http://lod.bco-dmo.org/id/dataset/783873
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
2019-12-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Diel proteomes of cultured Trichodesmium erythraeum sp. IMS101 from laboratory experiments conducted in November of 2018
2019-12-10
publication
2019-12-10
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-03-25
publication
https://doi.org/10.26008/1912/bco-dmo.783873.1
Mak A. Saito
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. (2020) Diel proteomes of cultured Trichodesmium erythraeum sp. IMS101 from laboratory experiments conducted in November of 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-12-10 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.783873.1 [access date]
Dataset Description: <div>Diel proteomes of cultured&nbsp;<em>Trichodesmium erythraeum</em>&nbsp;sp. IMS101 from laboratory experiments conducted in November of 2018.</div>
<div>&nbsp;</div>
<div>The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD016332 and 10.6019/PXD016332 but are not yet public.</div>
<div>&nbsp;</div>
<div>&nbsp;Project Name: Trichodesmium erythraeum sp. IMS101 Diel proteomes</div>
<div>&nbsp;Project accession: PXD016332</div>
<div>&nbsp;Project DOI: 10.6019/PXD016332</div>
<div>&nbsp;</div>
<div>The format of these data in the BCO-DMO data system is tabular.&nbsp; For a version formatted as a matrix, see the "Data Files" section.</div> Methods and Sampling: <div><span style="font-size:13px">A batch culture (1.5L) of <em>Trichodesmium erythraeum</em> sp. IMS101 was grown in a 27°C incubator with a 14:10 light cycle that ramps up and down mimicking dawn and dusk. Sampling occurred every 1-3 hours with concentrated sampling at dawn and dusk. 70mL of the culture was sterically subsampled and collected on 0.2mm Supor filters, then frozen at -80°C. 10mL was collected and filtered on combusted GFF filters for CHN analysis.</span></div>
<div>&nbsp;</div>
<div><span style="font-size:13px">Proteins were extracted in sodium dodecyl sulfate and digested in gel similar to Saito et al., 2014 (Science). Peptides were analyzed by LC-MS/MS on a Thermo Orbitrap Fusion using LC x LC/MS chromatography with high and low pH reversed phase chromatography.</span></div>
Funding provided by Gordon and Betty Moore Foundation: Marine Microbiology Initiative (MMI) Award Number: GBMF3934
Funding provided by Gordon and Betty Moore Foundation: Marine Microbiology Initiative (MMI) Award Number: GBMF3782 Award URL: https://www.moore.org/grant-detail?grantId=GBMF3782
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
asNeeded
Dataset Version: 1
Unknown
protein_name
hours_post_dawn
cnratio
relative_protein_abundance
Thermo Orbitrap Fusion mass spectrometer
theme
None, User defined
sample description
time_elapsed
Carbon to Nitrogen ratio (C:N)
protein concentration
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.
Marine Microbiology Initiative
https://www.moore.org/initiative-strategy-detail?initiativeId=marine-microbiology-initiative
Marine Microbiology Initiative
A Gordon and Betty Moore Foundation Program.
Forging a new paradigm in marine microbial ecology:
Microbes in the ocean produce half of the oxygen on the planet and remove vast amounts of carbon dioxide, a greenhouse gas, from the atmosphere. Yet, we have known surprisingly little about these microscopic organisms. As we discover answers to some long-standing puzzles about the roles that marine microorganisms play in supporting the ocean’s food webs and driving global elemental cycles, we realized that we still need to learn much more about what these organisms do and how they do it—including how they evolved and contribute to our ocean's health and productivity.
The Marine Microbiology Initiative seeks to gain a comprehensive understanding of marine microbial communities, including their diversity, functions and behaviors; their ecological roles; and their origins and evolution. Our focus has been to enable researchers to uncover the principles that govern the interactions among microbes and that govern microbially mediated nutrient flow in the sea. To address these opportunities, we support leaders in the field through investigator awards, multidisciplinary team research projects, and efforts to create resources of broad use to the research community. We also support development of new instrumentation, tools, technologies and genetic approaches.
Through the efforts of many scientists from around the world, the initiative has been catalyzing new science through advances in methods and technology, and to reduce interdisciplinary barriers slowing progress. With our support, researchers are quantifying nutrient pools in the ocean, deciphering the genetic and biochemical bases of microbial metabolism, and understanding how microbes interact with one another. The initiative has five grant portfolios:
Individual investigator awards for current and emerging leaders in the field.
Multidisciplinary projects that support collaboration across disciplines.
New instrumentation, tools and technology that enable scientists to ask new questions in ways previously not possible.
Community resource efforts that fund the creation and sharing of data and the development of tools, methods and infrastructure of widespread utility.
Projects that advance genetic tools to enable development of experimental model systems in marine microbial ecology.
We also bring together scientists to discuss timely subjects and to facilitate scientific exchange.
Our path to marine microbial ecology was a confluence of new technology that could accelerate science and an opportunity to support a field that was not well funded relative to potential impact. Around the time we began this work in 2004, the life sciences were entering a new era of DNA sequencing and genomics, expanding possibilities for scientific research – including the nascent field of marine microbial ecology. Through conversations with pioneers inside and outside the field, an opportunity was identified: to apply these new sequencing tools to advance knowledge of marine microbial communities and reveal how they support and influence ocean systems.
After many years of success, we will wind down this effort and close the initiative in 2021. We will have invested more than $250 million over 17 years to deepen understanding of the diversity, ecological activities and evolution of marine microbial communities. Thanks to the work of hundreds of scientists and others involved with the initiative, the goals have been achieved and the field has been profoundly enriched; it is now positioned to address new scientific questions using innovative technologies and methods.
MMI
largerWorkCitation
program
New technology for high resolution analysis of proteins and other organic materials produced by marine microorganisms
https://www.moore.org/grant-detail?grantId=GBMF3934
New technology for high resolution analysis of proteins and other organic materials produced by marine microorganisms
<p>In support of acquiring a high resolution mass spectrometer that incorporates the latest technologies for analyzing proteins and other organic materials.</p>
MM Proteins and Organics Tech
largerWorkCitation
project
Marine Microbial Investigator Award: Investigator Mak Saito
https://osprey.bco-dmo.org/project/786672
Marine Microbial Investigator Award: Investigator Mak Saito
<p>In support of obtaining deeper knowledge of major biogeochemically relevant proteins to inform a mechanistic understanding of global marine biogeochemical cycles.</p>
MM Saito
largerWorkCitation
project
eng; USA
oceans
2018-11-01
2018-11-01
0
BCO-DMO catalogue of parameters from Diel proteomes of cultured Trichodesmium erythraeum sp. IMS101 from laboratory experiments conducted in November of 2018
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/786666.rdf
Name: protein_name
Units: unitless
Description: <p>Protein name</p>
http://lod.bco-dmo.org/id/dataset-parameter/786667.rdf
Name: hours_post_dawn
Units: hours
Description: <p>Hours post dawn. Hours after incubator light is on</p>
http://lod.bco-dmo.org/id/dataset-parameter/786668.rdf
Name: cnratio
Units: dimensionless
Description: <p>POC:PON ratio of culture. Ratio of particulate organic carbon to particulate organic nitrogen</p>
http://lod.bco-dmo.org/id/dataset-parameter/786669.rdf
Name: relative_protein_abundance
Units: unitless
Description: <p>Relative protein abundance. Normalized spectral counts.</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
3694943
https://darchive.mblwhoilibrary.org/bitstream/1912/25577/1/dataset-783873_diel-proteomes-trichodesmium-ims101__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.783873.1
download
onLine
dataset
<div><span style="font-size:13px">A batch culture (1.5L) of <em>Trichodesmium erythraeum</em> sp. IMS101 was grown in a 27°C incubator with a 14:10 light cycle that ramps up and down mimicking dawn and dusk. Sampling occurred every 1-3 hours with concentrated sampling at dawn and dusk. 70mL of the culture was sterically subsampled and collected on 0.2mm Supor filters, then frozen at -80°C. 10mL was collected and filtered on combusted GFF filters for CHN analysis.</span></div>
<div>&nbsp;</div>
<div><span style="font-size:13px">Proteins were extracted in sodium dodecyl sulfate and digested in gel similar to Saito et al., 2014 (Science). Peptides were analyzed by LC-MS/MS on a Thermo Orbitrap Fusion using LC x LC/MS chromatography with high and low pH reversed phase chromatography.</span></div>
Specified by the Principal Investigator(s)
<div><span style="font-size:13px">Peptide to spectrum matching was performed in SEQUEST implemented in Proteome Discoverer 2.2 using the <em>Trichodesmium erythraem</em> sp. IMS101 genome. Statistical validation was performed at the 1% protein and peptide FD levels calculated in Scaffold (Proteome Software).</span></div>
<div>&nbsp;</div>
<div><span style="font-size:13px">BCO-DMO Data Manager Processing Notes:</span></div>
<div><span style="font-size:13px">* originally submitted file "dielproteindata.csv" in matrix format added to "Data Files" section.</span></div>
<div><span style="font-size:13px">* a tabular version of dielproteindata.csv was created and imported into the BCO-DMO data system.&nbsp; Data was unpivoted to transform from the matrix into a table with columns for hours_post_dawn,cnratio,relative_protein_abundance.</span></div>
<div><span style="font-size:13px">* added a conventional header with dataset name, PI name, version date</span></div>
<div><span style="font-size:13px">* modified parameter names to conform with BCO-DMO naming conventions (spaces, +, and - changed to underscores).&nbsp; Units in parentheses removed and added to Parameter Description metadata section.</span></div>
<div><span style="font-size:13px">* blank values in this dataset are displayed as "nd" for "no data."&nbsp; nd is the default missing data identifier in the BCO-DMO system</span></div>
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 Orbitrap Fusion mass spectrometer
Thermo Orbitrap Fusion mass spectrometer
PI Supplied Instrument Name: Thermo Orbitrap Fusion 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/