Dataset: Proteomic data of dilution series of bacteria and diatoms using MS.

Name: Proteomic data of dilution series of bacteria and diatoms using MS.
Published: 2017-11-13
Keywords: biota, oceans

Cite This Dataset

Project:

Collaborative Research: Proteins as functional biomarkers: integrating organic characterization with proteomics to track routes for carbon and nitrogen recycling and preservation (Proteins as Biomarkers)

Principal Investigator:

Brook L. Nunn (University of Washington, UW)

Co-Principal Investigator:

Rodger Harvey (Old Dominion University, ODU)

William S. Noble (University of Washington, UW)

BCO-DMO Data Manager:

Megan Switzer (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2017-11-13

Restricted:

Proteomic data of dilution series of bacteria and diatoms using MS.

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Description

To mimic a complex marine sample, a dilution series of R. pomeroyi and T. pseudonana was created at different cellular ratios. These mixtures were filtered and proteins were extracted from the filter for tryptic digestion and LC-MS/MS analysis.

Biological fractions were lysed, digested and analyzed using proteomic mass spectrometry.

Data are available for download at the EBI PRIDE Archive.
Homepage: https://www.ebi.ac.uk/pride/archive
Project URL: https://www.ebi.ac.uk/pride/archive/projects/PXD004758
Data URL: https://www.ebi.ac.uk/pride/archive/projects/PXD004758/files

Methods & Sampling

Peptide samples were spiked with a quality control mix of PRTC-BSA peptides and 2 ul containing 1 ug of protein was injected on a 27 cm column (C18 beads) and 3 cm trap (C18). Data were collected in 4 m/z isolation width windows in 125 m/z ranges (400-525, 525-650, 650-775, 775-900). For each method, a gradient of 5-80% aceotnitrile over 90 minutes was applied for peptide spectra acquisition on a Q-Exactive-HF.

Instrument(s): QExactive Thermo Finnegan

Data Processing Description

In order to generate spectral libraries for targeted method development, Peptide Centric Analysis was completed with the software PECAN (Ting et al., 2015). Input files included the list of peptides generated for targeted proteomics and the mzML files generated from raw DIA files using MSConvert. PECAN correlates a list of peptide sequences of interest with the acquired DIA spectra in order to locate the peptide-specific spectra within the acquired DIA dataset. The PECAN .blib output file was then imported into Skyline daily for targeted method development. The selected reaction monitoring dataset is published in PeptideAtlas under Accession number PASS00917.

Data Files

File
Bacterial_detection_Timmins.csv (Comma Separated Values (.csv), 193 bytes) MD5:71ff326f3478ae0fb4a045d4bd1ebb17 Primary data file for dataset ID 719080

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1633939

Deployments

None available yet

Instruments

Mass Spectrometer

Supplied Name: QExactive Thermo Finnegan

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

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Repository	Name of database where data are currently served	unitless	no_bcodmo_term
Project	Unique project identifier for the database where data are currently served	unitless	project
Project_URL	Link to project page at the database where data are currently served	unitless	external_link

Status message

Database

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Dataset: Proteomic data of dilution series of bacteria and diatoms using MS.