MALDI Guided SpatialOMx® Reveals Proteomic Heterogeneity in Tumor Subpopulations of Breast Cancer

MALDI Guided SpatialOMx^® provides an excellent tool for discovering deep proteomics insights into heterogeneous tumor subpopulations. The timsTOF fleX system bridges a current gap by providing regiospecific targeting of a multi-molecular imaging technique with 4D-Proteomics™ analysis in just one instrument.

Figure 1. Proteomics of tumor subpopulations and biological process characterization. Proteins from microdissected tissue (approx 160 ng) were extracted, digested with trypsin and peptide extracts were run on the timsTOF fleX using PASEF. Number of protein IDs per tumor subpopulation segment A and biological process characterization per segment as revealed by PANTHER B.

The instrument offers all benefits of a timsTOF Pro for timeefficient and sensitive 4D-proteomics, combined with highresolution, label-free molecular imaging. Novel PASEF technology enables high protein ID rates with very small sample amounts typical of microextracted tumor subpopulations. Key findings: 1. SpatialOMx is a new workflow for in situ characterization of tissue subtypes based on molecular expression; 2. locations of selected subtypes guide laser-capture microdissection to cells of a specific molecular phenotype; 3. timsTOF fleX uses 4D-proteomic analysis of small microdissected tissue pieces to explore differences related to molecular phenotype; and 4. SpatialOMx, combining MALDI imaging and LC-MS/MS, with timsTOF fleX provides deeper proteomics profiling correlated to cell phenotype.

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