Integrated Single-Cell Mass Spectrometry Imaging and Immunofluorescence Microscopy for Multimodal Characterization of Human Immune Cells

This record contains the data associated with the publication: Integrated Single-Cell Mass Spectrometry Imaging and Immunofluorescence Microscopy for Multimodal Characterization of Human Immune Cells(https://doi.org/10.1021/acs.analchem.6c00381) In this study, we developed a workflow that combines immunocytochemistry with single-cell MALDI-2 mass spectrometry imaging (MSI) to enable multimodal characterization of human immune cells. The workflow was applied to investigate neutrophils isolated from patients with liver cirrhosis and from healthy control donors. This record contains the following .zip files: zip file description single_cell_data.zip .zip file containing single cell data as .csv ms_run_1.zip .zip file containing raw timsTOF fleX mass spectrometry data of mixed control and liver chirrhosis cells from experiment 1 ms_run_2.zip .zip file containing raw timsTOF fleX mass spectrometry data of mixed control and liver chirrhosis cells from experiment 2 ms_run_3.zip .zip file containing raw timsTOF fleX mass spectrometry data of mixed control and liver chirrhosis cells from experiment 3 icc_run_1.zip .zip file containing immunocytochemistry images of experiment 1 as .tif files icc_run_2.zip .zip file containing immunocytochemistry images of experiment 2 as .tif files icc_run_3.zip .zip file containing immunocytochemistry images of experiment 3 as .tif files MSMS.zip .zip file containing all MS/MS spectra as .mgf files bessler_et_al_lipid_annotation .zip file containing raw timsTOF fleX mass spectrometry data of neutrophils used for lipid annotation The single cell data were generated using FISCAS (https://doi.org/10.1021/jasms.4c00279, https://github.com/BioMedMS/FISCAS).Subsequent data processing and analysis were performed as described in the Methods section of the associated publication. The single-cell dataset is organized such that each row represents an individual cell. Columns correspond either to detected m/z features from mass spectrometry imaging or to immunocytochemistry parameters. Each cell is assigned a unique identifier. In addition, cells are annotated according to their experimental condition, indicating whether they originate from a healthy control donor or from stained samples.