Dataset: Single cell mass spec Cell-Cell interaction

Name: Single cell mass spectroscopy data collected to investigate metabolomics affected by cell-cell interactions in 2020 and 2021
Published: 2023-03-01
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.890877.1

Temporal Extent: 2020 - 2021

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)

Student:

Zongkai Peng (University of Oklahoma, OU)

BCO-DMO Data Manager:

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

Version:

Version Date:

2023-03-01

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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

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).

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2023-03-01	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.890877.1	2023-03-07

Methods & Sampling

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.

Data Processing Description

Data processing
Single cell data was exported from the mass spec .raw files into Excel Sheets and submitted to BCO-DMO. Each individual table was concatenated into a cohesive table (see BCO-DMO data manager processing notes).

Metabolites data from single cells were searched against three online metabolomics databases (Metlin, HMDB, and GNPS) for tentative labeling. Tandem MS (MS2) analyses were performed for molecular structure verifications.

BCO-DMO Data Manager Processing Notes:
* All Sheets from Excel files "Cell-cell interaction project_neg.xlsx" and "Cell-cell interaction project_pos.xlsx" were exported as a csv file per sheet. These sheets were bundled together with a sheet inventory providing experimental metadata to and made available as a supplemental file "single_cell_csvs.zip."
* Each cell table (csv) was imported into the BCO-DMO data system totaling 199 tables. These were concatenated into a cohesive table with additional columns to for metadata contained in the original excel filename, and sheet name.
* Additional Columns "Ion_mode" "Cell_Line" "Cell_Number" and "Description" were added to the combined data table using a lookup table provided by the data submitter that matched information about each Sheet position in the Excel file and which Cell line and cell number it corresponded to.
* sheet inventory and combined data table were reviewed by the original data submitter to ensure the provided metadata was represented accurately in the published data.

Data Files

File
Cell-cell interactions filename: cell_cell_interactions.csv (Comma Separated Values (.csv), 517.69 MB) MD5:68af5c134857c6a821a7e4c5cc4d218e Cell-cell interaction mass to charge, intensity, and sample metadata. See "Parameters" section for more details of the data columns. This is the main data table for this dataset and combines all single-cell subtables contained in "single_cell_csvs.zip."

Supplemental Files

File

Single-cell csv files (data in alternate format)
filename: single_cell_csvs.zip

(ZIP Archive (ZIP), 28.34 MB)
MD5:350d8dabecbbb24637723d9da4a6de18

This file bundle contains one csv file per cell in the experiment.  These files were concatenated together to form the main data table in this dataset.   This file bundle includes a "sheet_inventory.csv" which provides metadata for each csv file (cell-cell interaction cell line information).

Each csv file contains:
* m.z: This is the m/z (mass/charge) for ions detected in single cell
* Intensity: The intensity of ions at m/z
* Relative: relative intensity normalized by highest peak intensity (100%)

 Each file contains six header lines as output from the instrument-specific file format.  These header lines contain information about where each table was extracted from in the instrument .raw file.

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

Supplied Description:

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

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
Ion_Mode	Ion mode (pos=positive ion mode, neg=negative ion mode)	unitless	sampling_method
Cell_Line	The specific cell line that was used for studying cell-cell interactions in co-culture systems.	unitless	sample_descrip
Cell_Number	Cell number for each Cell_Line and Ion mode.	unitless	sample_descrip
Description	Cell with or without co-culture in cell-cell interaction experiments. (e.g. "Control cell line" or "Cell-cell interaction cell line (with resistance)").	unitless	sample_descrip
Mass_to_Charge	Mass to charge ratio (m/z). This is the m/z for ions detected in single cell	unitless	mass_to_charge
Intensity	The intensity of ions at m/z	unitless	intensity
Relative	relative intensity normalized by highest peak intensity (100%)	unitless	intensity
path_name	Path name of the same data in an alternate format. This path name is the corresponding csv file containing the same m.z,Intensity, Relative data columns within the file bundle "single_cell_csvs.zip" which contains a csv file per cell. See processing notes section for more information.	unitless	file_name

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Database

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Dataset: Single cell mass spec Cell-Cell interaction