http://lod.bco-dmo.org/id/dataset/720684
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
2017-12-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Raw LCMS data files from study of metabolomics of blue crab urine inducing fear in prey
2017-12-19
publication
2017-12-19
revision
BCO-DMO Linked Data URI
2017-12-19
creation
http://lod.bco-dmo.org/id/dataset/720684
Marc Weissburg
Georgia Institute of Technology
principalInvestigator
Julia Kubanek
Georgia Institute of Technology
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: Weissburg, M., Kubanek, J. (2017) Raw LCMS data files from study of metabolomics of blue crab urine inducing fear in prey. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 19 December 2017) Version Date 2017-12-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/720684 [access date]
Raw LCMS data files from study of metabolomics of blue crab urine inducing fear in prey Dataset Description: <p>This dataset includes the following files, packaged in a&nbsp;.zip file:</p>
<ul>
<li>"LCMS negative mode" = contains MS1 negative mode files.</li>
<li>"LCMS positive mode" = contains MS1 positive mode files.</li>
<li>LCMS File Summary.docx =&nbsp;document describing the files.</li>
<li>METADATA_CrabUrine.xlsx = metadata describing the study and the files.</li>
</ul>
<p>MS data files are also publicly available on the NIH Metabolomics Workbench (doi:&nbsp;<a href="http://dx.doi.org/10.21228/M86M4G" target="_blank">10.21228/M86M4G</a>).</p>
<p>The following PNAS paper contains the analyses of the processed data:<br />
Poulin RX, Lavoie S, Siegel K, Gaul D, Weissburg M, Kubanek J (2018) Chemical encoding of risk perception and predator detection among estuarine invertebrates. Proceedings of the National Academy of Sciences. 115:662-667; doi:<a href="http://dx.doi.org/10.1073/pnas.1713901115" target="_blank">10.1073/pnas.1713901115</a></p> Methods and Sampling: <p>MS data were aligned with an adaptive curve and metabolic features (retention time (Rt), m/z pairs) were detected after removal of isotopes and adducts in Compound Discoverer. Background peaks were removed from the dataset using a sample blank. Fill gaps and normalization by constant sum was applied to the data. Select features with a fold change greater or equal to 2 in urine from blue crabs fed mud crabs when compared to urine from blue crabs fed oysters and relative standard deviation of less than 30 were used to build an un-supervised PCA model with leave-one-out cross-validation using MATLAB R2012b (Version 8.0.0.783 The MathWorks, Inc.) and the PLS Toolbox (v.6.71, Eigenvector Research, Inc.). Data were preprocessed by auto-scaling the features’ peak areas across the samples.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1234449 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1234449
completed
Marc Weissburg
Georgia Institute of Technology
404-894-8433
School of Biological Sciences Georgia Institute of Technology
Atlanta
GA
30332-0230
USA
marc.weissburg@biology.gatech.edu
pointOfContact
Julia Kubanek
Georgia Institute of Technology
404-894-8424
School of Biological Sciences Georgia Institute of Technology
Atlanta
GA
30332-0230
USA
julia.kubanek@biosci.gatech.edu
pointOfContact
asNeeded
Dataset Version: 19 December 2017
Unknown
theme
None, User defined
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.
The role of the sensory environment and predator chemical signal properties in determining NCE strength in cascading interactions on oyster reefs
https://osprey.bco-dmo.org/project/565703
The role of the sensory environment and predator chemical signal properties in determining NCE strength in cascading interactions on oyster reefs
<p><em>Extracted from the NSF award abstract:</em></p>
<p>In this project, the investigators will examine the ability of top blue crab predators to indirectly benefit the abundance of basal oyster prey by reducing the density (consumptive effects, CEs) and suppressing foraging (non-consumptive effects, NCEs) of intermediate mud crab predators. These NCEs are mediated by chemical perception of aversive cues in blue crab urine and produce a behaviorally mediated trophic cascade. Through a series of manipulative experiments, the investigators will examine how the strength of this behaviorally-mediated trophic cascade is modulated and factors that influence perceptive range such as predator diet and intake rate, and the flow environment. The investigators will also determine the chemical identity, concentration and release rate of chemical cues.</p>
<p>Identifying the quantitative and molecular aspects of aversive cues, and linking them to behavioral responses that produce trophic cascades establishes the chemical basis of risk perception by prey and how this translates into cascading ecological effects. The use of perceptive range as a framework for evaluating the effects of both chemistry and environment provides an integrated view of processes affecting chemically-mediated NCEs. The use of a water borne predator-prey signaling system to test ideas on the strength of NCEs should have broad applications.</p>
SensoryNCE
largerWorkCitation
project
eng; USA
oceans
2017-12-19
Intertidal and subtidal oyster reefs in Wassaw Sound, Georgia, US
0
BCO-DMO catalogue of parameters from Raw LCMS data files from study of metabolomics of blue crab urine inducing fear in prey
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
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
2152765632
https://datadocs.bco-dmo.org/file/5AoA1r7UZmloKV/Chemical_encoding_of_risk_perception_MS_metabolomics_dataset.zip
Chemical_encoding_of_risk_perception_MS_metabolomics_dataset.zip
LCMS Raw data
download
https://osprey.bco-dmo.org/dataset/720684/data/download
download
onLine
dataset
<p>MS data were aligned with an adaptive curve and metabolic features (retention time (Rt), m/z pairs) were detected after removal of isotopes and adducts in Compound Discoverer. Background peaks were removed from the dataset using a sample blank. Fill gaps and normalization by constant sum was applied to the data. Select features with a fold change greater or equal to 2 in urine from blue crabs fed mud crabs when compared to urine from blue crabs fed oysters and relative standard deviation of less than 30 were used to build an un-supervised PCA model with leave-one-out cross-validation using MATLAB R2012b (Version 8.0.0.783 The MathWorks, Inc.) and the PLS Toolbox (v.6.71, Eigenvector Research, Inc.). Data were preprocessed by auto-scaling the features’ peak areas across the samples.</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
PI Supplied Instrument Name: 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/