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