http://lod.bco-dmo.org/id/dataset/934718
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
2024-08-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Peptides associated with scaffold-derived metaproteomic proteins from samples taken during R/V Atlantic Explorer cruise AE1913 from the Sargasso Sea to Northeast US shelf waters in June of 2019
2024-08-01
publication
2024-08-01
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-10-29
publication
https://doi.org/10.26008/1912/bco-dmo.934718.1
Mak A. Saito
Woods Hole Oceanographic Institution
principalInvestigator
Natalie Cohen
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., Cohen, N. (2024) Peptides associated with scaffold-derived metaproteomic proteins from samples taken during R/V Atlantic Explorer cruise AE1913 from the Sargasso Sea to Northeast US shelf waters in June of 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-08-01 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.934718.1 [access date]
Dataset Description: <p>Related data table and dataset descriptions:</p>
<p>Total spectral counts refer to the total number of spectra with peptide to spectrum matches (PSMs) that matches to each entry within the FASTA sequence database. This approach allows each peptide to map to multiple closely related sequences. In contrast, with exclusive spectral counts each peptide is only allowed to map to one sequence within the FASTA database, and when a peptide is found in multiple database sequences the one with the most peptides mapping (parsimony) to it is selected. There are pros and cons to each approach, where total spectral counts will double count peptides when two similar proteins are compared, and exclusive spectral counts will underrepresent less abundant proteins with shared peptides, favoring the most homolog with the most shared peptides. Considering protein groups with shared peptides or focusing on peptide-level analyses are alternative approaches that could be constructed from these results.&nbsp;&nbsp;</p>
<p>See "Related Datasets" section for:<br />
*&nbsp; "AE1913 Protein Spectral Counts" which includes the exclusive and total spectral counts associated with proteins.<br />
* "AE1913 Protein Identification FASTA"</p>
<p>CTD and other data from the same cruise are listed on deployment page AE1913: https://www.bco-dmo.org/deployment/916412</p>
<p>These data will become part of the Ocean Protein Portal (https://proteinportal.whoi.edu/; Saito et al., 2020).</p> Methods and Sampling: <p>Methods are reported in Cohen et al. 2023 (biorxiv preprint doi: <a href="http://doi.org/10.1101/2023.11.20.567900" target="_blank">10.1101/2023.11.20.567900</a>) and are summarized below.<br />
* This section describes how this and related datasets were generated (see "Related Datasets" section).</p>
<p>One half of the 142 mm filters (0.2-51 μm) collected by Clio were processed for metaproteomics. Proteins were extracted in an 1% SDS-based detergent in 50 mM HEPES at pH 8.5, reduced with dithiothreitol, alkylated with iodoacetamide, and purified using a polyacrylamide electrophoresis tube gel method. Protein quantification was performed using a BSA assay. Trypsin was added to the protein-bead mixture in a 1:20 trypsin:protein ratio. Peptides were purified using C18 tips and diluted to a concentration of 0.1 μg μL−1.&nbsp;</p>
<p>Approximately 2-5 µg of purified peptides were injected onto a Dionex UltiMate 3000 RSLCnano LC system with an additional RSLCnano pump, run in online 2D active modulation mode interfaced with a Thermo Fusion mass spectrometer. The mass spectrometer acquired MS1 scans from 380 to 1,580 m/z at 240K resolution in the Orbitrap. MS2 were collected in data dependent mode in the ion trap with a cycle time of 2 seconds between scans and acquisition of charge states 2 to 10. MS2 scans had 1.6 m/z isolation window, 50 ms maximum injection time and 5 s dynamic exclusion time.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1658030 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1658030
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
Natalie Cohen
Woods Hole Oceanographic Institution
919-519-8297
10 Ocean Science Circle
Savannah
GA
31411
USA
cohen@uga.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
row_id
protein_id
peptide_sequence
sample_id
spectral_count_sum
cruise_id
station_id
depth_m
minimum_filter_size_microns
maximum_filter_size_microns
date_y_m_d
latitude_dd
longitude_dd
Thermo Fusion mass spectrometer
Dionex UltiMate 3000 RSLCnano LC system
theme
None, User defined
No BCO-DMO term
protein_ID
sequence
sample identification
spectral counts
Cruise identfier
station
depth
filter_size
date
latitude
longitude
featureType
BCO-DMO Standard Parameters
AUV Clio
Mass Spectrometer
Ultra-high-performance liquid chromatography
instrument
BCO-DMO Standard Instruments
AE1913
service
Deployment Activity
St. George's, Bermuda to Woods Hole, MA
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.
Collaborative Research: Direct Characterization of Adaptive Nutrient Stress Responses in the Sargasso Sea using Protein Biomarkers and a Biogeochemical AUV
https://osprey.bco-dmo.org/project/765945
Collaborative Research: Direct Characterization of Adaptive Nutrient Stress Responses in the Sargasso Sea using Protein Biomarkers and a Biogeochemical AUV
<p><em>NSF Award Abstract:</em><br />
Microscopic communities in the ocean can be surprisingly diverse. This diversity makes it difficult to study the individual organisms and reactions that control specific reactions controlling nutrient cycles. Past studies confirm that iron and nitrogen are vital elements for biological growth. There is increasing evidence, however, that other chemicals such as silica, zinc, cobalt, and vitamin B12 may be just as important. This project will provide an unprecedented view of community distributions using new molecular methods to isolate and link active proteins to specific chemical cycles during the very first research deployment of a brand-new autonomous underwater vehicle (AUV). The AUV will collect samples in programed patterns by pumping water directly into its filtering mechanism and then return the samples to the ship for analysis. The Bermuda Atlantic Time-series Study (BATS) station, which provides abundant supporting data, is the site for this innovative investigation into the microbial ecology and chemistry of the open oceans. Additionally, data will be widely distributed to other scientists through the Ocean Protein Portal website being developed by the Woods Hole Oceanographic Institute (WHOI) and the Biological and Chemical Oceanography Data Management Office. Data will also contribute a new teaching module in the Marine Bioinorganic Chemistry course at WHOI.</p>
<p>This first scientific deployment of the newly engineered and constructed biogeochemical AUV, Clio, will generate a novel dataset to examine marine microbial biogeochemical cycles in the Northwestern Atlantic oligotrophic ocean in unprecedented detail and at high vertical resolution. First the project proposes to understand if the microbial community reflects the varying chemical composition and cyanobacterial species through nutrient response adaptations. Additionally, the research will determine if iron stress in the low light Prochlorococcus ecotyope found in the deep chlorophyll maximum is a persistent feature influenced by seasonal dust fluxes. The highly resolved vertical data from the in situ pumping capabilities of Clio are fundamental to a rigorous examination of these biogeochemical questions. This highly transformative dataset will greatly advance understanding of the nutrient and trace element cycling of this region and will be the first field validation of the potentially revolutionary capability these new approaches represent for the study of marine microbial biogeochemistry.</p>
Nutrient Stress Responses and AUV Clio
largerWorkCitation
project
eng; USA
oceans
St. George's, Bermuda to Woods Hole, MA
-70.840703
-64.165587
31.586387
38.527393
2019-06-16
2019-06-27
Bermuda Atlantic Time Series
0
BCO-DMO catalogue of parameters from Peptides associated with scaffold-derived metaproteomic proteins from samples taken during R/V Atlantic Explorer cruise AE1913 from the Sargasso Sea to Northeast US shelf waters in June of 2019
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/941074.rdf
Name: row_id
Units: unitless
Description: <p>sequential row identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/941075.rdf
Name: protein_id
Units: unitless
Description: <p>Identification parameter for protein sequence, typically shared with metagenomic database. An identifier that uniquely identifies this protein within this dataset and the FASTA file.</p>
http://lod.bco-dmo.org/id/dataset-parameter/941076.rdf
Name: peptide_sequence
Units: unitless
Description: <p>Peptide genomic sequence (unique sequence in dataset)</p>
http://lod.bco-dmo.org/id/dataset-parameter/941077.rdf
Name: sample_id
Units: unitless
Description: <p>Identifies the sample associated with this annotation</p>
http://lod.bco-dmo.org/id/dataset-parameter/941078.rdf
Name: spectral_count_sum
Units: unitless
Description: <p>Sum of spectral counts (+2, +3, +4 ions)</p>
http://lod.bco-dmo.org/id/dataset-parameter/941079.rdf
Name: cruise_id
Units: unitless
Description: <p>Cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/941080.rdf
Name: station_id
Units: unitless
Description: <p>Station identifier where sample was taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/941081.rdf
Name: depth_m
Units: meters
Description: <p>The depth in meters at which the sample as taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/941082.rdf
Name: minimum_filter_size_microns
Units: microns (um)
Description: <p>Minimum size of the collection filter</p>
http://lod.bco-dmo.org/id/dataset-parameter/941083.rdf
Name: maximum_filter_size_microns
Units: microns (um)
Description: <p>Maximum size of the collection filter</p>
http://lod.bco-dmo.org/id/dataset-parameter/941084.rdf
Name: date_y_m_d
Units: unitless
Description: <p>The date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/941085.rdf
Name: latitude_dd
Units: decimal degrees
Description: <p>The latitude at the station in decimal degrees (-90 to 90)</p>
http://lod.bco-dmo.org/id/dataset-parameter/941086.rdf
Name: longitude_dd
Units: decimal degrees
Description: <p>The longitude at the station in decimal degrees (-180 to 180)</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
12341217287
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/9fbc18e0-3128-4653-be72-65a59d6406fe/content
download
https://doi.org/10.26008/1912/bco-dmo.934718.1
download
onLine
dataset
<p>Methods are reported in Cohen et al. 2023 (biorxiv preprint doi: <a href="http://doi.org/10.1101/2023.11.20.567900" target="_blank">10.1101/2023.11.20.567900</a>) and are summarized below.<br />
* This section describes how this and related datasets were generated (see "Related Datasets" section).</p>
<p>One half of the 142 mm filters (0.2-51 μm) collected by Clio were processed for metaproteomics. Proteins were extracted in an 1% SDS-based detergent in 50 mM HEPES at pH 8.5, reduced with dithiothreitol, alkylated with iodoacetamide, and purified using a polyacrylamide electrophoresis tube gel method. Protein quantification was performed using a BSA assay. Trypsin was added to the protein-bead mixture in a 1:20 trypsin:protein ratio. Peptides were purified using C18 tips and diluted to a concentration of 0.1 μg μL−1.&nbsp;</p>
<p>Approximately 2-5 µg of purified peptides were injected onto a Dionex UltiMate 3000 RSLCnano LC system with an additional RSLCnano pump, run in online 2D active modulation mode interfaced with a Thermo Fusion mass spectrometer. The mass spectrometer acquired MS1 scans from 380 to 1,580 m/z at 240K resolution in the Orbitrap. MS2 were collected in data dependent mode in the ion trap with a cycle time of 2 seconds between scans and acquisition of charge states 2 to 10. MS2 scans had 1.6 m/z isolation window, 50 ms maximum injection time and 5 s dynamic exclusion time.&nbsp;</p>
Specified by the Principal Investigator(s)
<p>The metatranscriptomic ORFs were used as the protein database, and peptide-spectrum matches were performed using Sequest algorithm within IseNode Proteome Discoverer 2.2.0.388 with a parent ion tolerance of 10 ppm and fragment tolerance of 0.6 Da, and 0 max missed cleavage. Identification criteria consisted of a peptide threshold of 98% (false discovery rate [FDR] = 0.1%) and protein threshold of 99% (1 peptide minimum, FDR = 1.5%) in Scaffold 5.1.2 (Proteome Software) resulting in 77,438 proteins and 3,155,061 exclusive spectral counts.&nbsp;<br />
<br />
"NA" in the spectral_count_sum column represents annotations not available, or no counts detected.</p>
Specified by the Principal Investigator(s)
* Submitted file "opp_peptides.csv" was modified to name the first un-named column with name "row_id". Data were not modified further. Due to table size the data were not imported into the data system and instead was attached to this dataset as a csv a Data File directly named .
** In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values.
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]
* Date converted to ISO 8601 format
* ISO DateTime with timezone (UTC) column added in ISO 8601 format.
* Species names corrected. World Register of Marine Species taxa match tool used to find misspellings and unaccepted names. Name changes reviewed and accepted by the data contributor Species name spelling corrected to the accepted spelling (as of 2018-05-09)
Specified by BCO-DMO Data Managers
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: AUV Clio Instrument Short Name: Instrument Description: Clio is an autonomous underwater vehicle (AUV) created to accomplish the dual goals of global ocean mapping and biochemistry sampling. The ability to sample dissolved and particulate seawater biochemistry across ocean basins while capturing fine-scale biogeochemical processes sets it apart from other AUVs. Clio is designed to efficiently and precisely move vertically through the ocean, drift laterally to observe water masses, and integrate with research vessel operations to map large horizontal scales up to a depth of 6,000 meters. More information is available at https://www2.whoi.edu/site/deepsubmergencelab/clio/
Thermo Fusion mass spectrometer
Thermo Fusion mass spectrometer
PI Supplied Instrument Name: Thermo 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/
Dionex UltiMate 3000 RSLCnano LC system
Dionex UltiMate 3000 RSLCnano LC system
PI Supplied Instrument Name: Dionex UltiMate 3000 RSLCnano LC system Instrument Name: Ultra-high-performance liquid chromatography Instrument Short Name:UHPLC Instrument Description: Ultra high-performance liquid chromatography: Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small (< 2 microm) particles and the inlet pressure is relatively high.
Cruise: AE1913
AE1913
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1913
Mak A. Saito
Woods Hole Oceanographic Institution
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel