http://lod.bco-dmo.org/id/dataset/739337
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
2018-06-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Spectral data from high pressure liquid chromatography coupled to mass spectrometry from R/V Thomas G. Thompson cruise TN303 in the Eastern Tropical Pacific from October to December 2013
2018-06-27
publication
2018-06-27
revision
BCO-DMO Linked Data URI
2018-06-27
creation
http://lod.bco-dmo.org/id/dataset/739337
Daniel J. Repeta
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
documentDigital
Cite this dataset as: Repeta, D. J. (2018) Spectral data from high pressure liquid chromatography coupled to mass spectrometry from R/V Thomas G. Thompson cruise TN303 in the Eastern Tropical Pacific from October to December 2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-06-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/739337 [access date]
Spectral data from high pressure liquid chromatography coupled to mass spectrometry Dataset Description: <p>The mass spectral datafiles have been deposited at the <a href="https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=69e813d2ab8a4cc48eadf4788596f576" target="_blank">Center for Computational Mass Spectrometry</a>.</p> Methods and Sampling: <p><strong>Sample collection and processing:&nbsp;</strong>Trace-metal clean filtered seawater was pumped by a tow-fish from 3m depth along the cruise track of the US GEOTRACES EPZT (GP16) cruise from October-December 2013 (Boiteau et al. 2016, Table S1). Each sample represents an integrated average signal across a wide region. Between 400-600L of seawater was filtered continuously at a flow rate of 250mL/min and extracted through custom-made solid phase extraction (SPE) columns packed with 20g ENV resin (Bondesil, Agilent). Prior to sample collection, SPE columns were activated with distilled methanol, flushed with ultra-high purity water (qH<sub>2</sub>O), acidified to pH 2 with dilute hydrochloric acid, and finally rinsed with qH<sub>2</sub>O. Samples were stored at -20 degrees C and returned to the laboratory for further analyses. Thawed SPE columns were rinsed with 500mL of qH<sub>2</sub>O, to remove salts and organic ligands were eluted with 250mL of methanol (MeOH). Extracts were concentrated by rotary evaporation and the final volume was adjusted to 6mL with qH<sub>2</sub>O. Samples were stored at -20 degrees C in polytetrafluoroethylene (PTFE) vials. Aliquots (1mL) of each concentrated sample were removed and spiked with 20uL of 50uM cyanocobalamin (Sigma Aldrich) as an internal standard. A sample blank was also collected by pumping only 200mL of filtered seawater through an SPE column, which was frozen, processed, and analyzed with the six seawater samples.</p>
<p><strong>Liquid chromatography:&nbsp;</strong>Organic extracts were separated on an Agilent 1260 series bioinert high pressure liquid chromatography (HPLC) system fitted with a C8 column (Hamilton, 2.1x100mm, 3um particle size) and polyetheretherketone (PEEK) tubing and connectors. Ligands were eluted with (A) 5mM aqueous ammonium formate and (B) 5mM ammonium formate in distilled MeOH using a 50 minute gradient from 10-90% B, followed by isocratic elution at 90% B for 10 minutes at a flow rate of 0.2mL/min. A post column PEEK flow splitter directed 50uL/min into the ICPMS or ESIMS.</p>
<p><strong>Inductively coupled plasma mass spectrometry (ICPMS):&nbsp;</strong>The method for LC-ICPMS analysis was modified from Boiteau<em> </em>et al. (Analytical Chemistry, 2013). &nbsp;The flow of the LC column was coupled directly to a quadrupole ICPMS (iCAP Q, Thermo Scientific) using a perfluoroalkoxy micronebulizer (PFA-ST, Elemental Scientific) and a cyclonic spray chamber cooled to 0 degrees C. Oxygen gas was introduced to the plasma at 25 mL/min to prevent the deposition of reduced organics on the cones. The ICPMS was equipped with platinum sampler and skimmer cones. <sup>56</sup>Fe, <sup>57</sup>Fe, and <sup>59</sup>Co were monitored with an integration time of 0.05 seconds each. Measurements were made in kinetic energy discrimination mode with a He collision gas introduced at a rate of 4.2 mL/min to remove ArO<sup>+</sup> interferences on <sup>56</sup>Fe. Peak areas were integrated and used to calculate concentrations with a six-point calibration curve of a ferrioxamine E standard solution (retention time = 19.8 min). Since only the iron-bound form is quantified by LC-ICPMS, samples were titrated with excess iron citrate and re-analyzed to quantify total siderophore concentrations. A 1:10 addition of the iron citrate stock solution was sufficient to saturate the unbound iron complexes.</p>
<p><strong>Electrospray ionization mass spectrometry (ESIMS) analysis:&nbsp;</strong>For determination of the siderophore mass, the flow from the LC was coupled to an Orbitrap Fusion mass spectrometer (Thermo Scientific) equipped with a heated electrospray ionization source. ESI source parameters were set to a capillary voltage of 3500 V, sheath, auxiliary and sweep gas flow rates of 12, 6, and 2 (arbitrary units), and ion transfer tube and vaporizer temperatures of 300 degrees C and 75 degrees C. MS1 scans were collected in high resolution (450 K) positive mode. High energy collision induced dissociation (HCD) MS2 spectra were collected on the ion trap mass analyzer. Ions were trapped using a quadrupole isolation window of 1 m/z and were then fragmented using an HCD collision energy of 35%. Details of data analysis (41) are provided in the Supporting information.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1356747 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1356747
onGoing
Daniel J. Repeta
Woods Hole Oceanographic Institution
508-289-2635
360 Woods Hole Rd. MS #51 Watson Laboratory
Woods Hole
MA
02543
USA
drepeta@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Thermo-scientific iCap-Q mass spectrometer
Thermo-scientific Orbitrap Fusion masss spectrometer
theme
None, User defined
Mass Spectrometer
Mass Spectrometer
instrument
BCO-DMO Standard Instruments
TN303
service
Deployment Activity
Eastern Tropical Pacific - Transect from Peru to Tahiti
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 Biogeochemistry of Dissolved Iron-ligands in Marine Cyanobacteria and Seawater
http://www.whoi.edu/page.do?pid=130796
The Biogeochemistry of Dissolved Iron-ligands in Marine Cyanobacteria and Seawater
<p>NSF Award Abstract:</p>
<p>Micronutrient trace metals, such as iron and cobalt, are critical to all life on earth, and their availability in the environment can regulate the primary productivity in a region. In the ocean, up to 99.9% of dissolved iron, and to a lesser extent cobalt, are bound by strong organic binding molecules, known as ligands which control what fraction of these metals is available to organisms. To understand carbon and nutrient cycling in many remote areas of the ocean where trace metals limit primary production, it is important to understand the distribution and cycling of ligands. In this study, a researcher at the Woods Hole Oceanographic Institute will use novel techniques to assess the diversity and composition of natural iron and cobalt binding ligands in laboratory cultures of the globally abundant marine cyanobacteria Prochlorococcus and in seawater samples from the South Pacific Subtropical Gyre. This study will add significantly to the interpretation of iron and cobalt availability, and help to link measurements of elemental metal distributions, ligand concentrations and binding strengths, and assessments of the microbial community.</p>
<p>Broader Impacts: Results from the project would be incorporated into graduate level organic geochemistry classes taught by the proponent and be made publically available through the Massachusetts Institute of Technology and Woods Hole Oceanographic Institution websites. One graduate student would be supported and trained as part of this project. It is anticipated that undergraduate students would also have the opportunity to participate in the study during the summer months and learn about organic geochemistry, microbial biogeochemistry, and modeling.</p>
Trace metal ligands
largerWorkCitation
project
eng; USA
oceans
Eastern Tropical Pacific - Transect from Peru to Tahiti
2018-06-27
Equatorial Pacific, Coastal California
0
BCO-DMO catalogue of parameters from Spectral data from high pressure liquid chromatography coupled to mass spectrometry from R/V Thomas G. Thompson cruise TN303 in the Eastern Tropical Pacific from October to December 2013
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
https://osprey.bco-dmo.org/dataset/739337/data/download
download
onLine
dataset
<p><strong>Sample collection and processing:&nbsp;</strong>Trace-metal clean filtered seawater was pumped by a tow-fish from 3m depth along the cruise track of the US GEOTRACES EPZT (GP16) cruise from October-December 2013 (Boiteau et al. 2016, Table S1). Each sample represents an integrated average signal across a wide region. Between 400-600L of seawater was filtered continuously at a flow rate of 250mL/min and extracted through custom-made solid phase extraction (SPE) columns packed with 20g ENV resin (Bondesil, Agilent). Prior to sample collection, SPE columns were activated with distilled methanol, flushed with ultra-high purity water (qH<sub>2</sub>O), acidified to pH 2 with dilute hydrochloric acid, and finally rinsed with qH<sub>2</sub>O. Samples were stored at -20 degrees C and returned to the laboratory for further analyses. Thawed SPE columns were rinsed with 500mL of qH<sub>2</sub>O, to remove salts and organic ligands were eluted with 250mL of methanol (MeOH). Extracts were concentrated by rotary evaporation and the final volume was adjusted to 6mL with qH<sub>2</sub>O. Samples were stored at -20 degrees C in polytetrafluoroethylene (PTFE) vials. Aliquots (1mL) of each concentrated sample were removed and spiked with 20uL of 50uM cyanocobalamin (Sigma Aldrich) as an internal standard. A sample blank was also collected by pumping only 200mL of filtered seawater through an SPE column, which was frozen, processed, and analyzed with the six seawater samples.</p>
<p><strong>Liquid chromatography:&nbsp;</strong>Organic extracts were separated on an Agilent 1260 series bioinert high pressure liquid chromatography (HPLC) system fitted with a C8 column (Hamilton, 2.1x100mm, 3um particle size) and polyetheretherketone (PEEK) tubing and connectors. Ligands were eluted with (A) 5mM aqueous ammonium formate and (B) 5mM ammonium formate in distilled MeOH using a 50 minute gradient from 10-90% B, followed by isocratic elution at 90% B for 10 minutes at a flow rate of 0.2mL/min. A post column PEEK flow splitter directed 50uL/min into the ICPMS or ESIMS.</p>
<p><strong>Inductively coupled plasma mass spectrometry (ICPMS):&nbsp;</strong>The method for LC-ICPMS analysis was modified from Boiteau<em> </em>et al. (Analytical Chemistry, 2013). &nbsp;The flow of the LC column was coupled directly to a quadrupole ICPMS (iCAP Q, Thermo Scientific) using a perfluoroalkoxy micronebulizer (PFA-ST, Elemental Scientific) and a cyclonic spray chamber cooled to 0 degrees C. Oxygen gas was introduced to the plasma at 25 mL/min to prevent the deposition of reduced organics on the cones. The ICPMS was equipped with platinum sampler and skimmer cones. <sup>56</sup>Fe, <sup>57</sup>Fe, and <sup>59</sup>Co were monitored with an integration time of 0.05 seconds each. Measurements were made in kinetic energy discrimination mode with a He collision gas introduced at a rate of 4.2 mL/min to remove ArO<sup>+</sup> interferences on <sup>56</sup>Fe. Peak areas were integrated and used to calculate concentrations with a six-point calibration curve of a ferrioxamine E standard solution (retention time = 19.8 min). Since only the iron-bound form is quantified by LC-ICPMS, samples were titrated with excess iron citrate and re-analyzed to quantify total siderophore concentrations. A 1:10 addition of the iron citrate stock solution was sufficient to saturate the unbound iron complexes.</p>
<p><strong>Electrospray ionization mass spectrometry (ESIMS) analysis:&nbsp;</strong>For determination of the siderophore mass, the flow from the LC was coupled to an Orbitrap Fusion mass spectrometer (Thermo Scientific) equipped with a heated electrospray ionization source. ESI source parameters were set to a capillary voltage of 3500 V, sheath, auxiliary and sweep gas flow rates of 12, 6, and 2 (arbitrary units), and ion transfer tube and vaporizer temperatures of 300 degrees C and 75 degrees C. MS1 scans were collected in high resolution (450 K) positive mode. High energy collision induced dissociation (HCD) MS2 spectra were collected on the ion trap mass analyzer. Ions were trapped using a quadrupole isolation window of 1 m/z and were then fragmented using an HCD collision energy of 35%. Details of data analysis (41) are provided in the Supporting information.</p>
Specified by the Principal Investigator(s)
<p>The in-house algorithms used to process the data are&nbsp;deposited here:&nbsp;<a href="https://github.com/rboiteau/LC-ICPMS-ESIMS-feature-detection" target="_blank">https://github.com/rboiteau/LC-ICPMS-ESIMS-feature-detection</a></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
Thermo-scientific iCap-Q mass spectrometer
Thermo-scientific iCap-Q mass spectrometer
PI Supplied Instrument Name: Thermo-scientific iCap-Q 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/
Thermo-scientific Orbitrap Fusion masss spectrometer
Thermo-scientific Orbitrap Fusion masss spectrometer
PI Supplied Instrument Name: Thermo-scientific Orbitrap Fusion masss 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/
Cruise: TN303
TN303
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN303
James W. Moffett
University of Southern California
http://dmoserv3.whoi.edu/data_docs/GEOTRACES/EPZT/GT13_EPZT_ODFReport_All.pdf
Report describing TN303
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel