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

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.