Dataset: Ruergeria pomeroyi DSS-3 replete proteome

Name: The global proteome of replete laboratory cultures of Ruergeria pomeroyi DSS-3
Published: 2022-06-14
Keywords: proteomics, marine bacteria, physiology, metabolites, biogeochemistry, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.875600.1

Temporal Extent: 2021-03-01 - 2021-05-01

Project:

C-CoMP Model Bacteria Physiological Studies (C-CoMP Model Bacteria)

Program:

Center for Chemical Currencies of a Microbial Planet (C-CoMP)

Principal Investigator:

Mak A. Saito (Woods Hole Oceanographic Institution, WHOI)

Co-Principal Investigator:

Mary Ann Moran (University of Georgia, UGA)

Data Manager:

Laura Gray (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

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

Version:

Version Date:

2022-06-14

Restricted:

Validated:

Yes

Current State:

Final no updates expected

The global proteome of replete laboratory cultures of Ruergeria pomeroyi DSS-3

Abstract:

This dataset represents the global proteome of replete laboratory cultures of Ruergeria pomeroyi DSS-3 (collected in triplicate). This dataset is an initial examination of the proteome allocation of this heterotrophic bacteria and will contribute to C-CoMP's efforts that are focused on understanding the physiology of model marine bacteria. A total of 2341 proteins were identified in DSS-3. The Moran laboratory at University of Georgia grew and prepared the cultures and the Saito laboratory at Woods Hole Oceanographic Institution conducted the proteomics analyses.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2022-06-14	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.875600.1	2022-06-15

Methods & Sampling

Cultures (50 ml each) of Ruergeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 were harvested in triplicate, centrifuged at 8000 x g for 10 minutes, flash frozen, stored at -80 degrees C, and shipped to Woods Hole Oceanographic Institution for proteomics analysis. Cultures were filtered and filters were extracted using SDS detergent and a SP3 magnetic bead purification followed by trypsin digestion alkylation and reduction. The methods are described in Saito et al. 2020 and were modified from the methods originally published by Hughes et al. 2014. Analysis was conducted by 2D active modulation Orbitrap mass spectrometry as described in McIlvin and Saito 2021.

This dataset reports results for the Ruergeria pomeroyi DSS-3 samples. See related datasets for the Alteromonas macleodii MIT1002 samples.

Note: the sample ids ending in a1, b1, and c1 differentiate biological triplicates from one another.

Data Processing Description

Data Processing:
The raw mass spectra files were searched against the SEQUEST high thread database within Proteome Discoverer software (v2.4). Processed files were then loaded into Proteome Software (Scaffold v5) and filtered to False Discovery Rates less than 1% using Percolator (0.7% peptide FDR and 0.03% Protein FDR using decoy database). Percolator was used for PSM validation based on PEP scoring. The output was reported as exclusive unique spectral counts. No normalization was applied to this dataset.

Raw data files are currently being submitted to the ProteomeXchange repository through PRIDE under accession number PXD034365. Raw file names are: 220427_CCoMP_AHANA_DSS_3_a1, 220427_CCoMP_AHANA_DSS_3_b1, 220427_CCoMP_AHANA_DSS_3_c1.

BCO-DMO Processing:
- modified parameter names;
- replaced commas with semi-colons in the protein_name column.

Data Files

File
DSS-3.csv (Comma Separated Values (.csv), 201.24 KB) MD5:c3e5bb475ef8216fe97f7ceebebd4d61 Primary data file for dataset ID 875600

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-2019589

Deployments

None available yet

Instruments

High-Performance Liquid Chromatograph

Supplied Name: Dionex nano-HPLC

Supplied Description:

Data were collected with a Thermo Fusion Orbitrap mass spectrometer interfaced with a Dionex nano-HPLC configured with 2D active modulation chromatography using the methods of McIlvin and Saito 2021.

Instrument Type

Generic Name: High-Performance Liquid Chromatograph

Acronym: HPLC

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/

Generic Description:

A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase.

Mass Spectrometer

Supplied Name: Thermo Fusion Orbitrap

Supplied Description:

Data were collected with a Thermo Fusion Orbitrap mass spectrometer interfaced with a Dionex nano-HPLC configured with 2D active modulation chromatography using the methods of McIlvin and Saito 2021.

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
protein_id	A numerical identifier that uniquely identifies this protein within this dataset	unitless	protein_ID
protein_name	A name identifying this protein	unitless	protein_ID
ncbi_id	unique ID (typically the NCBI protein accession number) assigned to each protein name	unitless	accession_number
molecular_weight_kDa	The molecular weight in kilo-Daltons of the protein	kilo-Daltons	molecular_weight
DSS3_a1_SC	Exclusive unique spectral counts for proteins in sample DSS3_a1	unnormalized spectral counts	spectral_counts
DSS3_b1_SC	Exclusive unique spectral counts for proteins in sample DSS3_b1	unnormalized spectral counts	spectral_counts
DSS3_c1_SC	Exclusive unique spectral counts for proteins in sample DSS3_c1	unnormalized spectral counts	spectral_counts

Status message

Database

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Dataset: Ruergeria pomeroyi DSS-3 replete proteome