Dataset: Trichodesmium field metaproteomes - protein spectral counts
Deployment: AT39-05

View Data: For data, See Dataset Metadata Page: https://osprey.bco-dmo.org/dataset/787147

Principal Investigator:

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

Student:

Noelle Held (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

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

Project:

Collaborative Research: Iron and phosphorus balanced limitation of nitrogen fixation in the oligotrophic ocean (TriCoLim)

Collaborative Research: Evolutionary, biochemical and biogeochemical responses of marine cyanobacteria to warming and iron limitation interactions (Cyanobacteria Warming Responses)

Marine Microbial Investigator Award: Investigator Mak Saito (MM Saito)

New technology for high resolution analysis of proteins and other organic materials produced by marine microorganisms (MM Proteins and Organics Tech)

Version:

Deployment Synonyms:

TriCoLim

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Description

Net tow metaproteome of Trichodesmium species mapped to a Trichodesmium metagenome plus cyanoGEBA species genomes, analyzed by 2D LC-MS/MS in units of normalized protein spectral counts. Samples were collected in North Atlantic surface waters, at station BATS (Bermuda Atlantic Time-series Study), and station ALOHA (A Long-Term Oligotrophic Habitat Assessment) between 2000 and 2018.

An alternative form of these data are available as dataset:
"Trichodesmium field metaproteomes - protein spectral counts in alternative format" https://www.bco-dmo.org/dataset/787078

Related datasets:
Trichodesmium field metaproteomes - sequence fasta: https://www.bco-dmo.org/dataset/787181
Trichodesmium field metaproteomes - peptide spectral counts: https://www.bco-dmo.org/dataset/787168
Trichodesmium sample provenance: https://www.bco-dmo.org/dataset/787093 - Sample provenance file, which includes sample locations, filter sizes

Methods & Sampling

Dataset acquisition description

A 200um plankton net net was deployed to ~20m depth, then recovered to just below surface, repeating five times. Trichodesmium colonies were hand picked into 0.2um filtered surface seawater, rinsed twice in 0.2um filtered surface seawater, and decanted onto a 0.2-4um Supor filter (indicated in sample provenance table, see dataset https://www.bco-dmo.org/dataset/787093).

Proteins were extracted and trypsin digested in-gel following Saito et al., 2014 (Science). Peptides were analyzed by LC-MS/MS in data discovery mode on a Thermo Orbitrap Fusion.

Data Processing Description

Dataset Processing Description

Thermo proteome discoverer 2.2 was used to search the data with the SEQUEST algorithm. Statistical validation was performed in Scaffold (Proteome Software) at the 1% protein and peptide false discovery rate (FDR) levels.

A publicly available Trichodesium metagenome was used in this search (IMG ID 2821474806) as well as the contents of the CyanoGEBA project (Shih et al, 2013).

BCO-DMO Data Manager Processing Notes:
* Time values "00009" changed to 09:00 after checking the sample log.
* Removed column of row numbers called "Unnamed:0"
* Column names were switched kegg_pathway and pfams_id so those column names were switched to correct that. kegg_id and ncbi_name were also switched.

More information about this dataset deployment

Funding

Award Number	Funding Source
GBMF3782	Gordon and Betty Moore Foundation: Marine Microbiology Initiative
GBMF3934	Gordon and Betty Moore Foundation: Marine Microbiology Initiative
OCE-1657766	NSF Division of Ocean Sciences
OCE-1850719	NSF Division of Ocean Sciences

Instruments

Mass Spectrometer

Supplied Name: Thermo Orbitrap Fusion mass spectrometer

Supplied Description:

Instrument Type

Generic Name: Mass Spectrometer

Acronym: Mass Spec

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic Description:

General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
sample_id	Unique sample location ID	unitless	sample
cruise_id	Cruise name	unitless	cruise_id
station_id	Station name	unitless	station
latitude_dd	Latitude (South is negative)	decimal degrees	lat
longitude_dd	Longitude (West is negative)	decimal degrees	lon
depth_m	Sample depth	meters (m)	depth
date_y-m-d	Date (Local ship time) in format yyyy-mm-dd (various time zones, see sample provenance dataset http://lod.bco-dmo.org/id/dataset/787093)	unitless	date_local
time_h-m-d	Time (Local ship time) of sampling in format HH:MM (various time zones, see sample provenance dataset http://lod.bco-dmo.org/id/dataset/787093)	unitless	time_local
minimum_filter_size_microns	Maxiumum phytoplankton net size	microns (uM)	filter_size
maximum_filter_size_microns	Minimum phytoplankton net size	microns (uM)	filter_size
protein_id	Unique protein accession number. Uniquely identifies a protein within the dataset and FASTA file	unitless	sample_descrip
protein_name	Protein descriptive name	unitless	sample_descrip
top3_precursor	Normalized precursor ion intensity of the top 3 most abundant peptide	unitless	no_bcodmo_term
molecular_weight_kDa	Molecular weight of the sample (no data, column included to comply with Ocean Protein Portal template)	kilodaltons (kDa)	weight
ncbi_id	NCBI protein ID. NCBI taxon identifier (txid)	unitless	taxon
ncbi_name	NCBI protein name. NCBI taxon name associated with the NCBI taxon identifier (ncbi_id)	unitless	taxon
kegg_id	KO ontology identifier	unitless	sample_descrip
kegg_description	Kegg description as it correlates to the Kegg identifier (kegg_id).(no data, column included to comply with Ocean Protein Portal template)	unitless	sample_descrip
kegg_pathway	Kegg pathway as it correlates to the Kegg identifier (kegg_id). (no data, column included to comply with Ocean Protein Portal template)	unitless	sample_descrip
pfams_id	PFams identifier	unitless	sample_descrip
pfams_name	pfams name (no data, column included to comply with Ocean Protein Portal template)	unitless	sample_descrip
uniprot_id	Uniprot database identifier (no data, column included to comply with Ocean Protein Portal template)	unitless	accession_number
enzyme_comm_id	Enzyme Commission identifer (no data, column included to comply with Ocean Protein Portal template)	unitless	sample_descrip
other_identified_proteins	Other protein identifiers in the FASTA file (no data, column included to comply with Ocean Protein Portal )	unitless	sample_descrip
sample_type	Sample type "Trichodesmium net tow"	unitless	sample_descrip

Database

Contribute Data

Dataset: Trichodesmium field metaproteomes - protein spectral counts
Deployment: AT39-05

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Trichodesmium field metaproteomes - protein spectral countsDeployment: AT39-05

Dataset acquisition description

Dataset Processing Description

Dataset: Trichodesmium field metaproteomes - protein spectral counts
Deployment: AT39-05