http://lod.bco-dmo.org/id/dataset/875622
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
2022-06-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sample information for metaproteomic samples taken from Station 2 from R/V Knorr KN210-04 in the Western Atlantic Ocean between Uruguay and Barbados from March 2013
2022-06-13
publication
2022-06-13
revision
BCO-DMO Linked Data URI
2022-06-13
creation
http://lod.bco-dmo.org/id/dataset/875622
Mak A. Saito
Woods Hole Oceanographic Institution
principalInvestigator
Matthew R. McIlvin
Woods Hole Oceanographic Institution
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: Saito, M. A., McIlvin, M. R. (2022) Sample information for metaproteomic samples taken from Station 2 from R/V Knorr KN210-04 in the Western Atlantic Ocean between Uruguay and Barbados from March 2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-06-13 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/875622 [access date]
Metaproteomic dataset from DeepDOM Station 2 Dataset Description: <p>The dataset includes total spectral counts for proteins and peptides. Four files and a link to raw data at the domain repository are included:</p>
<p>1) Sample metadata file with station locations, depth, time of collection and sample IDs described by this BCO-DMO page. (original file name:&nbsp;<strong>DeepDOM_sample_metadata_for_OPP.csv)</strong></p>
<p>2) Raw mass spectral data files are available on PRIDE and ProteomeXchange:</p>
<p><strong>ProteomeXchange title: </strong>Microbial Metaproteome from the Western Atlantic Ocean DeepDOM KN210-04 Expedition</p>
<p><strong>ProteomeXchange accession: </strong>PXD034035</p>
<p>&nbsp;<strong>Project Webpage: </strong>http://www.ebi.ac.uk/pride/archive/projects/PXD034035</p>
<p>&nbsp;<strong>FTP Download: </strong>ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/05/PXD034035</p> Methods and Sampling: <p>Samples were collected by McLane Pump and filtered onto GFF and GF75 glass filters and frozen at -80C until analysis.</p>
<p>Filters were extracted using SDS detergent and tube gel purification followed by trypsin digestion alkylation and reduction. Analysis was conducted by 2D active modulation Orbitrap mass spectrometry as described in McIlvin and Saito 2021.</p>
<p>Data was 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.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2019589 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2019589
onGoing
Mak A. Saito
Woods Hole Oceanographic Institution
508-289-2393
266 Woods Hole Rd. MS #51 Watson Lab
Woods Hole
MA
02543
USA
msaito@whoi.edu
pointOfContact
Matthew R. McIlvin
Woods Hole Oceanographic Institution
Watson 222A, Mail Stop: 52
Woods Hole
MA
02543
USA
mmcilvin@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample_id
ms_ms_sample_name
station_id
depth_m
latitude_dd
longitude_dd
date_ISO
time_h_m_s
minimum_filter_size_microns
maximum_filter_size_microns
cruise_id
event_number
ISO_DateTime_UTC
nano-HPLC
Thermo Fusion Orbitrap mass spectrometer
theme
None, User defined
sample identification
station
depth
latitude
longitude
date
time of day
filter_size
Cruise identfier
event
ISO_DateTime_UTC
featureType
BCO-DMO Standard Parameters
High-Performance Liquid Chromatograph
Thermal Ionization Mass Spectrometer
instrument
BCO-DMO Standard Instruments
KN210-04
service
Deployment Activity
Western Atlantic Ocean between Uruguay and Barbados
place
Locations
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.
Ocean Carbon and Biogeochemistry
http://us-ocb.org/
Ocean Carbon and Biogeochemistry
The Ocean Carbon and Biogeochemistry (OCB) program focuses on the ocean's role as a component of the global Earth system, bringing together research in geochemistry, ocean physics, and ecology that inform on and advance our understanding of ocean biogeochemistry. The overall program goals are to promote, plan, and coordinate collaborative, multidisciplinary research opportunities within the U.S. research community and with international partners. Important OCB-related activities currently include: the Ocean Carbon and Climate Change (OCCC) and the North American Carbon Program (NACP); U.S. contributions to IMBER, SOLAS, CARBOOCEAN; and numerous U.S. single-investigator and medium-size research projects funded by U.S. federal agencies including NASA, NOAA, and NSF.
The scientific mission of OCB is to study the evolving role of the ocean in the global carbon cycle, in the face of environmental variability and change through studies of marine biogeochemical cycles and associated ecosystems.
The overarching OCB science themes include improved understanding and prediction of: 1) oceanic uptake and release of atmospheric CO2 and other greenhouse gases and 2) environmental sensitivities of biogeochemical cycles, marine ecosystems, and interactions between the two.
The OCB Research Priorities (updated January 2012) include: ocean acidification; terrestrial/coastal carbon fluxes and exchanges; climate sensitivities of and change in ecosystem structure and associated impacts on biogeochemical cycles; mesopelagic ecological and biogeochemical interactions; benthic-pelagic feedbacks on biogeochemical cycles; ocean carbon uptake and storage; and expanding low-oxygen conditions in the coastal and open oceans.
OCB
largerWorkCitation
program
Center for Chemical Currencies of a Microbial Planet
https://ccomp-stc.org/
Center for Chemical Currencies of a Microbial Planet
Functions carried out by microscopic inhabitants of the surface ocean affect every aspect of life on our planet, regardless of distance from the coast. Ocean phytoplankton are responsible for half of the photosynthesis on Earth, the first step in a complex system that annually withdraws 50 billion metric tons of carbon from the atmosphere to sustain their growth. Of this, 25 billion metric tons participate in a rapid cycle in which biologically reactive material is released into seawater and converted back into carbon dioxide by marine bacteria within hours to days. The chemical-microbe network at the heart of this fast cycle remains poorly constrained; consequently, its primary currencies and controls remain elusive; its sensitivities to changing ocean conditions are unknown; and its responses to future climate scenarios are not predictable. The Center for Chemical Currencies of a Microbial Planet (C-CoMP) integrates research, education and knowledge transfer activities to develop a mechanistic understanding of surface ocean carbon flux within the context of a changing ocean and through increased participation in ocean sciences. C-CoMP supports science teams that merge biology, chemistry, modeling, and informatics to close long-standing knowledge gaps in the identities and dynamics of organic molecules that serve as the currencies of elemental transfer between the ocean and atmosphere. C-CoMP fosters education, outreach, and knowledge transfer activities that engage students of all ages, broaden participation in the next generation of ocean scientists, and extend novel open-science approaches into complementary academic and industrial communities. The Center framework is critical to this mission, uniquely facilitating an open exchange of experimental and computational science, methodological and conceptual challenges, and collaborations that establish integrated science and education partnerships. With expanded participation in ocean science research and ocean literacy across the US society, the next generation of ocean scientists will better reflect the diverse US population.
Climate-carbon feedbacks on the marine carbon reservoir are major uncertainties for future climate projections, and the trajectory and rate of ocean changes depend directly on microbial responses to temperature increases, ocean acidification, and other perturbations driven by climate change. C-CoMP research closes an urgent knowledge gap in the mechanisms driving carbon flow between ocean and atmosphere, with global implications for predictive climate models. The Center supports interdisciplinary science teams following open and reproducible science practices to address: (1) the chemical currencies of surface ocean carbon flux; (2) the structure and regulation of the chemical-microbe network that mediates this flux; and (3) sensitivity of the network and its feedbacks on climate. C-CoMP leverages emerging tools and technologies to tackle critical challenges in these themes, in synergy with existing ocean programs and consistent with NSF’s Big Ideas. C-CoMP education and outreach activities seek to overcome barriers to ocean literacy and diversify participation in ocean research. The Center is developing (1) initiatives to expand ocean literacy in K-12 and the broader public, (2) ocean sciences undergraduate curricula and research opportunities that provide multiple entry points into research experiences, (3) post-baccalaureate programs to transition undergraduates into graduate education and careers in ocean science, and (4) interdisciplinary graduate student and postdoctoral programs that prepare the next generation of ocean scientists. The C-CoMP team includes education faculty who evaluate the impacts of education and outreach activities and export successful STEM initiatives to the education community. C-CoMP is revolutionizing the technologies for studying chemical transformations in microbial systems to build understanding of the outsized impact of microbes on elemental cycles. Open science, cross-disciplinary collaborations, community engagement, and inclusive practices foster strategic advances in critical science problems and STEM initiatives. C-CoMP science, education, and knowledge-transfer themes are efficiently addressed through a sustained network of scientists addressing critical research challenges while broadening the workforce that will tackle multi-disciplinary problems with academic, industrial and policy partners.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
The Program's Data Management Plan (DMP) is available as a PDF document.
C-CoMP
largerWorkCitation
program
Center for Chemical Currencies of a Microbial Planet
https://ccomp-stc.org/
Center for Chemical Currencies of a Microbial Planet
Functions carried out by microscopic inhabitants of the surface ocean affect every aspect of life on our planet, regardless of distance from the coast. Ocean phytoplankton are responsible for half of the photosynthesis on Earth, the first step in a complex system that annually withdraws 50 billion metric tons of carbon from the atmosphere to sustain their growth. Of this, 25 billion metric tons participate in a rapid cycle in which biologically reactive material is released into seawater and converted back into carbon dioxide by marine bacteria within hours to days. The chemical-microbe network at the heart of this fast cycle remains poorly constrained; consequently, its primary currencies and controls remain elusive; its sensitivities to changing ocean conditions are unknown; and its responses to future climate scenarios are not predictable. The Center for Chemical Currencies of a Microbial Planet (C-CoMP) integrates research, education and knowledge transfer activities to develop a mechanistic understanding of surface ocean carbon flux within the context of a changing ocean and through increased participation in ocean sciences. C-CoMP supports science teams that merge biology, chemistry, modeling, and informatics to close long-standing knowledge gaps in the identities and dynamics of organic molecules that serve as the currencies of elemental transfer between the ocean and atmosphere. C-CoMP fosters education, outreach, and knowledge transfer activities that engage students of all ages, broaden participation in the next generation of ocean scientists, and extend novel open-science approaches into complementary academic and industrial communities. The Center framework is critical to this mission, uniquely facilitating an open exchange of experimental and computational science, methodological and conceptual challenges, and collaborations that establish integrated science and education partnerships. With expanded participation in ocean science research and ocean literacy across the US society, the next generation of ocean scientists will better reflect the diverse US population.
Climate-carbon feedbacks on the marine carbon reservoir are major uncertainties for future climate projections, and the trajectory and rate of ocean changes depend directly on microbial responses to temperature increases, ocean acidification, and other perturbations driven by climate change. C-CoMP research closes an urgent knowledge gap in the mechanisms driving carbon flow between ocean and atmosphere, with global implications for predictive climate models. The Center supports interdisciplinary science teams following open and reproducible science practices to address: (1) the chemical currencies of surface ocean carbon flux; (2) the structure and regulation of the chemical-microbe network that mediates this flux; and (3) sensitivity of the network and its feedbacks on climate. C-CoMP leverages emerging tools and technologies to tackle critical challenges in these themes, in synergy with existing ocean programs and consistent with NSF’s Big Ideas. C-CoMP education and outreach activities seek to overcome barriers to ocean literacy and diversify participation in ocean research. The Center is developing (1) initiatives to expand ocean literacy in K-12 and the broader public, (2) ocean sciences undergraduate curricula and research opportunities that provide multiple entry points into research experiences, (3) post-baccalaureate programs to transition undergraduates into graduate education and careers in ocean science, and (4) interdisciplinary graduate student and postdoctoral programs that prepare the next generation of ocean scientists. The C-CoMP team includes education faculty who evaluate the impacts of education and outreach activities and export successful STEM initiatives to the education community. C-CoMP is revolutionizing the technologies for studying chemical transformations in microbial systems to build understanding of the outsized impact of microbes on elemental cycles. Open science, cross-disciplinary collaborations, community engagement, and inclusive practices foster strategic advances in critical science problems and STEM initiatives. C-CoMP science, education, and knowledge-transfer themes are efficiently addressed through a sustained network of scientists addressing critical research challenges while broadening the workforce that will tackle multi-disciplinary problems with academic, industrial and policy partners.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
The Program's Data Management Plan (DMP) is available as a PDF document.
C-CoMP
largerWorkCitation
program
Dissolved Organic Matter Composition in the Deep Atlantic Ocean
https://osprey.bco-dmo.org/project/2204
Dissolved Organic Matter Composition in the Deep Atlantic Ocean
<p>Transformations of dissolved organic matter (DOM) in the deep ocean have profound impacts on the global carbon cycle due to the sequestration of carbon dioxide (CO2) away from the atmosphere. Although research has been conducted on the high molecular weight component of this material, the same cannot be said for low molecular weight DOM because the needed analytical techniques have not been available to determine its composition and reactivity.</p>
<p>In recent years, a research team at Woods Hole Oceanographic Institution has acquired the necessary analytical capability. As such, in this project, they will carry out the first systematic survey of deep ocean DOM in the western Atlantic Ocean to characterize the low molecular weight fraction of DOM in southward flowing North Atlantic Deep Water (NADW), northward flowing Antarctic Bottom Water (AABW), and Antarctic Intermediate Water (AAIW). Using ultrahigh resolution mass spectrometry and multi-stage fragmentation coupled to liquid chromatography, the scientists will determine the spatial variability in the composition of DOM along the flow path of the water masses, as well as assess the source water, transport, and surface processes that contribute to temporal changes in DOM composition. These results will be augmented with structural elucidation and quantitative assays of unique marker compounds for each water mass. Results will provide important insights into the biogeochemical reactions that govern DOM dynamics in the deep ocean.</p>
Deep Atlantic DOM
largerWorkCitation
project
Deep Dissolved Organic Matter Multi-omics Analyses
https://osprey.bco-dmo.org/project/875710
Deep Dissolved Organic Matter Multi-omics Analyses
<p>This project hosts additional dataset contributions to the Dissolved Organic Matter Composition in the Deep Atlantic Ocean Project (BCO-DMO Project 2204) that have been generated by the Center for Chemical Currencies of a Microbial Planet. This project will be focused on integrating data that has been collected using a variety of oceanographic sampling and 'omics techniques, including metabolomics and proteomics. </p>
DeepDom Multi-omics
largerWorkCitation
project
eng; USA
biota
oceans
Western Atlantic Ocean between Uruguay and Barbados
-45
-45
-38
-38
2013-03-27
2013-03-29
Western Atlantic Ocean
0
BCO-DMO catalogue of parameters from Sample information for metaproteomic samples taken from Station 2 from R/V Knorr KN210-04 in the Western Atlantic Ocean between Uruguay and Barbados from March 2013
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/891041.rdf
Name: sample_id
Units: unitless
Description: <p>sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/891042.rdf
Name: ms_ms_sample_name
Units: unitless
Description: <p>additional sample identifier that includes date of analysis run, method (2D), total amount of protein injected, cruise name, station number, pump cast number, filter type, and sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/891043.rdf
Name: station_id
Units: unitless
Description: <p>station identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/891044.rdf
Name: depth_m
Units: meters
Description: <p>Sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/891045.rdf
Name: latitude_dd
Units: decimal degrees
Description: <p>latitude of sampling location with positive values indicating North</p>
http://lod.bco-dmo.org/id/dataset-parameter/891046.rdf
Name: longitude_dd
Units: decimal degrees
Description: <p>longitude of sampling location with positive values indicating West</p>
http://lod.bco-dmo.org/id/dataset-parameter/891048.rdf
Name: date_ISO
Units: unitless
Description: <p>date of sample collection in ISO format</p>
http://lod.bco-dmo.org/id/dataset-parameter/891049.rdf
Name: time_h_m_s
Units: unitless
Description: <p>time of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/891050.rdf
Name: minimum_filter_size_microns
Units: microns
Description: <p>minimum filter sized used reported in microns</p>
http://lod.bco-dmo.org/id/dataset-parameter/891051.rdf
Name: maximum_filter_size_microns
Units: microns
Description: <p>maximum filter sized used reported in microns</p>
http://lod.bco-dmo.org/id/dataset-parameter/891052.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/891053.rdf
Name: event_number
Units: unitless
Description: <p>event identification number which includes sampling date in year-month-day format. This ID corresponds to the DeepDOM event log 'event' parameter. </p>
http://lod.bco-dmo.org/id/dataset-parameter/906502.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p> ISO standardized time and date of sampling.</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
2894
https://datadocs.bco-dmo.org/file/8XAyqRnUXokw2Z/deepdom_sample_metadata_for_opp.csv
deepdom_sample_metadata_for_opp.csv
Primary data file for dataset ID 875622.
download
https://osprey.bco-dmo.org/dataset/875622/data/download
download
onLine
dataset
<p>Samples were collected by McLane Pump and filtered onto GFF and GF75 glass filters and frozen at -80C until analysis.</p>
<p>Filters were extracted using SDS detergent and tube gel purification followed by trypsin digestion alkylation and reduction. Analysis was conducted by 2D active modulation Orbitrap mass spectrometry as described in McIlvin and Saito 2021.</p>
<p>Data was 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.</p>
Specified by the Principal Investigator(s)
<p>The raw mass spectra files were searched against 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. Protein and Peptide reports as well as discovered proteins fasta files will be generated. The files will be modified slightly to map to the Ocean Protein Portal data model for submission to BCO-DMO.</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
nano-HPLC
nano-HPLC
PI Supplied Instrument Name: nano-HPLC PI Supplied Instrument Description:Nano-HPLC configured with 2D active modulation chromatography. Instrument Name: High-Performance Liquid Chromatograph Instrument Short Name:HPLC Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/
Thermo Fusion Orbitrap mass spectrometer
Thermo Fusion Orbitrap mass spectrometer
PI Supplied Instrument Name: Thermo Fusion Orbitrap mass spectrometer PI Supplied Instrument Description:Thermo Fusion Orbitrap mass spectrometer interfaced with a Dionex nano-HPLC configured with 2D active modulation chromatography. Instrument Name: Thermal Ionization Mass Spectrometer Instrument Short Name:TI Mass Spec Instrument Description: A Thermal Ionization Mass Spectrometer (TIMS) is an instrument that measures isotopic ratios after electrical excitation of a sample causes ionization of the isotopes. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Cruise: KN210-04
KN210-04
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel
KN210-04
Elizabeth Kujawinski
Woods Hole Oceanographic Institution
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel