Dataset: Mass spec proteomics data
Deployment: EN509

Proteomics on diatom response to allelopathy from red tide dinoflagellate (Karenia brevis).

Principal Investigator:

Julia Kubanek (Georgia Institute of Technology, GA Tech)

Co-Principal Investigator:

Facundo Fernandez (Georgia Institute of Technology, GA Tech)

Brook L. Nunn (University of Washington, UW)

Contact:

Julia Kubanek (Georgia Institute of Technology, GA Tech)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Waterborne chemical cues in the plankton: a systems biology approach (Plankton Chemical Cues)

Current State:

Final no updates expected

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/536902/data

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Description

Data files in .raw format are available from the Chorus repository (https://chorusproject.org) under project ID number 650 (project name: "Diatom response to allelopathy"), experiment ID number 843.

Files can be downloaded from the following URL. Note the total file size is 13.4 GB: https://chorusproject.org/anonymous/download/experiment/6729965144923166962

The data files are in Thermo-Finnigan .raw format. Vendor software can be used to view these files, and there are free viewers that can also be used (one example is PVIEW). The files can also be converted to mzXML files using MSconvert.

Methods & Sampling

Dataset acquisition description

Field assemblages of plankton were sampled during two cruises (EN496 and EN509), and shipboard experiments were conducted to test the community-level effects of Karenia brevis allelopathy on Gulf of Mexico plankton. The sampling and shipboard experiments are described fully in:
Poulson-Ellestad et al. 2014. Are offshore phytoplankton susceptible to Karenia brevis allelopathy? J. Plankton Res. 36:1344-1356. doi: 10.1093/plankt/fbu064

All raw files collected in DDA fashion with 90 minute gradient. These diatom species (either A. glacialis or T. pseudonana) were grown in flasks containing the toxic red tide forming dinoflagellate K. brevis in dialisis bags. This experimental design allowed allelopathic chemicals to be released by the dinoflagellate to the diatom of interest without contaminating the diatoms collected.

See related publication:
Poulson-Ellestad, K.L., Jones, C.M., Roy, J., Viant, M.R., Fernandez, F.M., Kubanek, J., & Nunn, B.L. 2014. Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton. PNAS Proc Natl Acad Sci USA, 111(24): 9009-14. doi:10.1073/pnas.1402130111

Data Processing Description

Dataset Processing Description

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1060300	NSF Division of Ocean Sciences

Instruments

Global Positioning System Receiver

Supplied Name: GPS

Supplied Description:

Instrument Type

Generic Name: Global Positioning System Receiver

Acronym: GPS

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/POS03/

Generic Description:

The Global Positioning System (GPS) is a U.S. space-based radionavigation system that provides reliable positioning, navigation, and timing services to civilian users on a continuous worldwide basis. The U.S. Air Force develops, maintains, and operates the space and control segments of the NAVSTAR GPS transmitter system. Ships use a variety of receivers (e.g. Trimble and Ashtech) to interpret the GPS signal and determine accurate latitude and longitude.

Mass Spectrometer

Supplied Name: QEplus

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
description	Description of the data file.	text	brief_desc
repository	Name of the external repository where the data file is located.	text	brief_desc
project_id	Chorus project ID number.	integer	project
experiment_id	Chorus experiment ID number.	integer	exp_id
file_size	Size of the downloadable file.	GB	no_bcodmo_term
file_link	Link to the data file (.zip).	text	file_link

Database

Contribute Data

Dataset: Mass spec proteomics data
Deployment: EN509

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Mass spec proteomics dataDeployment: EN509

Dataset acquisition description

Dataset Processing Description

Dataset: Mass spec proteomics data
Deployment: EN509