biostudies-literatureTodorovic VNCI NIH HHSNIAMS NIH HHS351-61https://www.ebi.ac.uk/biostudies/studies/S-EPMC2830845biostudies-literatureUnknown9(2)The ability of cells to modulate interactions with each other and the substrate is essential for epithelial tissue remodeling during processes such as wound healing and tumor progression. However, despite strides made in the field of proteomics, proteins involved in adhesion have been difficult to study. Here, we report a method for the enrichment and analysis of proteins associated with the basal surface of the cell and its underlying matrix. The enrichment involves deroofing the cells with 20 mM ammonium hydroxide and the removal of cytosolic and organellar proteins by stringent water wash. Proteomic profiling was achieved by LC-FTMS, which allowed comparison of differentially expressed or shared proteins under different cell states. First, we analyzed and compared the basal cell componeMolecular & cellular proteomics : MCPDetection of differentially expressed basal cell proteins by mass spectrometry.PMC2830845F32 AR055444R01 AR041836R01 AR43380T32 CA070085R01 AR043380P30 AR057216R01 CA122151R01 AR41836Todorovic VDesai BVYin TMrksich MPatterson MJEigenheer RAGreen KJAmargo EVfalseDetection of differentially expressed basal cell proteins by mass spectrometry.The ability of cells to modulate interactions with each other and the substrate is essential for epithelial tissue remodeling during processes such as wound healing and tumor progression. However, despite strides made in the field of proteomics, proteins involved in adhesion have been difficult to study. Here, we report a method for the enrichment and analysis of proteins associated with the basal surface of the cell and its underlying matrix. The enrichment involves deroofing the cells with 20 mM ammonium hydroxide and the removal of cytosolic and organellar proteins by stringent water wash. Proteomic profiling was achieved by LC-FTMS, which allowed comparison of differentially expressed or shared proteins under different cell states. First, we analyzed and compared the basal cell compone2010-01-01T00:00:00Z2010 Feb2025-04-21T18:43:51.17Z2019-03-27T00:28:59ZS-EPMC28308451995507710.1074/mcp.M900358-MCP20010.1074/mcp.m900358-mcp200