Dataset: Mass spectrometry proteomics data

Name: Mass spectrometry proteomics data investigating morphological plasticity in a sulfur-oxidizing bacterium from the SUP05 clade enhances dark carbon fixation from cultures grown under under aerobic and anaerobic conditions
Published: 2019-12-17
Keywords: oceans

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Cite This Dataset

Project:

Characterizing the contribution of bacteria from the SUP05 clade to autotrophic and heterotrophic carbon cycling across ocean gradients (SUP05 Activities)

Principal Investigator:

Robert Morris (University of Washington, UW)

Co-Principal Investigator:

Anitra E. Ingalls (University of Washington, UW)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2019-12-17

Restricted:

Validated:

Current State:

Preliminary and in progress

Mass spectrometry proteomics data investigating morphological plasticity in a sulfur-oxidizing bacterium from the SUP05 clade enhances dark carbon fixation from cultures grown under under aerobic and anaerobic conditions

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Description

The mass spectrometry proteomics data files have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the data set identifier PXD013243 and title "Morphological plasticity in a sulfur-oxidizing bacterium from the SUP05 clade enhances dark carbon fixation"
(see https://www.ebi.ac.uk/pride/archive/projects/PXD013243).

These data were published in Shah et al. (2019).

Methods & Sampling

Methodology:

Ca. T. autotrophicus strain EF1 protein extracts were analyzed using a mass spectrometer. Protein identifications were determined using COMET and checked using PeptideProphet, ProteinProphet, and iProphet. The final list of protein identifications were then filtered to ensure that at least one peptide was observed consistently across individual injections and that the protein probability within each replicate was greater than 95%. A total of 802 proteins were observed, representing 53% of all predicted proteins in strain EF1.

Sampling and analytical procedures:

Protein samples for comparative analyses were extracted from axenic cultures grown under aerobic and anaerobic conditions.

Instruments:
Waters ACQUITY M-class UPLC coupled to a Thermo QExactive HF Orbitrap high-resolution mass spectrometer (HRMS) equipped with a nano-electrospray (NSI) source.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1558483

Deployments

None available yet

Instruments

Mass Spectrometer

Supplied Name: Waters ACQUITY M-class UPLC coupled to a Thermo QExactive HF Orbitrap high-resolution mass spectrometer (HRMS) equipped with a nano-electrospray (NSI) 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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Dataset: Mass spectrometry proteomics data