Dataset: Ross Sea metaproteome FASTA files

Name: FASTA file of protein identifications from net tows during RVIB Nathaniel B. Palmer cruise NBP0601 in December of 2015
Published: 2019-05-17
Keywords: metaproteomics, Ross Sea, Phaeocystis antarctica, Antartica, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.769266.1

Spatial Extent: N:-76.82 E:170.76 S:-76.82 W:170.76

Ross Sea

Temporal Extent: 2005-12-30

Project:

Controls of Ross Sea Algal Community Structure (CORSACS)

Program:

Ocean Carbon and Biogeochemistry (OCB)

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)

Version:

Version Date:

2019-05-17

Restricted:

Validated:

Yes

Current State:

Final no updates expected

FASTA file of protein identifications from net tows during RVIB Nathaniel B. Palmer cruise NBP0601 in December of 2015

Abstract:

A net tow metaproteome of a Phaeocystis antarctica bloom in the Ross Sea, mapped here to Phaeocystis metatranscriptomes analyzed by 2D LCMS, sequence file of discovered proteins, unitless.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2019-05-17	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.769266.1	2024-05-23

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., 2019).

Methods & Sampling

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

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.

BCO-DMO Processing

fasta file added to BCO-DMO data system, no changes.

Data Files

File
minio_v1/Sara_phaeo_field_161223_2d_assembly_1374_1871_V2.fasta (attached also to BCO-DMO draft page) filename: Sara_phaeo_field_161223_2d_assembly_1374_1871_V2.fasta (FASTA, 593.07 KB) MD5:34816c895836b3e2b7552b2fa2b4405c Primary file for dataset 769266 v1. Corresponds to Ocean Protein Portal Bender-Ross Sea data (version 1).

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
NBP0601	CORSACS I	2005-12-17	RVIB Nathaniel B. Palmer	Giacomo DiTullio (Chief Scientist)	data info

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

None available yet

Status message

Database

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Dataset: Ross Sea metaproteome FASTA files