http://lod.bco-dmo.org/id/dataset/851911
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
2021-05-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Reactive mass spectrometry determination of C=C bonds in unsaturated lipids in single cells from laboratory experiments performed in 2018 and 2019
2021-05-14
publication
2021-05-14
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-05-17
publication
https://doi.org/10.26008/1912/bco-dmo.851911.1
Zhibo Yang
University of Oklahoma
principalInvestigator
Linda Atkinson
University of Oklahoma
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: Yang, Z., Atkinson, L. (2021) Reactive mass spectrometry determination of C=C bonds in unsaturated lipids in single cells from laboratory experiments performed in 2018 and 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-05-14 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.851911.1 [access date]
Methods and Sampling: <p><span style="font-size:13px">The following are excerpts from Zhu et al., 2020. Please refer to this publication for more details.</span></p>
<p>Methodology</p>
<p>Fabrication of the Micropipette Needle. The micropipette needle (tip size ≈ 15 um) was pulled from a glass&nbsp;capillary tube (size: 0.8 × 90 mm2, Kimble Chase Life Science and Research Products, Rockwood, TN) using a pipet puller (KOPF, Tujunga, CA). UV epoxy (Prime-Dent, Chicago, IL) was used to connect the micropipette needle to a fused silica capillary (OD: 150 μm, ID: 75 μm, Polymicro Technologies, Phoenix, AZ). A syringe was connected to the fused silica capillary via a conductive union (IDEX Health &amp; Science LLC, Oak Harbor, WA).<br />
&nbsp;</p>
<p><strong>Sampling device </strong></p>
<p>The Micropipette Needle was produced for sampling. The micropipette needle (tip size ≈ 15 um) was pulled from a glass capillary tube (size: 0.8 × 90 mm2, Kimble Chase Life Science and Research Products, Rockwood, TN) using a pipet puller (KOPF, Tujunga, CA). UV epoxy (Prime-Dent, Chicago, IL) was used to connect the micropipette needle to a fused silica capillary (OD: 150 μm, ID: 75 μm, Polymicro Technologies,&nbsp; Phoenix, AZ). A syringe was connected to the fused silica capillary via a conductive union (IDEX Health &amp; Science LLC, Oak Harbor, WA). Using an Eppendorf cell manipulation system and a syringe pump, a target cell was sucked into the glass micropipette (flow rate 10 μL/min) containing prefilled acetone or benzophenone solution. Additional solution was drawn into the micropipette needle to ensure cell lysis. The syringe pump was turned on to deliver (flow rate 0.2 μL/min) the single cell lysate toward the nano-ESI emitter. Both the regular (no UV irradiation) and the reactive (after UV irradiation) single cell MS experiments can be conducted for the same single cell. Specifically, after accomplishing data acquisition of the regular SCMS experiment, the ionization energy was turned off and the syringe pump was paused. The UV lamp (BHK, Ontario, CA) was then turned on to generate UV radiation and initiate PB reactions between the reagents and unsaturated cellular lipids. After 15 min of reaction, the UV light was turned off, and then</p>
<p>the reactive single cell MS experiment was started by turning on the ionization voltage and resuming the syringe pump. Products from the PB reactions were analyzed using both MS scan (to obtain accurate m/z values of all ions) and tandem MS (MS/MS) analysis (to acquire fragments of selected ions).</p>
<p><strong>Instrument</strong></p>
<p>Thermo LTQ Orbitrap XL mass spectrometer (Thermo Scientific, Waltham, MA, United States). Mass analyze parameters were as follows: mass resolution 60,000, 1 microscan, 100 ms max injection time, and automatic gain control on. A DC ionization voltage (+4 kV in the positive ion mode or −4 kV in the negative ion mode) was applied on a conductive union and transmitted through the solvent to induce ionization of cell lysis at the tip of the micropipette for MS analysis.<br />
<br />
<span style="font-size:13px"><strong>Location of experiments</strong>: University of Oklahoma, Norman, OK 73019</span></p>
<div><span style="font-size:13px"><strong>Cell line:</strong> HCT-116 (human colon cancer cell line)</span></div>
<div><span style="font-size:13px"><strong>Reactions: </strong>Paternò-Büchi (PB) between unsaturated lipids (contain carbon-carbon double bonds) and acetone or benzophenone</span></div>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1634630 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1634630
completed
Zhibo Yang
University of Oklahoma
405-325-1772
101 Stephenson Parkway Department of Chemistry and Biochemistry
Norman
Oklahoma
73019
USA
zhibo.yang@ou.edu
pointOfContact
Linda Atkinson
University of Oklahoma
405-325-1267
K20-Center 3100 Monitor Ave, Suite 200
Norman
OK
73072
United States
latkinson@ou.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cell_Number
Ion_Mode
Before_or_After_PB
Mass_to_Charge
Thermo LTQ Orbitrap XL mass spectrometer (Thermo Scientific, Waltham, MA, United States)
theme
None, User defined
sample description
sampling_method
treatment
mass-to-charge ratio (m/z)
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.
Collaborative Research: Creatine Cycling in Marine Bacterial and Phytoplankton Assemblages
https://osprey.bco-dmo.org/project/709493
Collaborative Research: Creatine Cycling in Marine Bacterial and Phytoplankton Assemblages
<p><em>NSF Award Abstract:</em><br />
High rates of dissolved organic nitrogen (DON) production and utilization in aquatic systems are typically attributed to microbial activity. Though it is known that there is a tight coupling between the production and consumption of biologically available DON, the composition, dynamics, and ecological significance of this rapidly cycled DON pool are less well understood. This proposal focuses on a component of the DON pool, creatine, which is historically understood as a product of metazoan activity, but appears to be both produced by phytoplankton and consumed by marine bacteria. Creatine is present in seawater in measurable quantities, which led to the hypothesis that creatine may be a significant component of the marine DON cycle. DON cycling likely has a bearing on fundamental marine ecosystem processes with large implications for carbon and nitrogen turnover on a global scale. Broader impacts of this project will include outreach that focuses on connecting scientists with K-12 students through research experiences for teachers and lesson development in collaboration with the K20 Center for Educational and Community Renewal, a statewide education research and development center at the University of Oklahoma. The project will integrate the research with inquiry-based teaching of rural secondary science teachers through Authentic Research Experiences in oceanographic science and microbial ecology. The K20 network includes 96% of Oklahoma schools, providing a unique opportunity to impact STEM education in Oklahoma.</p>
<p>The results of this project will help develop a better understanding of DON cycling, the ecological context of creatine uptake activity, and identify both creatine-producing and consuming organisms in the marine environment. The importance of creatine cycling will be assessed via 15N tracer studies along the natural coastal-to-offshore productivity gradient observed in the North Atlantic. Tracer and molecular approaches will be used to investigate the importance of phytoplankton vs. bacteria in creatine uptake and, the taxonomic identities of creatine-utilizing bacteria will be interrogated via molecular, stable isotope probing (SIP), and RT-qPCR approaches.</p>
Creatine Cycling
largerWorkCitation
project
eng; USA
oceans
2018-12-01
2019-06-01
Atlantic bight
0
BCO-DMO catalogue of parameters from Reactive mass spectrometry determination of C=C bonds in unsaturated lipids in single cells from laboratory experiments performed in 2018 and 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/851943.rdf
Name: Cell_Number
Units: unitless
Description: <p>Cell Number</p>
http://lod.bco-dmo.org/id/dataset-parameter/851944.rdf
Name: Ion_Mode
Units: unitless
Description: <p>Ion mode (Pos=positive ion mode, Neg=negative ion mode)</p>
http://lod.bco-dmo.org/id/dataset-parameter/851945.rdf
Name: Before_or_After_PB
Units: unitless
Description: <p>Description of whether before or after Paternò-Büchi (PB) reaction between unsaturated lipids (contain carbon-carbon double bonds) and acetone or benzophenone</p>
http://lod.bco-dmo.org/id/dataset-parameter/851946.rdf
Name: Mass_to_Charge
Units: dimensionless
Description: <p>Mass to charge ratio (m/z)</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
1577883
https://darchive.mblwhoilibrary.org/bitstream/1912/27120/1/dataset-851911_single-cell-mass-spec-lipid-double-bonds__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.851911.1
download
onLine
dataset
<p><span style="font-size:13px">The following are excerpts from Zhu et al., 2020. Please refer to this publication for more details.</span></p>
<p>Methodology</p>
<p>Fabrication of the Micropipette Needle. The micropipette needle (tip size ≈ 15 um) was pulled from a glass&nbsp;capillary tube (size: 0.8 × 90 mm2, Kimble Chase Life Science and Research Products, Rockwood, TN) using a pipet puller (KOPF, Tujunga, CA). UV epoxy (Prime-Dent, Chicago, IL) was used to connect the micropipette needle to a fused silica capillary (OD: 150 μm, ID: 75 μm, Polymicro Technologies, Phoenix, AZ). A syringe was connected to the fused silica capillary via a conductive union (IDEX Health &amp; Science LLC, Oak Harbor, WA).<br />
&nbsp;</p>
<p><strong>Sampling device </strong></p>
<p>The Micropipette Needle was produced for sampling. The micropipette needle (tip size ≈ 15 um) was pulled from a glass capillary tube (size: 0.8 × 90 mm2, Kimble Chase Life Science and Research Products, Rockwood, TN) using a pipet puller (KOPF, Tujunga, CA). UV epoxy (Prime-Dent, Chicago, IL) was used to connect the micropipette needle to a fused silica capillary (OD: 150 μm, ID: 75 μm, Polymicro Technologies,&nbsp; Phoenix, AZ). A syringe was connected to the fused silica capillary via a conductive union (IDEX Health &amp; Science LLC, Oak Harbor, WA). Using an Eppendorf cell manipulation system and a syringe pump, a target cell was sucked into the glass micropipette (flow rate 10 μL/min) containing prefilled acetone or benzophenone solution. Additional solution was drawn into the micropipette needle to ensure cell lysis. The syringe pump was turned on to deliver (flow rate 0.2 μL/min) the single cell lysate toward the nano-ESI emitter. Both the regular (no UV irradiation) and the reactive (after UV irradiation) single cell MS experiments can be conducted for the same single cell. Specifically, after accomplishing data acquisition of the regular SCMS experiment, the ionization energy was turned off and the syringe pump was paused. The UV lamp (BHK, Ontario, CA) was then turned on to generate UV radiation and initiate PB reactions between the reagents and unsaturated cellular lipids. After 15 min of reaction, the UV light was turned off, and then</p>
<p>the reactive single cell MS experiment was started by turning on the ionization voltage and resuming the syringe pump. Products from the PB reactions were analyzed using both MS scan (to obtain accurate m/z values of all ions) and tandem MS (MS/MS) analysis (to acquire fragments of selected ions).</p>
<p><strong>Instrument</strong></p>
<p>Thermo LTQ Orbitrap XL mass spectrometer (Thermo Scientific, Waltham, MA, United States). Mass analyze parameters were as follows: mass resolution 60,000, 1 microscan, 100 ms max injection time, and automatic gain control on. A DC ionization voltage (+4 kV in the positive ion mode or −4 kV in the negative ion mode) was applied on a conductive union and transmitted through the solvent to induce ionization of cell lysis at the tip of the micropipette for MS analysis.<br />
<br />
<span style="font-size:13px"><strong>Location of experiments</strong>: University of Oklahoma, Norman, OK 73019</span></p>
<div><span style="font-size:13px"><strong>Cell line:</strong> HCT-116 (human colon cancer cell line)</span></div>
<div><span style="font-size:13px"><strong>Reactions: </strong>Paternò-Büchi (PB) between unsaturated lipids (contain carbon-carbon double bonds) and acetone or benzophenone</span></div>
Specified by the Principal Investigator(s)
processed using Genna 2 oneline software, unpublished.
BCO-DMO data manager processing notes:
* Loaded Sheet 1 "mz list using Script A" from file "Double bond single cell_BCODMO.xlsx" into the BCO-DMO data system.
* Unpivoted data. Transformed from many mass to charge ratio columns with multiple header rows containing information for Cell number, ion mode, before or after PB reaction into a data table with one column for mass to charge ratio and added columns (Cell_Number,Ion_Mode,Before_or_After_PB).
* metadata included in the data file extracted to metadata.
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 LTQ Orbitrap XL mass spectrometer (Thermo Scientific, Waltham, MA, United States)
Thermo LTQ Orbitrap XL mass spectrometer (Thermo Scientific, Waltham, MA, United States)
PI Supplied Instrument Name: Thermo LTQ Orbitrap XL mass spectrometer (Thermo Scientific, Waltham, MA, United States) PI Supplied Instrument Description:Mass analyze parameters were as follows: mass resolution 60,000, 1 microscan, 100 ms max injection time, and automatic gain control on. A DC ionization voltage (+4 kV in the positive ion mode or −4 kV in the negative ion mode) was applied on a conductive union and transmitted through the solvent to induce ionization of cell lysis at the tip of the micropipette for MS analysis. 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/