Research by Daucke et. el, has been introduced to revolutionize the analysis of Formalin-fixed paraffin-embedded (FFPE) tissues, catering to the intricate demands of spatial proteomics. FFPE tissue, widely employed for its ability to preserve biological specimens, has long posed challenges in extracting molecular information due to the need for substantial sample quantities. This limitation hampers comprehensive retrospective studies, particularly in understanding cell heterogeneity and identifying tissue-specific signatures, crucial in fields such as cancer research.

The newly devised workflow addresses these challenges with remarkable efficiency. Leveraging Liquid Chromatography-Mass Spectrometry (LC-MS) advancements, particularly the IonOpticks Aurora Elite XT S 15 cm nanoflow UHPLC column, it enables the extraction of proteins even from ultra-low input material. Through meticulous optimization and validation, the workflow achieves deep proteome coverage across varying sample sizes, from as low as 1,166 µm² to ∼800,000 µm², surpassing previous limitations.

The protocol’s adaptability is showcased in its compatibility with diverse archival tissues, employing stains like EpCAM and H&E. Through Laser Capture Microdissection (LCM), specific cell populations can be isolated, allowing for the identification of tissue-specific signatures and clustering of cell populations.

This transformative approach not only unlocks the potential of FFPE repositories for retrospective studies but also lays the groundwork for broader applications in cancer research and beyond. With its ease of implementation and profound insights into spatial biology, this workflow stands as a valuable tool for researchers seeking comprehensive molecular analysis of FFPE tissues.

‌This study utilizes IonOpticks Aurora Elite XT 15 cm nanoflow UHPLC column, it enables the extraction of proteins even from ultra-low input material.

Pre – Published in BioRxiv, January 29, 2024.

Authors

Rune Daucke, Charlotte V. Rift, Nicolai S. Bager, Kartikey Saxena, Peter R. Koffeldt, Jakob Woessmann, Valdemaras Petrosius, Eric Santoni-Rugiu,Bjarne W. kristensen, Pia Klausen, Erwin M. Schoof

Title

Refining Spatial Proteomics by Mass Spectrometry: An Efficient Workflow Tailored for Archival Tissue