http://lod.bco-dmo.org/id/dataset/719129
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)
Metaproteomics of Bering Strait Ship-board 10 day bacterial Incubations.
2017-11-13
publication
2017-11-13
revision
BCO-DMO Linked Data URI
2017-11-13
creation
http://lod.bco-dmo.org/id/dataset/719129
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) Metaproteomics of Bering Strait Ship-board 10 day bacterial Incubations. 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/719129 [access date]
Dataset Description: <pre>
Data are available for download at the EBI PRIDE Archive.
Homepage: <a href="http://www.ebi.ac.uk/pride/archive" target="_blank">http://www.ebi.ac.uk/pride/archive</a>
Project URL: <a href="http://www.ebi.ac.uk/pride/archive/projects/PXD006688" target="_blank">http://www.ebi.ac.uk/pride/archive/projects/PXD006688</a>
Data URL: <a href="http://www.ebi.ac.uk/pride/archive/projects/PXD006688/files" target="_blank">http://www.ebi.ac.uk/pride/archive/projects/PXD006688/files</a></pre>
<p>Data are published in&nbsp;Timmins-Schiffman, E., May, D.H., Mikan, M., Riffle, M., Frazar, C., Harvey, H.R., Noble, W.S., Nunn, B.L. (2016) Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns. The ISME Journal. DOI:&nbsp;<a href="https://www.nature.com/articles/ismej2016132" target="_blank">10.1038/ismej.2016.132</a></p> Methods and Sampling: <p>Water samples were collected in August of 2013 using a 24 bottle (10 L General Oceanics Niskin X) rosette equipped with CTD sensors; 160 liters of water were collected from the Bering Strait (BSt) chlorophyll maximum layer (7 m depth; 65° 43.44”N, 168° 57.42”W). The integrated initial <em>Chl a</em> measurement was 226.88 mg/m<sup>2</sup>, temperature was 2.06°C and salinity was 32.15.</p>
<p>Water was prefiltered to remove all eukaryotic grazers and particles by sequential filtration: 10.0 µm followed by a 1.0 µm polycarbonate (PC) filter. For the generation of a site/time-specific metagenome, seven 1-L aliquots of 1.0 µm prefiltered water was filtered onto 0.2 µm PC filters for a total of 7 filters.&nbsp; Metaproteomics samples of free-living ocean microbes were collected on 0.2 µm Nuclepore Track-Etch membrane PC filters (Whatman, Maidstone, UK) from shipboard incubations at 0 ºC in the dark over 10 days (T0 = day 0, T10 = day 10). The 10-day incubation was designed to follow the changes in community composition and metabolism with and without an exogenous source of carbon. Upon collection, all filters were immediately frozen in liquid nitrogen and stored at -80 ºC. In the full experiment, multiple parameters (in addition to proteomics) were measured at several time points over the 10-day incubation (manuscript in prep.).&nbsp; There are, of course, limitations to measuring community function during an incubation in a closed system, but those limitations will be addressed more fully in the biologically- and ecologically-focused future manuscript.</p>
<p>Filters for the metaproteomics analysis were sliced and submerged in 100 µl of 6 M urea and 600 µl of 50 mM NH<sub>4</sub>HCO<sub>3</sub>. Whole cell lysing was accomplished with a Branson 250 probe sonicator (duty cycle 40%; output control 3) for 20 seconds (Branson Ultrasonics, Danbury, CT). Between sonication events, each filter was flash-frozen in liquid nitrogen to reduce protease activity.&nbsp; Protease inhibitors are avoided because they interfere with downstream digestion and mass spectrometry.&nbsp; This sonication-freezing cycle was repeated five times. Filters were rinsed two times in 100 µl of ultrapure water<sub> </sub>to remove remaining cellular debris from the filter. Protein extraction and desalting followed the protocol outlined in Nunn et al., (2015).</p>
<p>Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was done on a nanoAcquity UPLC (Waters Corp, Milford, MA) connected to a Q-Exactive-HF (Thermo Fisher Scientific, Waltham, MA) on technical duplicates for each sample. A total of 11 mixed microbial samples were analyzed.</p>
<p>Analytical and trapping columns were made and packed in-house. Laser-pulled analytical columns were packed with 3 µm C18 beads (Dr. Maisch HPLC GmBH, Germany) to 15 cm (75 µm ID) and 2 cm trapping columns (100 µm ID) were packed with 3 µm C12 beads (Dr. Maisch) with a Kasil-frit.&nbsp; Peptides were eluted from the column with 5%-30% ACN, 0.1% formic acid in 90 minutes using a 300 nl/min flow rate. The mass spectrometer was operated in Top 20 DDA mode with an MS1 scan range of 400-1000 m/z, 15 second dynamic exclusion, and to increase sensitivity of microbial peptides, 5 trypsin peptide ions were added to the exclusion list (421.7598, 842.5121, 532.2871, and 1045.5664).&nbsp; Mass accuracy and chromatographic retention time were monitored using a quality control standard of 15 peptides (PRTC-BSA, Thermo Fisher Scientific).</p>
<p>Instrument(s):&nbsp;QExactive Thermo Finnegan: DDA data</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
Experiment_ID
Project_URL
nanoAcquity UPLC (Waters Corp, Milford MA) connected to a Q-Exactive-HF (Thermo-Fisher Scientific, Waltham MA)
10 L General Oceanics Niskin X
theme
None, User defined
No BCO-DMO term
project
experiment id
external_link
featureType
BCO-DMO Standard Parameters
CTD - profiler
Mass Spectrometer
Niskin bottle
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
oceans
2017-11-13
Multiple locations: Canadian and US Beaufort Sea
0
BCO-DMO catalogue of parameters from Metaproteomics of Bering Strait Ship-board 10 day bacterial Incubations.
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/719873.rdf
Name: Repository
Units: unitless
Description: <p>Name of database where data are currently served</p>
http://lod.bco-dmo.org/id/dataset-parameter/719874.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/719875.rdf
Name: Experiment_ID
Units: unitless
Description: <p>unknown</p>
http://lod.bco-dmo.org/id/dataset-parameter/719876.rdf
Name: Project_URL
Units: unitless
Description: <p>Link to project page 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
210
https://datadocs.bco-dmo.org/file/N77GgLAT0GZpBm/BeringSt_Incubations_Mikan_Timmins.csv
BeringSt_Incubations_Mikan_Timmins.csv
Primary data file for dataset ID 719129
download
https://osprey.bco-dmo.org/dataset/719129/data/download
download
onLine
dataset
<p>Water samples were collected in August of 2013 using a 24 bottle (10 L General Oceanics Niskin X) rosette equipped with CTD sensors; 160 liters of water were collected from the Bering Strait (BSt) chlorophyll maximum layer (7 m depth; 65° 43.44”N, 168° 57.42”W). The integrated initial <em>Chl a</em> measurement was 226.88 mg/m<sup>2</sup>, temperature was 2.06°C and salinity was 32.15.</p>
<p>Water was prefiltered to remove all eukaryotic grazers and particles by sequential filtration: 10.0 µm followed by a 1.0 µm polycarbonate (PC) filter. For the generation of a site/time-specific metagenome, seven 1-L aliquots of 1.0 µm prefiltered water was filtered onto 0.2 µm PC filters for a total of 7 filters.&nbsp; Metaproteomics samples of free-living ocean microbes were collected on 0.2 µm Nuclepore Track-Etch membrane PC filters (Whatman, Maidstone, UK) from shipboard incubations at 0 ºC in the dark over 10 days (T0 = day 0, T10 = day 10). The 10-day incubation was designed to follow the changes in community composition and metabolism with and without an exogenous source of carbon. Upon collection, all filters were immediately frozen in liquid nitrogen and stored at -80 ºC. In the full experiment, multiple parameters (in addition to proteomics) were measured at several time points over the 10-day incubation (manuscript in prep.).&nbsp; There are, of course, limitations to measuring community function during an incubation in a closed system, but those limitations will be addressed more fully in the biologically- and ecologically-focused future manuscript.</p>
<p>Filters for the metaproteomics analysis were sliced and submerged in 100 µl of 6 M urea and 600 µl of 50 mM NH<sub>4</sub>HCO<sub>3</sub>. Whole cell lysing was accomplished with a Branson 250 probe sonicator (duty cycle 40%; output control 3) for 20 seconds (Branson Ultrasonics, Danbury, CT). Between sonication events, each filter was flash-frozen in liquid nitrogen to reduce protease activity.&nbsp; Protease inhibitors are avoided because they interfere with downstream digestion and mass spectrometry.&nbsp; This sonication-freezing cycle was repeated five times. Filters were rinsed two times in 100 µl of ultrapure water<sub> </sub>to remove remaining cellular debris from the filter. Protein extraction and desalting followed the protocol outlined in Nunn et al., (2015).</p>
<p>Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was done on a nanoAcquity UPLC (Waters Corp, Milford, MA) connected to a Q-Exactive-HF (Thermo Fisher Scientific, Waltham, MA) on technical duplicates for each sample. A total of 11 mixed microbial samples were analyzed.</p>
<p>Analytical and trapping columns were made and packed in-house. Laser-pulled analytical columns were packed with 3 µm C18 beads (Dr. Maisch HPLC GmBH, Germany) to 15 cm (75 µm ID) and 2 cm trapping columns (100 µm ID) were packed with 3 µm C12 beads (Dr. Maisch) with a Kasil-frit.&nbsp; Peptides were eluted from the column with 5%-30% ACN, 0.1% formic acid in 90 minutes using a 300 nl/min flow rate. The mass spectrometer was operated in Top 20 DDA mode with an MS1 scan range of 400-1000 m/z, 15 second dynamic exclusion, and to increase sensitivity of microbial peptides, 5 trypsin peptide ions were added to the exclusion list (421.7598, 842.5121, 532.2871, and 1045.5664).&nbsp; Mass accuracy and chromatographic retention time were monitored using a quality control standard of 15 peptides (PRTC-BSA, Thermo Fisher Scientific).</p>
<p>Instrument(s):&nbsp;QExactive Thermo Finnegan: DDA data</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
PI Supplied Instrument Name: Instrument Name: CTD - profiler Instrument Short Name: Instrument Description: The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.
This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
nanoAcquity UPLC (Waters Corp, Milford MA) connected to a Q-Exactive-HF (Thermo-Fisher Scientific, Waltham MA)
nanoAcquity UPLC (Waters Corp, Milford MA) connected to a Q-Exactive-HF (Thermo-Fisher Scientific, Waltham MA)
PI Supplied Instrument Name: nanoAcquity UPLC (Waters Corp, Milford MA) connected to a Q-Exactive-HF (Thermo-Fisher Scientific, Waltham MA) 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/
10 L General Oceanics Niskin X
10 L General Oceanics Niskin X
PI Supplied Instrument Name: 10 L General Oceanics Niskin X Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/