Dataset: Raw LC-MS/MS

Name: Raw LC-MS/MS data with list of identified peptides in xml format from a proteomic analysis performed on protein extracts of M. ferrooxydans
Published: 2016-01-27
Keywords: oceans

Cite This Dataset

Project:

Proteomic profiling of neutrophilic, iron-oxidizing Mariprofundus ferrooxydans, strain PV-1 (Proteomic profiling of Mariprofundus ferrooxydans)

Program:

Center for Dark Energy Biosphere Investigations (C-DEBI)

Principal Investigator:

Roman A. Barco (Bigelow Laboratory for Ocean Sciences)

Co-Principal Investigator:

Katrina Edwards (University of Southern California, USC)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

27 Jan 2016

Version Date:

2016-01-27

Validated:

Yes

Current State:

Final no updates expected

Raw LC-MS/MS data with list of identified peptides in xml format from a proteomic analysis performed on protein extracts of M. ferrooxydans

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Description

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

Related publications:
Barco, RA, Edwards, KJ. 2014. Interactions of proteins with biogenic iron oxyhydroxides and a new culturing technique to increase biomass yields of neutrophilic, iron-oxidizing bacteria. Front. Microbiol. 5:259. doi: 10.3389/fmicb.2014.00259

Methods & Sampling

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.

Data 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

Data Files

File
raw_LCMS.csv (Comma Separated Values (.csv), 246 bytes) MD5:2667b4d139d1de4dd5a8251604d38180 Primary data file for dataset ID 636621

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0939564

Deployments

None available yet

Instruments

Mass Spectrometer

Supplied Name: Thermo LTQ-Orbitrap XL

Supplied 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.

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

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
taxon	Taxon studied.	dimensionless	taxon
description	Description of method.	dimensionless	brief_desc
PRIDE_project	PRIDE database project ID number.	dimensionless	accession_number
data_URL	Link to PRIDE database.	dimensionless	external_link

Status message

Database

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Dataset: Raw LC-MS/MS