Dataset: Ross Sea metaproteome FASTA files
Deployment: NBP0601

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/769266

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

These data are part of the Ocean Protein Portal "Ross Sea Net Tow (Bender)" dataset version 1 (https://proteinportal.whoi.edu/; Saito et al., 2020).

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.

This .fasta file is a standard FASTA format for sequences with first line of entry starting with ">" and a text description, followed by the associated amino acid sequence. This file is unitless (all sequence, no integers).

Organism identifier (LifeSciences Identifier, LSID):
Phaeocystis antarctica, urn:lsid:marinespecies.org:taxname:341585

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 FASTA generated from Phaeocystis culture transcriptome study. FASTA of discovered protein sequences exported from Proteome Software. Data processing was documented in Bender et al. 2018.

More information about this dataset deployment

Funding

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

Instruments

Mass Spectrometer

Supplied Name: Thermo Scientific Q-Exactive Orbitrap mass spectrometer with a Michrom Advance CaptiveSpray source

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

Contribute Data

Dataset: Ross Sea metaproteome FASTA files
Deployment: NBP0601

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Ross Sea metaproteome FASTA filesDeployment: NBP0601

Dataset acquisition description

Dataset Processing Description

Dataset: Ross Sea metaproteome FASTA files
Deployment: NBP0601