V Falkor 160115 SOI ProteOMZ Expedition

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
FK160115	ProteOMZ	2016-01-16	R/V Falkor	Mak A. Saito (Chief Scientist)	data info

Instruments

Alpkem RFA300

Supplied Name: Alpkem Autosampler

Supplied Description:

Used in nutrient analysis

Instrument Type

Generic Name: Alpkem RFA300

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0414/

Generic Description:

A rapid flow analyser (RFA) that may be used to measure nutrient concentrations in seawater. It is an air-segmented, continuous flow instrument comprising a sampler, a peristaltic pump which simultaneously pumps samples, reagents and air bubbles through the system, analytical cartridge, heating bath, colorimeter, data station, and printer. The RFA-300 was a precursor to the smaller Alpkem RFA/2 (also RFA II or RFA-2).

CTD Sea-Bird

Supplied Name: SeaBird SBE19 CTD

Supplied Description:

Used for water sampling

Instrument Type

Generic Name: CTD Sea-Bird

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics, no specific unit identified. This instrument designation is used when specific make and model are not known. See also other SeaBird instruments listed under CTD. More information from Sea-Bird Electronics.

Technicon AutoAnalyzer II

Supplied Description:

Used to measure phosphate and ammonium

Instrument Type

Generic Name: Technicon AutoAnalyzer II

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0291/

Generic Description:

A rapid flow analyzer that may be used to measure nutrient concentrations in seawater. It is a continuous segmented flow instrument consisting of a sampler, peristaltic pump, analytical cartridge, heating bath, and colorimeter. See more information about this instrument from the manufacturer.

Trace Metal Bottle

Supplied Name: Trace Metal Rosette

Supplied Description:

Used for nutrient sampling

Instrument Type

Generic Name: Trace Metal Bottle

Acronym: TM Bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/30/

Generic Description:

Trace metal (TM) clean rosette bottle used for collecting trace metal clean seawater samples.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
sample_id	Identifies the sample associated with this annotation	untiless	sample
MS_MS_sample_name	RAW file name; crossreferences to proteomexchange or OPP repository	untiless	no_bcodmo_term
station_id	Station number	unitless	station
depth_m	Cast depth where sample was taken	meters	depth
latitude_dd	Latitude	decimal degrees	lat
longitude_dd	Longitude	decimal degrees	lon
date_ymd	Date at station (local time zone HST) Format: %Y-%m-%d	unitless	date
time_hms	Time at station (local time zone HST) Format: %H:%M:%S	unitless	time
minimum_filter_size_microns	Minimum size of the collection filter in microns	microns	filter_size
maximum_filter_size_microns	Maximum size of the collection filter in microns	microns	filter_size
cruise_id	Cruise number	unitless	cruise_id
protein_id	An identifier that uniquely identifies this protein within this dataset and the FASTA file (see Related Datasets).	unitless	protein_ID
spectral_count_sum	Spectral count of each protein	count	spectral_counts
molecular_weight_kDa	The molecular weight in kilo-Daltons of the sample	kDa	weight
protein_name	A name identifying this protein	unitless	accession_number
ncbi_id	The NCBI taxon identifier.	taxon	species
ncbi_name	The name as it corresponds to the preceding NCBI identifier	verbatimIdentifiation	taxon
kegg_id	The Kegg Orthology Entry identifier for the best Kegg match.	unitless	accession_number
kegg_description	The Kegg Orthology Entry definition of corresponding Kegg ID.	unitless	no_bcodmo_term
kegg_pathway	The relevant Kegg Pathway names for the corresponding Kegg ID.	unitless	no_bcodmo_term
pfams_id	Protein family ID number	unitless	accession_number
pfams_name	Protein family description	unitless	no_bcodmo_term
uniprot_id	Uniprot database ID number	unitless	accession_number
enzyme_comm_id	Enzyme Commission ID number	unitless	accession_number
ISO_DateTime_UTC	Datetime with timezone (UTC) in ISO 8601 format Format: %Y-%m-%dT%H:%MZ	unitless	ISO_DateTime_UTC

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Dataset: ProteOMZ Protein Level Spectral Counts