URLhttps://www.bco-dmo.org/dataset/636621
Download URLhttps://www.bco-dmo.org/dataset/636621/data/download
Media Typetext/tab-separated-values
CreatedJanuary 27, 2016
ModifiedAugust 19, 2016
StateFinal no updates expected
Brief DescriptionRaw 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.

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.

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

PRIDE_project [accession number]
Details
PRIDE_project

PRIDE database project ID number.

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

Link to PRIDE database.

Link to an external data entry.

Dataset Maintainers

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

BCO-DMO Project Info

Project TitleProteomic profiling of neutrophilic, iron-oxidizing Mariprofundus ferrooxydans, strain PV-1
AcronymProteomic profiling of Mariprofundus ferrooxydans
URLhttps://www.bco-dmo.org/project/632643
CreatedJanuary 13, 2016
ModifiedJanuary 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.

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