http://lod.bco-dmo.org/id/dataset/719080
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2017-11-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Proteomic data of dilution series of bacteria and diatoms using MS.
2017-11-13
publication
2017-11-13
revision
BCO-DMO Linked Data URI
2017-11-13
creation
http://lod.bco-dmo.org/id/dataset/719080
Brook L. Nunn
University of Washington
principalInvestigator
Rodger Harvey
Old Dominion University
principalInvestigator
William S. Noble
University of Washington
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Nunn, B. L., Noble, W. S., Harvey, R. (2017) Proteomic data of dilution series of bacteria and diatoms using MS. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-11-13 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/719080 [access date]
Dataset Description: <p>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.</p>
<p>Biological fractions were lysed, digested and analyzed using proteomic mass spectrometry.</p>
<p>Data are available for download at the EBI PRIDE Archive.<br />
Homepage:&nbsp;<a href="https://www.ebi.ac.uk/pride/archive" target="_blank">https://www.ebi.ac.uk/pride/archive</a><br />
Project URL:&nbsp;<a href="https://www.ebi.ac.uk/pride/archive/projects/PXD004758" target="_blank">https://www.ebi.ac.uk/pride/archive/projects/PXD004758</a><br />
Data URL:&nbsp;<a href="https://www.ebi.ac.uk/pride/archive/projects/PXD004758/files" target="_blank">https://www.ebi.ac.uk/pride/archive/projects/PXD004758/files</a></p> Methods and Sampling: <p>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.</p>
<p>Instrument(s):&nbsp;QExactive Thermo Finnegan</p>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1633939 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1633939
onGoing
Brook L. Nunn
University of Washington
206-616-9023
Department of Genome Sciences, Foege Building S113 3720 15th Ave NE
Seattle
WA
98195
USA
brookh@uw.edu
pointOfContact
Rodger Harvey
Old Dominion University
757-683-5657
4600 Elkhorn Ave
Norfolk
VA
23508
US
rharvey@odu.edu
pointOfContact
William S. Noble
University of Washington
Department of Genome Sciences Foege Building S113, 3720 15th Ave NE
Seattle
WA
98195
USA
wnoble@uw.edu
pointOfContact
asNeeded
Unknown
Repository
Project
Project_URL
QExactive Thermo Finnegan
theme
None, User defined
No BCO-DMO term
project
external_link
featureType
BCO-DMO Standard Parameters
Mass Spectrometer
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: Proteins as functional biomarkers: integrating organic characterization with proteomics to track routes for carbon and nitrogen recycling and preservation
https://osprey.bco-dmo.org/project/682497
Collaborative Research: Proteins as functional biomarkers: integrating organic characterization with proteomics to track routes for carbon and nitrogen recycling and preservation
<p>NSF Award Abstract:<br />
Proteins are a major contributor to organic carbon and nitrogen in the ocean and their amino acid building blocks comprise a major fraction of the total nitrogen identified in coastal and oceanic waters and sediments. Over the last decade, tandem mass spectrometry methods developed for the analysis of peptides and protein reconstruction together with informatics developments have re-assembled the amino acid signatures and unlocked the information inherent in the proteins they represent. This interdisciplinary research team has the combined expertise in marine organic biogeochemistry, proteomics, and bioinformatics to help determine the fate of individual proteins during degradation and likely mechanisms for their preservation. This research aims to identify and quantify the proteins responsible for chemical transformations of organic matter in the ocean, thereby exposing how microbial communities control and contribute to the carbon and nitrogen cycle and to organic matter preservation. This project has the potential to trigger a fundamental change in how we view, analyze, and model microbial degradation processes.</p>
<p>Recent findings from microbial ecologists show that bacteria with broad responses to various nutrients (i.e. the generalists) can fine-tune the gene expression of various proteins as a reflection of substrate availability; the proponents of this project have observed a suite of bacterial proteins present during organic matter recycling and that this protein expression changes as degradation proceeds. These observations hint that bacterial proteins have potential as organic biomarkers to reflect the taxonomic distribution of the functioning catalysts in degradation processes. The investigators propose to build on these results to investigate the potential for organic matter preservation to be linked to proteomic expression of the microbial community that drive carbon and nitrogen cycling. The project objectives are: 1) to address the relationship between marine organic matter composition and protein expression by the bacterial community (metaproteome) which act as catalysts for degradation; 2) to detail protein expression in the context of detailed organic matter characterization and 3) to distinguish how proteins present in oceanic sediments derived from different kingdoms of life (e.g. eukaryotic or bacterial) reflect the complex process of organic matter preservation. The overall goal is to capture proteins as critical markers of both presence and process in marine systems. The investigators will link the rapid advances in protein identification to track bacterial proteins to act as "functional biomarkers" and indicators of carbon and nitrogen utilization.</p>
<p>The project would provide multiple opportunities for interdisciplinary student training in marine geochemistry and proteomics, and address the goal of disseminating results and tools to a broad audience. In the more traditional role, the project will expand the career for a female research faculty member in marine proteomics and support both graduate and undergraduate student research at each participating institution. On the broader community level, both Harvey and Nunn are also heavily involved in high school outreach programs.</p>
Proteins as Biomarkers
largerWorkCitation
project
eng; USA
biota
oceans
2017-11-13
Multiple locations: Canadian and US Beaufort Sea
0
BCO-DMO catalogue of parameters from Proteomic data of dilution series of bacteria and diatoms using MS.
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/719878.rdf
Name: Repository
Units: unitless
Description: <p>Name of database where data are currently served</p>
http://lod.bco-dmo.org/id/dataset-parameter/719879.rdf
Name: Project
Units: unitless
Description: <p>Unique project identifier for the database where data are currently served</p>
http://lod.bco-dmo.org/id/dataset-parameter/719880.rdf
Name: Project_URL
Units: unitless
Description: <p>Link to project page at the database where data are currently served</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
193
https://datadocs.bco-dmo.org/file/wnnxzVDI00Rzlg/Bacterial_detection_Timmins.csv
Bacterial_detection_Timmins.csv
Primary data file for dataset ID 719080
download
https://osprey.bco-dmo.org/dataset/719080/data/download
download
onLine
dataset
<p>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.</p>
<p>Instrument(s):&nbsp;QExactive Thermo Finnegan</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
<p>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.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
QExactive Thermo Finnegan
QExactive Thermo Finnegan
PI Supplied Instrument Name: QExactive Thermo Finnegan Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/