PRISM-MS: Mass-Guided Single-Cell MALDI Imaging of Low-Mass Metabolites

DOI: 10.1002/advs.202410506

This repository hosts the PRISM-MS application and related resources for the study described in our publication: Mass‐Guided Single‐Cell MALDI Imaging of Low‐Mass Metabolites Reveals Cellular Activation Markers.

Table of Contents

• Overview
• Installation
• Usage Instructions
• Supplementary Data

Overview

PRISM-MS is a Shiny application designed for MALDI imaging analysis workflows. The app simplifies the selection of regions of interest in MALDI datasets and enables guided DeepScan measurements. PRISM-MS is fully self-contained, requiring no additional installation of R or other software.

Installation

Clone or download this repository.

git clone https://github.com/CeMOS-Mannheim/PRISM-MS.git

Quick Start (without cloning the repository) :

1. Download PRISM-MS.rar Direct Download newest Release

2. Unzip the downloaded PRISM-MS.rar to a local directory, such as your Desktop.

Usage Instructions

Step 1: Run the Application

1. Navigate to the unzipped PRISM-MS folder.
2. Double-click on the run.bat file.
   • This will open a command prompt and launch the PRISM-MS Shiny application.
   • No additional installations (e.g., R) are required.

Step 2: Load Your Data

1. Load an .imzML file and the corresponding .idb file from your measurements.
   • Sample data is available in the folder: sample data\231027_GUVs_A.
2. Load the corresponding .mis file.
   • A sample file is also included in the same directory.

Step 3: Configure Analysis Settings

1. Select a normalization method (usually "none" is sufficient).
2. Set your mass range and tolerance values.
   • Preset values work well for the sample dataset.

Step 4: Process Data

1. If all data is loaded correctly, a Load button will appear. Click it to proceed.
2. Specify your target m/z value (e.g., 786.6 or 678.5 for the GUV dataset).

Step 5: Adjust Visualization

1. Manually adjust threshold levels to refine the selected mask.
   • Use the Otsu thresholding method until the desired mask is achieved.
2. Enter the acquisition path and adjust spatial resolution and spot dilation as needed.
   • Adjustments will affect the resulting .mis file.

Step 6: Export Data

1. The thresholded image (bottom right of the app) will be converted into a new .mis file upon pressing the Write MIS File button.
2. Save the .mis file to a designated folder for further measurements.

Step 7: Measurement

1. Use the generated .mis file to guide your DeepScan measurement.
2. Example output: 231027_GUVs_A_5_1.mis (from the sample dataset) demonstrates a DeepScan with 5-micron spatial resolution and a spot dilation factor of 1.

Supplementary Data

Supplementary datasets used in the manuscript are included in this repository. Notably:

• Supplementary Dataset S1: Available as a zip file from figshare.
• Measurement Data: Available as .imzML and .ibd files https://metaspace2020.eu/project/PRISM-MS