Enhanced Proteomic Coverage in Tissue Microenvironment by Immune Cell Subtype Library-assisted DIA-MS

The objective of the protject is to develop an immune cell-enrich library-assisted DIA method that enables the comprehensive identification and quantification of immunological proteins from micro-scale samples with high sensitivity. In the project, six immune cell subtype-specific libraries including CD8+ and CD4+ T cell, B cell, NK cell, DC and MP were established, and the six subtype libraries can be consolidated into a larger library termed the immune cell-enriched library. By integrating either a single cell-type specific library or multiple libraries into the conventional library-based DIA search, the method enhances the identification coverage of the immune landscape for micro-scale colonic polyps in CRC mice. Application of the method on the MLNs of the CRC mice offers an enlarged TME landscape that reveals proteomic changes in the MLN from different tumor growth of progrssion.