http://lod.bco-dmo.org/id/dataset/938909
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
2024-09-26
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Raw proteome mass spectrometry data (.mzML files) from pacific herring embryos sampled at Semiahmoo Bay between February and April 2022
2024-11-12
publication
2024-11-12
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-11-12
publication
https://doi.org/10.26008/1912/bco-dmo.938909.1
Brooke Love
Western Washington University
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: Love, B. (2024) Raw proteome mass spectrometry data (.mzML files) from pacific herring embryos sampled at Semiahmoo Bay between February and April 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-11-12 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.938909.1 [access date]
Raw proteome mass spectrometry data (.mzML files) herring embryo's 2022 Dataset Description: Methods and Sampling: <p>Embryos collected with a rake from small boat on 5 dates across three months and kept in a cooler with ambient seawater for 1-5 hours until returned to the lab.&nbsp; 1-5 embryos flash frozen and stored cyogenically for 3-6 months until processing.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2219978 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2219978
completed
Brooke Love
Western Washington University
(360) 650-2894
516 High St. Mail Stop 9181
Bellingham
WA
98225
United States
brooke.love@wwu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Location
Date_Sampling
Latitude
Longitude
Sample_ID
Cohort
Replicate
Mass_Spec_Run_Number
Date_Mass_Spec
Sample_Type
Filename
Lumos Orbitrap
theme
None, User defined
region
date
latitude
longitude
sample identification
sample description
replicate
sample type
file_name
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.
MCA: Utilizing high-throughput proteomics to build a conceptual model of the effects of environmental change on early life stages of genetically diverse herring populations
https://osprey.bco-dmo.org/project/905208
MCA: Utilizing high-throughput proteomics to build a conceptual model of the effects of environmental change on early life stages of genetically diverse herring populations
<p><em>NSF Award Abstract:</em><br />
Pacific Herring represent a critical link in marine food webs along the West Coast of the United States, connecting the plankton they eat with larger predators (fish, sea birds, and marine mammals). Temperature strongly influences the development and success of herring. This investigation targets the underlying pathways that drive their temperature response by examining seasonal differences in protein expression. The outcome will be a better understanding of the processes most influenced by temperature, such as specific metabolic processes or stress responses. The project supports training for the investigator in new proteomics techniques and for undergraduate students at a Primarily Undergraduate Institution. Outreach includes engagement with local stakeholders and coastal indigenous communities. Societal benefits include a better understanding of population differences to inform conservation and recovery efforts for a culturally, economically, and ecologically important species.</p>
<p>Pacific Herring are ecologically important forage fish; fluctuations in their biomass drive far reaching food web responses. Climate variability is suspected to be a major driver of population trends, but the underlying mechanisms driving physiological responses remain unknown. Protein expression is a sensitive indicator of sub-lethal differences in stress response and metabolic state; therefore, comparisons across seasons unveil the cellular processes driving organismal responses to climate factors. Project goals are 1) a deeper understanding of the mechanisms driving the response of a key forage fish species to temperature and 2) workforce development, bringing cutting-edge molecular capabilities to faculty and students at a primarily undergraduate institution. Through a comparison between the robust Semiahmoo Bay (SB) population and the genetically and behaviorally distinct, and much depleted, Cherry Point (CP) herring population, the research team is detecting biomarker molecules of key physiological differences. Investigators are profiling SB and CP embryos collected from January through June using proteomic analyses, then developing targeted assays for peptides of interest, with total lipids and relevant environmental variables (T, Salinity, pH) providing meaningful context. Cohorts of embryos are also being reared to hatch from each collection date for comparison of protein biomarkers associated with survival or morphometric differences in the hatched larvae. This project provides the first large-scale survey of proteins present in early life stage Pacific Herring under different temperature regimes, advancing our understanding of herring response to environmental conditions associated with global change and ocean/atmosphere cycles.</p>
<p>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.</p>
Herring Proteomics
largerWorkCitation
project
eng; USA
oceans
-122.78378231373
-122.78378231373
48.992824917812
48.992824917812
2022-02-02
2022-04-30
Salish Sea - NE Pacific
0
BCO-DMO catalogue of parameters from Raw proteome mass spectrometry data (.mzML files) from pacific herring embryos sampled at Semiahmoo Bay between February and April 2022
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/940434.rdf
Name: Location
Units: unitless
Description: <p>Sampling area: Semiahmoo Bay</p>
http://lod.bco-dmo.org/id/dataset-parameter/940435.rdf
Name: Date_Sampling
Units: unitless
Description: <p>Sampling date</p>
http://lod.bco-dmo.org/id/dataset-parameter/940436.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Approximate sample latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/940437.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Approximate sample longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/940438.rdf
Name: Sample_ID
Units: unitless
Description: <p>Sample ID: cohort + sampling id</p>
http://lod.bco-dmo.org/id/dataset-parameter/940439.rdf
Name: Cohort
Units: unitless
Description: <p>Cohorts of pacific herring embryos: 1 - 5</p>
http://lod.bco-dmo.org/id/dataset-parameter/940440.rdf
Name: Replicate
Units: unitless
Description: <p>Sample replicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/940441.rdf
Name: Mass_Spec_Run_Number
Units: unitless
Description: <p>Mass spectrometry run number</p>
http://lod.bco-dmo.org/id/dataset-parameter/940442.rdf
Name: Date_Mass_Spec
Units: unitless
Description: <p>Date of spectrometry run</p>
http://lod.bco-dmo.org/id/dataset-parameter/940443.rdf
Name: Sample_Type
Units: unitless
Description: <p>Description of single sample vs pool samples.</p>
http://lod.bco-dmo.org/id/dataset-parameter/940444.rdf
Name: Filename
Units: unitless
Description: <p>Filename of .mzml file in supplemental files. File name convention: DateRun_Intrument_project_sampleID_RunNumber</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
5945
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/3f0ab88f-88f1-43d5-9a87-65a3699a6a04/content
download
https://doi.org/10.26008/1912/bco-dmo.938909.1
download
onLine
dataset
<p>Embryos collected with a rake from small boat on 5 dates across three months and kept in a cooler with ambient seawater for 1-5 hours until returned to the lab.&nbsp; 1-5 embryos flash frozen and stored cyogenically for 3-6 months until processing.</p>
Specified by the Principal Investigator(s)
<p>Embryos were physically broken with a micropestle in a microcentriguge tube, then processed 3x 30 seconds with stainless steel beads in a bullet blender.&nbsp; Homogenate was removed from the bead then sonicated 3x. and digested using trypsin and a standard s-trap protocol.&nbsp; Tubes were dried using a speed vap and reconstituted in water/ACN.&nbsp;</p>
<p>Samples were spiked with Pierce retention time standards and with yeast enolase as a standard in some cases.&nbsp; A 90 minute gradient was run on the LC serving the Lumos.&nbsp;</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
Lumos Orbitrap
Lumos Orbitrap
PI Supplied Instrument Name: Lumos Orbitrap 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/