Dataset: Trichodesmium field metaproteomes - sequence fasta

Name: FASTA file of sequences in Trichodesmium field metaproteomes mapped to a Trichodesmium metagenome plus cyanoGEBA species genomes from samples collected in the Atlantic and Pacific Ocean between 2000 and 2018
Published: 2020-01-14
Keywords: Trichodesmium, metaproteomics, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.787181.1

Spatial Extent: N:23.22 E:-21.59 S:0.17 W:-158

Temporal Extent: 2000-07-27 - 2018-03-18

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)

Program:

Marine Microbiology Initiative (MMI)

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)

Version:

Version Date:

2020-01-14

Restricted:

Validated:

Yes

Current State:

Final no updates expected

FASTA file of sequences in Trichodesmium field metaproteomes mapped to a Trichodesmium metagenome plus cyanoGEBA species genomes from samples collected in the Atlantic and Pacific Ocean between 2000 and 2018

Abstract:

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

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2020-01-14	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.787181.1	2020-04-30

Description

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

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

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.

Data Files

File
trimmed_fasta_trichoWT.fasta filename: trimmed_fasta_forportal_trichoWT.fasta (FASTA, 1.01 MB) MD5:f81d4d95ca7411c2bac7d9e0ebd1a55e Contents include sequences of all identified proteins in fasta format

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AT39-05	TriCoLim	2018-02-11	R/V Atlantis	David A. Hutchins (Chief Scientist)	data info
JC150	Ziploc	2017-06-26	RRS James Cook	Claire Mahaffey (Chief Scientist)	data info

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

None available yet

Status message

Database

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Dataset: Trichodesmium field metaproteomes - sequence fasta