Dataset: Single cell mass spec lipid double bonds

Name: Reactive mass spectrometry determination of C=C bonds in unsaturated lipids in single cells from laboratory experiments performed in 2018 and 2019
Published: 2021-05-14
Keywords: Single cell mass spectrometry, chemical reactions of single cells, Paternò–Büchi (PB) reaction, unsaturated lipids, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.851911.1

Temporal Extent: 2018-12 - 2019-06

Project:

Collaborative Research: Creatine Cycling in Marine Bacterial and Phytoplankton Assemblages (Creatine Cycling)

Principal Investigator:

Zhibo Yang (University of Oklahoma, OU)

Co-Principal Investigator:

Linda Atkinson (University of Oklahoma, OU)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2021-05-14

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Reactive mass spectrometry determination of C=C bonds in unsaturated lipids in single cells from laboratory experiments performed in 2018 and 2019

Abstract:

Reactive mass spectrometry determination of C=C bonds in unsaturated lipids in single cells from laboratory experiments performed in 2018 and 2019. These data were used to create Table 1 in the results publication Zhu et al. (2020).

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2021-05-14	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.851911.1	2021-05-17

Methods & Sampling

The following are excerpts from Zhu et al., 2020. Please refer to this publication for more details.

Methodology

Fabrication of the Micropipette Needle. 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, Phoenix, AZ). A syringe was connected to the fused silica capillary via a conductive union (IDEX Health & Science LLC, Oak Harbor, WA).

Sampling device

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, Phoenix, AZ). A syringe was connected to the fused silica capillary via a conductive union (IDEX Health & 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

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).

Instrument

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.

Location of experiments: University of Oklahoma, Norman, OK 73019

Cell line: HCT-116 (human colon cancer cell line)

Reactions: Paternò-Büchi (PB) between unsaturated lipids (contain carbon-carbon double bonds) and acetone or benzophenone

Data Processing Description

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.

Data Files

File
mass_spec_double_bonds.csv (Comma Separated Values (.csv), 1.50 MB) MD5:53b963a7b8d807563b7c5b8b5ce9bf7c Primary data file for dataset ID 851911

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1634630

Deployments

None available yet

Instruments

Mass Spectrometer

Supplied Name: Thermo LTQ Orbitrap XL mass spectrometer (Thermo Scientific, Waltham, MA, United States)

Supplied 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 Type

Generic Name: Mass Spectrometer

Acronym: Mass Spec

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic 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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Cell_Number	Cell Number	unitless	sample_descrip
Ion_Mode	Ion mode (Pos=positive ion mode, Neg=negative ion mode)	unitless	sampling_method
Before_or_After_PB	Description of whether before or after Paternò-Büchi (PB) reaction between unsaturated lipids (contain carbon-carbon double bonds) and acetone or benzophenone	unitless	treatment
Mass_to_Charge	Mass to charge ratio (m/z)	dimensionless	mass_to_charge

Status message

Database

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Dataset: Single cell mass spec lipid double bonds