Abstract
The timsTOF fleX system bridges a current gap by providing MALDI Imaging and in-depth proteomics analysis in just one instrument. The instrument offers all benefits of a timsTOF Pro for timeefficient and sensitive proteomics, combined with a high-resolution MALDI source and stage. Using PASEF technology, it is possible to retrieve high protein ID rates with small sample amounts. Here we present the new SpatialOMx workflow to identify distinct proteomic profiles for different tumor subpopulations in breast cancer as an example for this powerful approach.
Introduction
Since tissue and disease are correlated, SpatialOMx provides the unique opportunity to combine regiospecific information from MALDI Imaging with deep proteomic coverage for biomarker discovery and molecular characterization. MALDI Imaging has
MALDI Imaging has the advantage of providing spatial and molecular information that can be used to detect Region of Interests (ROIs) in tissue sections. As a discovery tool, MALDI Imaging lacks the possibility of in-depth molecular characterization of classical LC-MS/MS based OMICs methods. Classical OMICs strategies, however, do not retain the spatial information. Here, we present SpatialOMx for microproteomic characterization of tumor subpopulations in breast cancer. In this efficient workflow, unsupervised segmentation of MALDI Imaging data with SCiLS Lab is used to define ROIs. Image processing strategies provide boundary information of segments of tumor subpopulations for laser capture microdissection (LMD). Protein extraction and tryptic digestion of small microdissected material is followed by proteomic analysis on the timsTOF fleX using PASEF (Parallel Accumulation Serial Fragmentation). Analysis of proteomics data provides a comprehensive mechanistic understanding of cell-type specific biological processes in-situ to complement the workflow.
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