Dataset: Ross Sea metaproteome protein spectral counts
Deployment: NBP0601

View Data: For data, See Dataset Metadata Page: https://osprey.bco-dmo.org/dataset/768237

Principal Investigator:

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

Contact:

Sara Bender (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

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

Project:

Controls of Ross Sea Algal Community Structure (CORSACS)

Version:

Deployment Synonyms:

CORSACS I

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Description

A net tow metaproteome of a Phaeocystis antarctica bloom in the Ross Sea, mapped here to Phaeocystis metatranscriptomes analyzed by 2D LCMS, in units of protein spectral counts.

Related dataset (generated from the same sampling event and methodology):
Ross Sea metaproteome peptide spectral counts: https://www.bco-dmo.org/dataset/768259
Ross Sea metaproteome FASTA files: https://www.bco-dmo.org/dataset/769266

Methods & Sampling

Dataset acquisition description

Sampling was conducted with a 20 micron plankton net on 12/30/2005 at about 1am (local time), near station 137, was extracted for total protein using an SDS detergent method followed by tube gel purification, reduction, alkylation, and tryptic digestion and analyzed on a Thermo Orbitrap Fusion using 2-dimensional separation scheme to maximize metaproteome depth. Detailed methods available in Bender et al. 2018.

Data Processing Description

Dataset Processing Description

Mass spectra from 2D LC-MS was peptide-to-spectrum matched using the SEQUEST algorithm within Proteome Discoverer software, followed by spectral counting with Proteome Software's Scaffold software using the submitted FASTA (see supplemental files) generated from Phaeocystis culture transcriptome study. Data processing documented in Bender et al. 2018.

BCO-DMO Data Manager Processing Notes:

Data version 1: 2019-05-17
Modified lat/lon and time to meet requirements to submit data to the Ocean Protein Portal.
* Modified formatting of latitude and longitude to make it valid decimal degree format. Removed the decimal symbol and direction letter. For S changed latitude to negative. For East did not since East is positive.
* Modified time format from HH-MM-SS to HH:MM:SS.
* Stripped ||_GAP_ prefix and _GAP_|| suffix from pfams_id and pfams_name.
* converted fields with internal delimiters inside the cell from || to semicolon;.

More information about this dataset deployment

Funding

Award Number	Funding Source
OPP-0338097	NSF Office of Polar Programs (formerly NSF PLR)

Instruments

None available yet

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
sample_id	Sample identifier. Identifies the sample associated with this annotation	unitless	no_bcodmo_term
cruise_id	Cruise identifier	unitless	cruise_id
station_id	Station identifier where sample was taken	unitless	station
latitude_dd	Station latitude	decimal degrees (DD)	lat
longitude_dd	Station longitude	decimal degrees (DD)	lon
depth_m	Sample depth	meters (m)	depth
date_y-m-d	Date (local) of sample collection in format YYYY-mm-dd. Time zone is Antarctica/McMurdo (NZST/NZDT, UTC+12/UTC+13)	unitless	date_local
time_h-m-s	Time (local) of sample collection in format HH:MM:SS. Time zone is Antarctica/McMurdo (NZST/NZDT, UTC+12/UTC+13)	unitless	time_local
minimum_filter_size_microns	Minimum size of the collection filter	microns (μm)	filter_size
maximum_filter_size_microns	Maximum size of the collection filter	microns (μm)	filter_size
protein_id	Protein identifier. Uniquely identifies a protein within the dataset and FASTA file	unitless	no_bcodmo_term
protein_name	Protein descriptive name	unitless	sample_descrip
spectral_count	Spectral count	count	spectral_counts
molecular_weight_kDa	Molecular weight of the sample	kilo-Daltons (kDa)	weight
ncbi_id	NCBI taxon identifier (txid)	unitless	taxon
ncbi_name	NCBI taxon name associated with the NCBI taxon identifier (ncbi_id)	unitless	taxon
kegg_id	Kegg identifier	unitless	accession_number
kegg_description	Kegg description as it correlates to the Kegg identifier (kegg_id)	unitless	sample_descrip
kegg_pathway	Kegg pathway as it correlates to the Kegg identifier (kegg_id)	unitless	sample_descrip
pfams_id	PFams identifier	unitless	accession_number
pfams_name	PFams name as it correlates to the PFams identifier (pfams_id)	unitless	no_bcodmo_term
uniprot_id	Uniprot database identifier	unitless	accession_number
enzyme_comm_id	Enzyme Commission identifer	unitless	no_bcodmo_term
other_identified_proteins	Other protein identifiers in the FASTA file	unitless	sample_descrip
ISO_DateTime_UTC	Timestamp (UTC) in standard ISO 8601:2004(E) format YYYY-mm-ddTHH:MM:SSZ	unitless	ISO_DateTime_UTC

Database

Contribute Data

Dataset: Ross Sea metaproteome protein spectral counts
Deployment: NBP0601

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Ross Sea metaproteome protein spectral countsDeployment: NBP0601

Dataset acquisition description

Dataset Processing Description

Dataset: Ross Sea metaproteome protein spectral counts
Deployment: NBP0601