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: 2018-12-10
Keywords: oceans

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

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:

2018-12-10

Restricted:

Yes

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

-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: 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.

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
EC	Enzyme Commission ID number	unitless	accession_number
uniprot	Uniprot database ID number	unitless	accession_number
best_hit_annotation	Product name	unitless	accession_number
KO	Kegg ID	unitless	accession_number
cast	Cast number	unitless	cast
cruise	Cruise number	unitless	cruise_id
date; yyyy/mm/dd	Date at station	unitless	date
depth	Cast depth	meters	depth
min_filter_size	Minimum filter size	microns	filter_size
max_filter_size	Maximum filter size	microns	filter_size
ISO_DateTime_UTC	DateTime UTC ISO formatted	unitless	ISO_DateTime_UTC
lat	Latitude	decimal degrees	lat
lon	Longitude	decimal degrees	lon
PFams_desc	Protein family description	unitless	no_bcodmo_term
row_id	Row number	unitless	no_bcodmo_term
KO_desc	Kegg name	unitless	no_bcodmo_term
KO_pathway	Kegg pathway	unitless	no_bcodmo_term
PFams	Protein family ID number	unitless	proteins
Identified_Proteins	JCVI metagenome ID number	unitless	proteins
best_hit_species	Taxon	unitless	species
spectral_count	Spectral count of each protein	count	spectral_counts
station	Station number	unitless	station
best_hit_taxon_id	Taxon ID	unitless	taxon
time; hh:mm	Time at station	unitless	time
Molecular_Weight	Useful for calculated information	kDa	weight

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Dataset: ProteOMZ Protein Level Spectral Counts