Dataset: Single cell mass spectroscopy data collected to investigate metabolomics affected by cell-cell interactions in 2020 and 2021

Final no updates expectedDOI: 10.26008/1912/bco-dmo.890877.1Version 1 (2023-03-01)Dataset Type:experimental

Principal Investigator: Zhibo Yang (University of Oklahoma)

Co-Principal Investigator: Linda Atkinson (University of Oklahoma)

Student: Zongkai Peng (University of Oklahoma)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)


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


Abstract

Single-cell mass spectrometry (SCMS) was integrated with fluorescence microscopy to investigate metabolomics affected by cell-cell interactions in 2020 and 2021. These data were used to create a table in the publication of the results by Chen et al. (2022).

Cell-cell interaction systems: the device utilized for the indirect co-culture system was Corning Transwell inserts (Corning Incorporated Life Science, Tewsbury, MA, USA) in the format of a 6-well plate with a permeable membrane (pore size: 0.4 µm). Gridded glass coverslips (ibidi USA Incorporation, Fitchburg, WI, USA) were used for cell attachment in the direct co-culture system.

The materials used to fabricate the single-probe include dual-bore quartz tubing (O.D. 500 µm, I.D. 127 µm, Friedrich & Dimmock, Inc., Millville, NJ, USA) and fused silica capillary (O.D. 105 µm, I.D. 40 µm, Polymicro Technologies, Phoenix, AZ, USA). The Single-probe was fabricated following our published protocols. Briefly, three major components (i.e., a Nano-ESI emitter, a dual-bore quartz tip, and a fused silica capillary) were integrated to prepare a Single-probe. Dual-bore quartz needles were produced by pulling the dual-bore quartz tubing using a laser micropipette puller (Sutter P-2000, Sutter Instrument, Novato, CA). The nano-ESI emitters were pulled from the fused silica capillaries using a butane micro torch. A Single-probe was fabricated by embedding a fused silica capillary and a nano-ESI emitter into those two channels of a dual-bore quartz needle. The Single-probe was coupled to a Thermo LTQ Orbitrap XL mass spectrometer for SCMS analysis. The sampling solvent (acetonitrile supplemented with 1% formic acid) was used for the SCMS experiment at a flow rate of ~0.05 µl/min.

Instruments
The Thermo LTQ Orbitrap XL mass spectrometer (Thermo Scientific, Waltham, MA, United States) was used. The SCMS experiment parameters included a mass range of m/z 200-1500 for positive ion mode and m/z 50-900 for negative ion mode, mass resolution 60,000, ionization voltage 4.5 kV, 1 microscan, and 100 ms max injection time.


Related Datasets

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Related Publications

Results

Chen, X., Peng, Z., & Yang, Z. (2022). Metabolomics studies of cell–cell interactions using single cell mass spectrometry combined with fluorescence microscopy. Chemical Science, 13(22), 6687–6695. https://doi.org/10.1039/d2sc02298b
Methods

Liu, R., Zhang, G., Sun, M., Pan, X., & Yang, Z. (2019). Integrating a generalized data analysis workflow with the Single-probe mass spectrometry experiment for single cell metabolomics. Analytica Chimica Acta, 1064, 71–79. doi:10.1016/j.aca.2019.03.006
Methods

Pan, N., Rao, W., Kothapalli, N. R., Liu, R., Burgett, A. W. G., & Yang, Z. (2014). The Single-Probe: A Miniaturized Multifunctional Device for Single Cell Mass Spectrometry Analysis. Analytical Chemistry, 86(19), 9376–9380. doi:10.1021/ac5029038
Methods

Pan, N., Rao, W., Standke, S. J., & Yang, Z. (2016). Using Dicationic Ion-Pairing Compounds To Enhance the Single Cell Mass Spectrometry Analysis Using the Single-Probe: A Microscale Sampling and Ionization Device. Analytical Chemistry, 88(13), 6812–6819. doi:10.1021/acs.analchem.6b01284
Methods

Rao, W., Pan, N., & Yang, Z. (2016). Applications of the Single-probe: Mass Spectrometry Imaging and Single Cell Analysis under Ambient Conditions. Journal of Visualized Experiments, (112). doi:10.3791/53911