http://lod.bco-dmo.org/id/dataset/737596
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
2018-05-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Total spectral counts of peptides from the R/V Falkor cruise 160115 in the Central Pacific for the ProteOMZ expedition in 2016
2022-06-03
publication
2022-06-03
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-11-06
publication
https://doi.org/10.26008/1912/bco-dmo.737596.1
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. A. (2024) Total spectral counts of peptides from the R/V Falkor cruise 160115 in the Central Pacific for the ProteOMZ expedition in 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-06-03 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.737596.1 [access date]
Total spectral counts of peptides from the R/V Falkor cruise 160115 in the Central Pacific for the ProteOMZ expedition in 2016. Dataset Description: <p>These data are part of the Ocean Protein Portal "ProteOMZ" dataset v3 (https://proteinportal.whoi.edu/; Saito et al., 2019).</p> Methods and Sampling:
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
Funding provided by Schmidt Ocean Institute (SOI) Award Number: R/V Falkor 160115 SOI ProteOMZ Expedition
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
sample_id
MS_MS_sample_name
protein_id
protein_molecular_weight_kDa
best_protein_id_probability
peptide_sequence
peptide_start_index
peptide_stop_index
plus2H_spectra_count
plus3H_spectra_count
plus4H_spectra_count
best_sequest_DCn_score
best_sequest_Xcorr_score
median_retention_time
total_precursor_intensity
TIC
spectral_count_sum
other_protein_ids
station_id
depth_m
latitude_dd
longitude_dd
date_ymd
time_hms
minimum_filter_size_microns
maximum_filter_size_microns
cruise_id
ISO_DateTime_UTC
Alpkem Autosampler
SeaBird SBE19 CTD
Technicon AutoAnalyzer II
Trace Metal Rosette
theme
None, User defined
sample identification
No BCO-DMO term
protein_ID
weight
sequence
spectral counts
station
depth
latitude
longitude
date
time of day
filter_size
Cruise identfier
ISO_DateTime_UTC
featureType
BCO-DMO Standard Parameters
Alpkem RFA300
CTD Sea-Bird
Technicon AutoAnalyzer II
Trace Metal Bottle
instrument
BCO-DMO Standard Instruments
FK160115
service
Deployment Activity
Central Pacific
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.
The ProteOMZ Expedition: Investigating Life Without Oxygen in the Pacific Ocean
https://schmidtocean.org/cruise/investigating-life-without-oxygen-in-the-tropical-pacific/#team
The ProteOMZ Expedition: Investigating Life Without Oxygen in the Pacific Ocean
<p>From Schmidt Ocean Institute's ProteOMZ Project page:</p>
<p>Rising temperatures, ocean acidification, and overfishing have now gained widespread notoriety as human-caused phenomena that are changing our seas. In recent years, scientists have increasingly recognized that there is yet another ingredient in that deleterious mix: a process called deoxygenation that results in less oxygen available in our seas.</p>
<p>Large-scale ocean circulation naturally results in low-oxygen areas of the ocean called oxygen deficient zones (ODZs). The cycling of carbon and nutrients – the foundation of marine life, called biogeochemistry – is fundamentally different in ODZs than in oxygen-rich areas. Because researchers think deoxygenation will greatly expand the total area of ODZs over the next 100 years, studying how these areas function now is important in predicting and understanding the oceans of the future. This first expedition of 2016 led by Dr. Mak Saito from the Woods Hole Oceanographic Institution (WHOI) along with scientists from University of Maryland Center for Environmental Science, University of California Santa Cruz, and University of Washington aimed to do just that, investigate ODZs.</p>
<p>During the 28 day voyage named “ProteOMZ,” researchers aboard R/V <em>Falkor </em>traveled from Honolulu, Hawaii to Tahiti to describe the biogeochemical processes that occur within this particular swath of the ocean’s ODZs. By doing so, they contributed to our greater understanding of ODZs, gathered a database of baseline measurements to which future measurements can be compared, and established a new methodology that could be used in future research on these expanding ODZs.</p>
ProteOMZ (Proteomics in an Oxygen Minimum Zone)
largerWorkCitation
project
eng; USA
oceans
Central Pacific
-157.3022
-139.1089
-0.4708
17.4465
2016-01-19
2016-01-28
Central Pacific Ocean (Hawaii to Tahiti)
0
BCO-DMO catalogue of parameters from Total spectral counts of peptides from the R/V Falkor cruise 160115 in the Central Pacific for the ProteOMZ expedition in 2016
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/943158.rdf
Name: sample_id
Units: unitless
Description: <p>Unique sample name for the specific filter collected (station/depth/version if applicable)</p>
http://lod.bco-dmo.org/id/dataset-parameter/943159.rdf
Name: MS_MS_sample_name
Units: unitless
Description: <p>Unique name for the mass spec sample and run</p>
http://lod.bco-dmo.org/id/dataset-parameter/943160.rdf
Name: protein_id
Units: unitless
Description: <p>The specific name of the full protein length sequence assembled in the metagenome that was used for peptide identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/943161.rdf
Name: protein_molecular_weight_kDa
Units: kDa
Description: <p>Molecular weight of the full length protein sequences</p>
http://lod.bco-dmo.org/id/dataset-parameter/943162.rdf
Name: best_protein_id_probability
Units: unitless
Description: <p>Probability of the protein assignment for the peptide</p>
http://lod.bco-dmo.org/id/dataset-parameter/943163.rdf
Name: peptide_sequence
Units: unitless
Description: <p>Amino acid sequence of the identified peptide. Unique Peptide sequence; this is the most unique identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/943164.rdf
Name: peptide_start_index
Units: unitless
Description: <p>Starting amino acid in the full length protein sequence for the identified peptide</p>
http://lod.bco-dmo.org/id/dataset-parameter/943165.rdf
Name: peptide_stop_index
Units: unitless
Description: <p>Stopping amino acid in the full length protein sequence for the identified peptide</p>
http://lod.bco-dmo.org/id/dataset-parameter/943166.rdf
Name: plus2H_spectra_count
Units: count
Description: <p>Number of identified spectral counts for a peptide of the +2 charge state</p>
http://lod.bco-dmo.org/id/dataset-parameter/943167.rdf
Name: plus3H_spectra_count
Units: count
Description: <p>Number of identified spectral counts for a peptide of the +3 charge state</p>
http://lod.bco-dmo.org/id/dataset-parameter/943168.rdf
Name: plus4H_spectra_count
Units: count
Description: <p>Number of identified spectral counts for a peptide of the +4 charge state</p>
http://lod.bco-dmo.org/id/dataset-parameter/943169.rdf
Name: best_sequest_DCn_score
Units: unitless
Description: <p>Delta CN score for peptide spectrum match (PSM). Metric of peptide quality</p>
http://lod.bco-dmo.org/id/dataset-parameter/943170.rdf
Name: best_sequest_Xcorr_score
Units: unitless
Description: <p>XCorr score for peptide spectrum match (PSM). Metric of peptide quality</p>
http://lod.bco-dmo.org/id/dataset-parameter/943171.rdf
Name: median_retention_time
Units: minutes
Description: <p>Median amount of time for a peptide in LC before it was identified via MS/MS</p>
http://lod.bco-dmo.org/id/dataset-parameter/943172.rdf
Name: total_precursor_intensity
Units: unitless
Description: <p>Total precursor intensity.</p>
http://lod.bco-dmo.org/id/dataset-parameter/943173.rdf
Name: TIC
Units: unitless
Description: <p>Total Ion Chromatogram (TIC).</p>
http://lod.bco-dmo.org/id/dataset-parameter/943174.rdf
Name: spectral_count_sum
Units: count
Description: <p>The sum of spectral counts for all peptide proton ionzation states. Sum of +2 +3 +4 data = total unnormalized spectral counts; Quantitative Value</p>
http://lod.bco-dmo.org/id/dataset-parameter/943175.rdf
Name: other_protein_ids
Units: unitless
Description: <p>All other possible proteins in the metagenome that contain the same peptide as the protein assigned. Other protein IDs from the FASTA file (see Related Datasets)</p>
http://lod.bco-dmo.org/id/dataset-parameter/943176.rdf
Name: station_id
Units: unitless
Description: <p>Station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/943177.rdf
Name: depth_m
Units: meters
Description: <p>Depth of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/943178.rdf
Name: latitude_dd
Units: decimal degrees
Description: <p>Latitude of station</p>
http://lod.bco-dmo.org/id/dataset-parameter/943179.rdf
Name: longitude_dd
Units: decimal degrees
Description: <p>Longitude of station</p>
http://lod.bco-dmo.org/id/dataset-parameter/943180.rdf
Name: date_ymd
Units: unitless
Description: <p>Date of sampling; (local time zone HST)</p>
http://lod.bco-dmo.org/id/dataset-parameter/943181.rdf
Name: time_hms
Units: unitless
Description: <p>Time of sampling; (local time zone HST)</p>
http://lod.bco-dmo.org/id/dataset-parameter/943182.rdf
Name: minimum_filter_size_microns
Units: microns
Description: <p>Minimum filter size</p>
http://lod.bco-dmo.org/id/dataset-parameter/943183.rdf
Name: maximum_filter_size_microns
Units: microns
Description: <p>Maximum filter size</p>
http://lod.bco-dmo.org/id/dataset-parameter/943184.rdf
Name: cruise_id
Units: unitless
Description: <p>The unique cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/943185.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>DateTime with timezone (UTC)of sampling in ISO 8601 format</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
813435085
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/d34a4d31-db7f-4009-a700-bf8c26440f65/content
download
https://doi.org/10.26008/1912/bco-dmo.737596.1
download
onLine
dataset
<p>The raw mass spectra files were searched against SEQUEST within Proteome Discoverer v2.2 software. Processed files were then loaded into Proteome Software and protein and peptide reports as well as and fasta files were exported. The files were modified slightly to map to the Protein Portal data model for submission to BCO-DMO. The peptide report was too large to work with within Excel and was modified in Pandas/Python to produce a CSV file.<br />
&nbsp;</p>
Specified by the Principal Investigator(s)
Preprocessing:
-Date, time, filter min, filter max, lat, lon, and cruise columns added based on information from the Falkor 160115 Event log and CTD log.
-Column names reformatted to comply with BCO-DMO standards.
Dataset Version 1: This file version (2022-06-03) replaces a previous revision of dataset version 1 from 2019-02-24.
* Data from source file "ProteOMZ_peptides_for_OPP.csv" was imported into the BCO-DMO data system for this dataset. This file "ProteOMZ_peptides_for_OPP.csv" is from Ocean Protein Portal "ProteOMZ" dataset v3 (file version 2022-06-03)
** 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] e.g. date_y-m-d changed to date_ymd
* ISO DateTime with timezone (UTC) column added in ISO 8601 format from local date and times in HST.
* Data table attached to dataset as Data File:"737596_v1_proteomz-peptides.csv"
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
Alpkem Autosampler
Alpkem Autosampler
PI Supplied Instrument Name: Alpkem Autosampler PI Supplied Instrument Description:Used in nutrient analysis Instrument Name: Alpkem RFA300 Instrument Short Name:Alpkem RFA300 Instrument Description: A rapid flow analyser (RFA) that may be used to measure nutrient concentrations in seawater. It is an air-segmented, continuous flow instrument comprising a sampler, a peristaltic pump which simultaneously pumps samples, reagents and air bubbles through the system, analytical cartridge, heating bath, colorimeter, data station, and printer. The RFA-300 was a precursor to the smaller Alpkem RFA/2 (also RFA II or RFA-2). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0414/
SeaBird SBE19 CTD
SeaBird SBE19 CTD
PI Supplied Instrument Name: SeaBird SBE19 CTD PI Supplied Instrument Description:Used for water sampling Instrument Name: CTD Sea-Bird Instrument Short Name:CTD Sea-Bird Instrument Description: A Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics. This instrument designation is used when specific make and model are not known or when a more specific term is not available in the BCO-DMO vocabulary. Refer to the dataset-specific metadata for more information about the specific CTD used. More information from: http://www.seabird.com/ Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Technicon AutoAnalyzer II
Technicon AutoAnalyzer II
PI Supplied Instrument Name: Technicon AutoAnalyzer II PI Supplied Instrument Description:Used to measure phosphate and ammonium Instrument Name: Technicon AutoAnalyzer II Instrument Short Name: Instrument Description: A rapid flow analyzer that may be used to measure nutrient concentrations in seawater. It is a continuous segmented flow instrument consisting of a sampler, peristaltic pump, analytical cartridge, heating bath, and colorimeter. See more information about this instrument from the manufacturer. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0291/
Trace Metal Rosette
Trace Metal Rosette
PI Supplied Instrument Name: Trace Metal Rosette PI Supplied Instrument Description:Used for nutrient sampling Instrument Name: Trace Metal Bottle Instrument Short Name:TM Bottle Instrument Description: Trace metal (TM) clean rosette bottle used for collecting trace metal clean seawater samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/30/
Cruise: FK160115
FK160115
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
FK160115
Mak A. Saito
Woods Hole Oceanographic Institution
https://service.rvdata.us/data/cruise/FK160115/doc/FK160115_OfficialCruiseReport_Saito_v3.pdf
Report describing FK160115
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel