CENTER for DARK ENERGY BIOSPHERE INVESTIGATIONS
Datasets
Raw LC-MS/MS
Data Project: Proteomic profiling of neutrophilic, iron-oxidizing Mariprofundus ferrooxydans, strain PV-1
Dataset Maintainers: Roman A. Barco, Katrina J. Edwards, Shannon Rauch, Shannon Rauch, Shannon Rauch
Data Project Maintainers: Roman A. Barco, Katrina J. Edwards
Last Modified: August 19, 2016
URLhttps://www.bco-dmo.org/dataset/636621
Download URLhttps://www.bco-dmo.org/dataset/636621/data/download
Media Type text/tab-separated-values
Created January 27, 2016
Modified August 19, 2016
State Final no updates expected
Brief Description

Raw LC-MS/MS data with list of identified peptides in xml format.

Acquisition Description

Proteomic analysis was performed on protein extracts of M. ferrooxydans by following two methodologies: osmotic shock and alkaline lysis (extraction with NaOH). A total of 8 liters of M. ferrooxydans PV-1 was harvested on 0.22 um filters and treated for osmotic-shock per Neu and Heppel (1965). For the alkaline lysis protocol (crude extract), of a total 8 L of M. ferrooxydans PV-1 was harvested on 0.22 um filters and immersed in a total of 80 mL 0.1 N NaOH. Samples were run on SDS-PAGE gels. 

Processing Description

Excised bands were trypsin-digested and submitted for LC-MS/MS analysis a Thermo LTQ-Orbitrap XL mass spectrometer equipped with an Eksigent Nanoliquid Chromatography 1-D plus system. The resulting MS/MS spectra were searched against the proteome of Mariprofundus ferrooxydans PV-1 in the Uniprot database using the Proteome Discoverer SEQUEST Daemon search engine.

Raw files are publicly available through the PRIDE Archive at http://www.ebi.ac.uk/pride/archive/projects/PXD000937

Instruments

Thermo LTQ-Orbitrap XL [Mass Spectrometer]
Details
Instance Description (Thermo LTQ-Orbitrap XL)

Excised bands were trypsin-digested and submitted for LC-MS/MS analysis a Thermo LTQ-Orbitrap XL mass spectrometer equipped with an Eksigent Nanoliquid Chromatography 1-D plus system.

Mass Spectrometer
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

taxon [taxon]
Details
taxon

Taxon studied.

taxon

taxonomic group or entity. This may be a family, class, genus, species, etc.; usually this parameter will contain a mixture of taxonomic entities.

description [brief_desc]
Details
description

Description of method.

brief_desc

brief description, open ended, specific to the data set in which it appears

PRIDE_project [accession number]
Details
PRIDE_project

PRIDE database project ID number.

accession number
Database identifier assigned by repository and linked to GenBank or other repository.
data_URL [external_link]
Details
data_URL

Link to PRIDE database.

external_link

Link to an external data entry.

Dataset Maintainers

NameAffiliationContact
Roman A. BarcoBigelow Laboratory for Ocean Sciences✓
Katrina J. EdwardsBigelow Laboratory for Ocean Sciences✓
Shannon RauchUniversity of Southern California (USC)
Shannon RauchUniversity of Southern California (USC)
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title Proteomic profiling of neutrophilic, iron-oxidizing Mariprofundus ferrooxydans, strain PV-1
Acronym Proteomic profiling of Mariprofundus ferrooxydans
URLhttps://www.bco-dmo.org/project/632643
Created January 13, 2016
Modified January 13, 2016
Project Description

Description from C-DEBI website:
The aim of this proposal is to gain a better understanding of what subsets of proteins are actually being expressed during neutrophilic, microbial iron (Fe)-oxidation. The recently isolated Mariprofundus ferrooxydans, strain PV-1, will be used as a marine model organism to investigate proteomic differences under different Fe substrates: aqueous Fe2+ and solid Fe0. Two-dimensional gel electrophoresis (2D-GE) and shotgun proteomic methods (LC-MS/MS) will be employed to obtain results from the cultures grown under different conditions. The research being proposed would constitute the foundation for the development of diagnostic tools for the accordance, distribution, and activity level of Fe-oxidation, a globally important biogeochemical process at and below the ocean floor.

This project was funded by a C-DEBI Graduate Student Fellowship.

Data Project Maintainers
NameAffiliationRole
Roman A. BarcoBigelow Laboratory for Ocean SciencesPrincipal Investigator
Katrina J. EdwardsUniversity of Southern California (USC)Co-Principal Investigator

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