http://lod.bco-dmo.org/id/dataset/719073
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)
Shotgun Proteomics of Pseudonitzschia multiseries Multi stress 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/719073
Brook L. Nunn
University of Washington
principalInvestigator
Philip W. Boyd
University of Tasmania
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., Boyd, P. W. (2017) Shotgun Proteomics of Pseudonitzschia multiseries Multi stress 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/719073 [access date]
Dataset Description: <pre>
Cultures were&nbsp; collected, filtered, and bacterial fractions were lysed, digested and analyzed using proteomic mass spectrometry.
Data are available for download at the EBI PRIDE Archive and at the Chorus Project Archive.
EBI PRIDE
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/PXD006468" target="_blank">http://www.ebi.ac.uk/pride/archive/projects/PXD006468</a>
Data URL: <a href="http://www.ebi.ac.uk/pride/archive/projects/PXD006468/files" target="_blank">http://www.ebi.ac.uk/pride/archive/projects/PXD006468/files</a>
Chorus Project
Data URL: <a href="https://chorusproject.org/anonymous/download/experiment/-896697234228528487" target="_blank">https://chorusproject.org/anonymous/download/experiment/-896697234228528487</a>
</pre>
<p>Data are published in&nbsp;Boyd, P.W., Dillingham, P.W., McGraw, C.M., Armstrong, E.A., Cornwall, C.E., Feng, Y.y., Hurd, C.L., Gault-Ringold, M., Roleda, M.Y., Timmins-Schiffman, E., Nunn, B.L. (2016). Physiological responses of a Southern Ocean diatom to complex future ocean conditions. Nature Climate Change 6, 207-213. DOI:&nbsp;<a href="https://www.nature.com/articles/nclimate2811?WT.feed_name=subjects_marine-biology" target="_blank">10.1038/nclimate2811</a>&nbsp;</p> Methods and Sampling: <p>Bottles were removed from the incubators, and the sampling ports carefully disconnected within the laminar flow hood. The cells were then re-suspended by gently inverting each bottle. Samples for pH were taken after the bottles were returned to the incubator. Sampling for all experimental parameters in each bottle was carried out on day 0, 4 and 9 (all treatments), and then days 11 and 14 for treatments B and D and on day 15 for A and day 17 for A and C. The following protocols were employed at each sampling point. For cell counts 1 ml samples were fixed with 50% glutaraldehyde to a final concentration of 0.5% and stored at 4 °C. Cells were counted with an Olympus CKX 41 inverted microscope using a 0.1 ml nannoplankton chamber (PhycoTech). Protocols for in vivo and in vitro chlorophyll analysis, active fluorescence, and the calculation of chlorophyll-based cell growth rates followed those in refs 56, 57. Cellular particulate C and N were analysed in a Thermo Flash 2000 CHN Elemental Analyser. Particulate P and biogenic Si were analysed following procedures in ref. 60 and ref. 61, respectively, and converted to cellular elemental composition based on cell counts. The low cell abundances in treatment C resulted in some assays being close to the limits of detection and in some cases being lower than the blanks. No subsamples were taken for dissolved iron analysis during the experiment, but confirmation of no trace-metal contamination of the treatments was obtained indirectly by monitoring several physiological metrics—such as C/chlorophyll, growth rate or cellular silica (see Supplementary Table 4)—that are sensitive to iron supply.</p>
<p>Data-dependent tandem mass spectrometry was carried out on a Thermo Scientific Q-Exactive tandem mass spectrometer following protocols detailed in (Poulson-Ellestad, K. L.&nbsp;<em>et al</em>.&nbsp;Metabolomics and proteomics reveal impacts of chemically mediated competition on plankton.&nbsp;<em>Proc. Natl Acad. Sci. USA</em>&nbsp;<strong>111</strong>,&nbsp;9009–9014&nbsp;(2014).</p>
<p>Cells were pelleted (10,000 × g; 10 min) on ice and lysed using a titanium microtip sonicating probe. Each sample received 10 sonication events (10–15 s each) in 0.2% sodium 3-(4-(1,1-bis(hexyloxy)ethyl)pyridinium-1-yl) propane-1-sulfonate (PPS silent surfactant; Agilent Technologies)&nbsp; in 50 mM ammonium bicarbonate. The details of the digestion were per the manufacturer’s guidelines. Disulfide bonds were reduced with DTT and alkylated with iodoacetamide. Each sample received trypsin at an enzyme-to-protein ratio of 1:50, were vortexed, and were incubated on a Thermomixer for 4 h at 37 °C. Peptide concentrations were measured for each sample using a Thermo Scientific NanoDrop 2000/2000c spectrophotometer. The peptide bond absorbance was monitored at 205 nm, and samples were diluted to yield a final concentration of 100 μg protein·mL−1 . Mass Spectrometry-Based Proteomics. Samples were separated and introduced into the Thermo Scientific Q-Exactive tandem mass spectrometer by reversed-phase chromatography using a 30-cm-long, 75-μm-i.d. fused silica capillary column packed with C18 silica particles (Magic C18AQ, 100 Å, 5 μ; Michrom, Bioresources) fitted with a 2-cm-long, 100-μm-i.d. precolumn (Magic C18AQ, 200 Å, 5 μ; Michrom) . Peptides were eluted using an acidified [formic acid, 0.1% (vol/vol)] water/acetonitrile gradient (2–35% acetonitrile over 90 min). Mass spectrometry was performed on a Thermo Fisher QExactive (QE). Based on peptide concentrations, a total of 1 μg of peptide digest in 10 μL of 2% acetonitrile, 0.1% formic acid was sampled per LC/MS analysis.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1233589 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1233589
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
Philip W. Boyd
University of Tasmania
NIWA Centre for Chemical and Physical OceanographyDepartment of Chemistry PO Box 56
Dunedin
9003
New Zealand
Pboyd@chemistry.otago.ac.nz
pointOfContact
asNeeded
Unknown
Repository
Project
URL
Thermo Flash 2000 CHN Elemental Analyser
Olympus CKX 41 inverted microscope
Thermo Scientific Q-Exactive tandem mass spectrometer
theme
None, User defined
No BCO-DMO term
project
external_link
featureType
BCO-DMO Standard Parameters
Elemental Analyzer
Inverted Microscope
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: Linking geochemistry and proteomics to reveal the impact of bacteria on protein cycling in the ocean
https://osprey.bco-dmo.org/project/675324
Collaborative Research: Linking geochemistry and proteomics to reveal the impact of bacteria on protein cycling in the ocean
<p><em>Text from NSF</em><em> award abstract:</em></p>
<p>Although proteins represent the primary source of new organic nitrogen in the ocean, the identification of individual proteins and mechanisms modulating their preservation has faced analytical and computational challenges in deciphering the vast suite of possible sequences and degradation by-products. Recent efforts to link geochemical cycling, biomedical proteomics and bioinformatics has demonstrated that only a small subset of the suite of proteins produced by marine diatoms appear to survive the degradation process, and those that do are largely protected by physical and enthalpic barriers to microbial attack. Although these discoveries help to explain the survival of individual proteins, they also generate multiple questions regarding bacteria as the dominant recyclers of organic nitrogen and carbon and needs for specific approaches to characterize modified protein products. Bacteria dominate the water column and sedimentary systems in both numbers and diversity, yet their relative contribution to the preserved proteomic pool appears low.</p>
<p>In this project, researchers at Old Dominion Universityand the University of Washington will join forces to decipher the bacterial role in protein recycling and their potential contribution. By integrating high mass accuracy tandem mass spectrometry-based proteomics with stable isotope-based geochemical analysis, they hope to identify those bacterial proteins initially synthesized during organic matter recycling. Three research objectives drive this investigation: (1) to determine the potential contribution of bacteria proteins to marine organic matter; (2) to identify those protein(s) synthesized by heterotrophic marine bacteria during initial stages of organic matter degradation; (3) to determine if glycan (carbohydrate) modifications represent an important component of preserved, yet unidentified, peptides seen in our analysis of oceanic particles and sediments.</p>
<p>Broader Impacts: This project will provide multiple opportunities for interdisciplinary student training in marine chemistry and proteomics as well as address the goal of disseminating results and tools to a broad audience. In the more traditional role, this project will expand the career for a female principal investigator in marine proteomics, support both graduate and undergraduate students at ODU which include opportunities for minority enrichment and provide training for a postdoctoral fellow at UW. On the broader level, the ODU PI participates in high school outreach programs for high achieving students in the local school which provides for summer internships and enrichment programs.</p>
<p><strong>Relevant Links:</strong></p>
<p>Old Dominion University: <a href="http://mogel.cbl.umces.edu/" target="_blank">Marine Organic Geochemistry and Ecology Laboratory (MOGEL) Lab Website</a><br />
Bering Sea Ecosystem Study: <a href="https://www.eol.ucar.edu/projects/best/" target="_blank">Data Archive</a><br />
Environmental Proteomics: <a href="http://www.environmentalproteomics.org/bacterial-degradation-of-proteins.html" target="_blank">Bacteria Recyclers in the Ocean</a><br />
Environmental Proteomics: <a href="http://www.environmentalproteomics.org/proteomics-at-subzero-temperatures.html" target="_blank">Proteomics of Colwellia psychretheca at subzero temperatures </a></p>
Bacterial Recyclers
largerWorkCitation
project
eng; USA
oceans
2017-11-13
0
BCO-DMO catalogue of parameters from Shotgun Proteomics of Pseudonitzschia multiseries Multi stress 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/719800.rdf
Name: Repository
Units: unitless
Description: <p>Name of database where data are currently served</p>
http://lod.bco-dmo.org/id/dataset-parameter/719801.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/719803.rdf
Name: URL
Units: unitless
Description: <p>Link to the data.</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
389
https://datadocs.bco-dmo.org/file/oAAmoVrH8rOVmr/PsNitz_multiseries_PRIDE_boyd.csv
PsNitz_multiseries_PRIDE_boyd.csv
Primary data file for dataset ID 719073
download
https://osprey.bco-dmo.org/dataset/719073/data/download
download
onLine
dataset
<p>Bottles were removed from the incubators, and the sampling ports carefully disconnected within the laminar flow hood. The cells were then re-suspended by gently inverting each bottle. Samples for pH were taken after the bottles were returned to the incubator. Sampling for all experimental parameters in each bottle was carried out on day 0, 4 and 9 (all treatments), and then days 11 and 14 for treatments B and D and on day 15 for A and day 17 for A and C. The following protocols were employed at each sampling point. For cell counts 1 ml samples were fixed with 50% glutaraldehyde to a final concentration of 0.5% and stored at 4 °C. Cells were counted with an Olympus CKX 41 inverted microscope using a 0.1 ml nannoplankton chamber (PhycoTech). Protocols for in vivo and in vitro chlorophyll analysis, active fluorescence, and the calculation of chlorophyll-based cell growth rates followed those in refs 56, 57. Cellular particulate C and N were analysed in a Thermo Flash 2000 CHN Elemental Analyser. Particulate P and biogenic Si were analysed following procedures in ref. 60 and ref. 61, respectively, and converted to cellular elemental composition based on cell counts. The low cell abundances in treatment C resulted in some assays being close to the limits of detection and in some cases being lower than the blanks. No subsamples were taken for dissolved iron analysis during the experiment, but confirmation of no trace-metal contamination of the treatments was obtained indirectly by monitoring several physiological metrics—such as C/chlorophyll, growth rate or cellular silica (see Supplementary Table 4)—that are sensitive to iron supply.</p>
<p>Data-dependent tandem mass spectrometry was carried out on a Thermo Scientific Q-Exactive tandem mass spectrometer following protocols detailed in (Poulson-Ellestad, K. L.&nbsp;<em>et al</em>.&nbsp;Metabolomics and proteomics reveal impacts of chemically mediated competition on plankton.&nbsp;<em>Proc. Natl Acad. Sci. USA</em>&nbsp;<strong>111</strong>,&nbsp;9009–9014&nbsp;(2014).</p>
<p>Cells were pelleted (10,000 × g; 10 min) on ice and lysed using a titanium microtip sonicating probe. Each sample received 10 sonication events (10–15 s each) in 0.2% sodium 3-(4-(1,1-bis(hexyloxy)ethyl)pyridinium-1-yl) propane-1-sulfonate (PPS silent surfactant; Agilent Technologies)&nbsp; in 50 mM ammonium bicarbonate. The details of the digestion were per the manufacturer’s guidelines. Disulfide bonds were reduced with DTT and alkylated with iodoacetamide. Each sample received trypsin at an enzyme-to-protein ratio of 1:50, were vortexed, and were incubated on a Thermomixer for 4 h at 37 °C. Peptide concentrations were measured for each sample using a Thermo Scientific NanoDrop 2000/2000c spectrophotometer. The peptide bond absorbance was monitored at 205 nm, and samples were diluted to yield a final concentration of 100 μg protein·mL−1 . Mass Spectrometry-Based Proteomics. Samples were separated and introduced into the Thermo Scientific Q-Exactive tandem mass spectrometer by reversed-phase chromatography using a 30-cm-long, 75-μm-i.d. fused silica capillary column packed with C18 silica particles (Magic C18AQ, 100 Å, 5 μ; Michrom, Bioresources) fitted with a 2-cm-long, 100-μm-i.d. precolumn (Magic C18AQ, 200 Å, 5 μ; Michrom) . Peptides were eluted using an acidified [formic acid, 0.1% (vol/vol)] water/acetonitrile gradient (2–35% acetonitrile over 90 min). Mass spectrometry was performed on a Thermo Fisher QExactive (QE). Based on peptide concentrations, a total of 1 μg of peptide digest in 10 μL of 2% acetonitrile, 0.1% formic acid was sampled per LC/MS analysis.</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
Thermo Flash 2000 CHN Elemental Analyser
Thermo Flash 2000 CHN Elemental Analyser
PI Supplied Instrument Name: Thermo Flash 2000 CHN Elemental Analyser Instrument Name: Elemental Analyzer Instrument Short Name: Instrument Description: Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/
Olympus CKX 41 inverted microscope
Olympus CKX 41 inverted microscope
PI Supplied Instrument Name: Olympus CKX 41 inverted microscope Instrument Name: Inverted Microscope Instrument Short Name: Instrument Description: An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).
Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.
The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Thermo Scientific Q-Exactive tandem mass spectrometer
Thermo Scientific Q-Exactive tandem mass spectrometer
PI Supplied Instrument Name: Thermo Scientific Q-Exactive tandem mass spectrometer 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/