MALDImID: Spatialomics R package and Shiny app for more specific identification of MALDI imaging proteolytic peaks...

Area of Science:

• Proteomics
• Molecular Pathology
• Biotechnology

Background:

• Matrix-assisted laser desorption/ionization (MALDI) imaging is valuable for protein localization in formalin-fixed paraffin-embedded (FFPE) tissues.
• Protein identification using traditional MALDI-time-of-flight (TOF) and post-source decay (PSD) fragmentation is often challenging and time-consuming.

Purpose of the Study:

• To develop a method for more specific identification of peaks in bottom-up MALDI imaging data.
• To leverage liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic data for enhanced MALDI imaging analysis.

Main Methods:

• Implementation of an R package for data analysis.
• Development of a Shiny application for user-friendly access to the analytical tools.
• Integration of LC-MS/MS proteomic biomarker discovery data with MALDI imaging datasets.

Main Results:

• The developed R package and Shiny app facilitate the specific identification of MALDI imaging peaks.
• The approach enhances the utility of MALDI imaging in molecular pathology by improving protein identification accuracy.
• The Shiny app provides direct access to the implemented tool for researchers.

Conclusions:

• The new R package and Shiny app significantly improve protein identification in MALDI imaging of FFPE tissues.
• This integration bridges the gap between proteomic biomarker discovery and spatial proteomics.
• The tools enhance the application of MALDI imaging in tissue classification and molecular pathology workflows.