Dataset: Trichodesmium field metaproteomes - sequence fasta
Deployment: JC150

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/787181

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:

Ziploc

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Description

FASTA file of sequences in Trichodesmium field metaproteomes analyzed by 2D LC-MS/MS mapped to a Trichodesmium metagenome (IMG ID 2821474806) plus cyanoGEBA species genomes (Shih et al, 2013). 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.

Related datasets:
Trichodesmium field metaproteomes - peptide spectral counts: https://www.bco-dmo.org/dataset/787168
Trichodesmium field metaproteomes - protein spectral counts: https://www.bco-dmo.org/dataset/787147
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.t

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). This fasta file contains the sequences that were identified in the metaproteome analysis.

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

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Database

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Dataset: Trichodesmium field metaproteomes - sequence fasta
Deployment: JC150

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Trichodesmium field metaproteomes - sequence fastaDeployment: JC150

Dataset acquisition description

Dataset Processing Description

Dataset: Trichodesmium field metaproteomes - sequence fasta
Deployment: JC150