http://lod.bco-dmo.org/id/dataset/875600
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)
The global proteome of replete laboratory cultures of Ruergeria pomeroyi DSS-3
2022-06-14
publication
2022-06-14
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-06-15
publication
https://doi.org/10.26008/1912/bco-dmo.875600.1
Mak A. Saito
Woods Hole Oceanographic Institution
principalInvestigator
Mary Ann Moran
University of Georgia
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., Moran, M. A. (2022) The global proteome of replete laboratory cultures of Ruergeria pomeroyi DSS-3. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-06-14 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.875600.1 [access date]
Ruergeria pomeroyi DSS-3 replete proteome Dataset Description: Methods and Sampling: <p>Cultures (50 ml each) of <em>Ruergeria pomeroyi </em>DSS-3 and <em>Alteromonas macleodii </em>MIT1002 were harvested in triplicate, centrifuged at 8000 x g for 10 minutes, flash frozen, stored at -80 degrees C, and shipped to Woods Hole Oceanographic Institution for proteomics analysis. Cultures were filtered and filters were extracted using SDS detergent and a SP3 magnetic bead purification followed by trypsin digestion alkylation and reduction. The methods are described in Saito et al. 2020 and were modified from the methods originally published by Hughes et al. 2014. Analysis was conducted by 2D active modulation Orbitrap mass spectrometry as described in McIlvin and Saito 2021.</p>
<p>This dataset reports results for the&nbsp;<em>Ruergeria pomeroyi&nbsp;</em>DSS-3 samples. See related datasets for the&nbsp;<em>Alteromonas macleodii&nbsp;</em>MIT1002 samples.</p>
<p>Note: the sample ids ending in a1, b1, and c1 differentiate biological triplicates from one another.</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
completed
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
Mary Ann Moran
University of Georgia
706-542-6481
Department of Marine Sciences
Athens
GA
30602
USA
mmoran@uga.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
protein_id
protein_name
ncbi_id
molecular_weight_kDa
DSS3_a1_SC
DSS3_b1_SC
DSS3_c1_SC
Dionex nano-HPLC
Thermo Fusion Orbitrap
theme
None, User defined
protein_ID
accession number
molecular weight
spectral counts
featureType
BCO-DMO Standard Parameters
High-Performance Liquid Chromatograph
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.
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
C-CoMP Model Bacteria Physiological Studies
https://osprey.bco-dmo.org/project/875254
C-CoMP Model Bacteria Physiological Studies
<p>The Center for Chemical Currencies of a Microbial Planet (C-CoMP) is focused on understanding how marine microorganisms determine the fate of labile carbon in the surface ocean. To study these chemical-biological dynamics across a variety of scales and in response to changing environmental conditions, the physiology of marine bacteria that drive chemical exchange must be explored in depth using a variety of microbiological, molecular biological, and integrative ’omics (e.g. proteomics, metabolomics, and genomics) methodologies. This project has been created to host data generated via these methods to investigate the physiological mechanisms underpinning the biogeochemical functions of model marine bacteria.</p>
C-CoMP Model Bacteria
largerWorkCitation
project
eng; USA
oceans
2021-03-01
2021-05-01
0
BCO-DMO catalogue of parameters from The global proteome of replete laboratory cultures of Ruergeria pomeroyi DSS-3
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/875687.rdf
Name: protein_id
Units: unitless
Description: <p>A numerical identifier that uniquely identifies this protein within this dataset</p>
http://lod.bco-dmo.org/id/dataset-parameter/875688.rdf
Name: protein_name
Units: unitless
Description: <p>A name identifying this protein</p>
http://lod.bco-dmo.org/id/dataset-parameter/875689.rdf
Name: ncbi_id
Units: unitless
Description: <p>unique ID (typically the NCBI protein accession number) assigned to each protein name</p>
http://lod.bco-dmo.org/id/dataset-parameter/875690.rdf
Name: molecular_weight_kDa
Units: kilo-Daltons
Description: <p>The molecular weight in kilo-Daltons of the protein</p>
http://lod.bco-dmo.org/id/dataset-parameter/875691.rdf
Name: DSS3_a1_SC
Units: unnormalized spectral counts
Description: <p>Exclusive unique spectral counts for proteins in sample DSS3_a1</p>
http://lod.bco-dmo.org/id/dataset-parameter/875692.rdf
Name: DSS3_b1_SC
Units: unnormalized spectral counts
Description: <p>Exclusive unique spectral counts for proteins in sample DSS3_b1</p>
http://lod.bco-dmo.org/id/dataset-parameter/875693.rdf
Name: DSS3_c1_SC
Units: unnormalized spectral counts
Description: <p>Exclusive unique spectral counts for proteins in sample DSS3_c1</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
206071
https://darchive.mblwhoilibrary.org/bitstream/1912/29016/1/dataset-875600_ruergeria-pomeroyi-dss-3-replete-proteome__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.875600.1
download
onLine
dataset
<p>Cultures (50 ml each) of <em>Ruergeria pomeroyi </em>DSS-3 and <em>Alteromonas macleodii </em>MIT1002 were harvested in triplicate, centrifuged at 8000 x g for 10 minutes, flash frozen, stored at -80 degrees C, and shipped to Woods Hole Oceanographic Institution for proteomics analysis. Cultures were filtered and filters were extracted using SDS detergent and a SP3 magnetic bead purification followed by trypsin digestion alkylation and reduction. The methods are described in Saito et al. 2020 and were modified from the methods originally published by Hughes et al. 2014. Analysis was conducted by 2D active modulation Orbitrap mass spectrometry as described in McIlvin and Saito 2021.</p>
<p>This dataset reports results for the&nbsp;<em>Ruergeria pomeroyi&nbsp;</em>DSS-3 samples. See related datasets for the&nbsp;<em>Alteromonas macleodii&nbsp;</em>MIT1002 samples.</p>
<p>Note: the sample ids ending in a1, b1, and c1 differentiate biological triplicates from one another.</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong><br />
The raw mass spectra files were searched against the 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 (0.7% peptide FDR and 0.03% Protein FDR using decoy database). Percolator was used for PSM validation based on PEP scoring. The output was reported as exclusive unique spectral counts. No normalization was applied to this dataset.</p>
<p>Raw data files are currently being submitted to the ProteomeXchange repository through PRIDE under accession number <a href="https://www.ebi.ac.uk/pride/archive/projects/PXD034365" target="_blank">PXD034365</a>. Raw file names are:<em> 220427_CCoMP_AHANA_DSS_3_a1, 220427_CCoMP_AHANA_DSS_3_b1, 220427_CCoMP_AHANA_DSS_3_c1</em>.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- modified parameter names;<br />
- replaced commas with semi-colons in the protein_name column.</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
Dionex nano-HPLC
Dionex nano-HPLC
PI Supplied Instrument Name: Dionex nano-HPLC PI Supplied Instrument Description:Data were 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. 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
Thermo Fusion Orbitrap
PI Supplied Instrument Name: Thermo Fusion Orbitrap PI Supplied Instrument Description:Data were 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. 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/