msiFlow: Automated Workflows for Reproducible and Scalable Multimodal Mass Spectrometry Imaging and Immunofluorescence Microscopy Data Processing and Analysis

This record contains example and result data of msiFlow. msiFlow is a collection of automated workflows for reproducible and scalable multimodal mass spectrometry imaging (MSI) and immunofluorescence microscopy (IFM) data processing and analysis. Using an experimental mouse model for urinary tract infection, induced by uropathogenic E.coli (UPEC), we generated data by matrix-assisted laser desorption ionisation mass spectrometry imaging with laser-induced postionisation (MALDI-2 MSI) using the Bruker timsTOFfleX instrument transmission-mode MALDI-2 MSI (t-MALDI-2) immunofluorescence microscopy (IFM) using the MACSima system from Miltenyi msiFlow was tested on MALDI-2 MSI, t-MALDI-2 MSI and IFM data of control and UPEC-infected mouse bladder sections. In IFM we used Ly6G and actin for staining neutrophils and the muscle layer. We validated msiFlow on MALDI MSI data of bone marrow (BM)-derived neutrophils. Tentative lipid annotations were validated by MALDI DDA MSI and MALDI MS/MS. All data used and results generated by msiFlow are included in this dataset (besides the intermediate results of the MALDI-2 preprocessing due to data size). The dataset contains the following zip files: zip file description ly6g_heterogeneity.zip example and result data (Ly6G clusters) for molecular_heterogeneity_flow if_segmentation.zip example and result data (Ly6G segmentation) for if_segmentation_flow ly6g_heterogeneity_signatures.zip example and result data (lipids for Ly6G clusters) for molecular_signatures_flow ly6g_molecular_signatures.zip example and result data (lipids for Ly6G) for molecular_signatures_flow msi_if_registration.zip example and result data for msi_if_registration_flow msi_segmentation.zip example and result data (segmented MSI bladder data) for msi_segmentation_flow region_group_analysis.zip example and result data (regulated lipids in different bladder tissue regions) for region_group_analysis_flow macsima.zip raw IFM data of UPEC-infected bladders containing Ly6G, actin and autofluorescence images maldi-bm-neutrophils.zip raw and pre-processed MALDI MSI data of BM-derived neutrophils t-maldi-2.zip raw t-MALDI-2 MSI data of a UPEC-infected bladder section maldi-2-group-sampleno.zip raw MALDI-2 MSI data of a control/UPEC bladder section MALDI_DDA_MSI.zip raw MALDI MSI data acquired in DDA mode TIMS_MS_MS.zip raw MALDI TIMS MS/MS data