Tissue Mild Extraction Enriches Membrane, Cytoplasmic, and Secreted Proteomes for Biomarker Discovery

Clinical blood biomarkers provide important diagnostic information and are generally secreted, cytoplasmic, membrane, and other soluble proteins. However, in the mass spectrometry-based proteomic biomarker discovery phase, the whole tissue is often lysed directly for analysis, and this increases protein complexity in the sample, limiting the detection of soluble proteins as biomarkers. Here, we use a mild extraction method that includes a low salt buffer and 1% Triton X-100 to isolate proteins from mouse tissues followed by proteomic analyses. This mild condition extracts membrane, cytoplasmic, and secreted proteins efficiently while preserving nuclear proteins largely from the mouse brain and 16 other tissues. Further in-depth proteomic analysis of the mild extract from an Alzheimer mouse brain tissue has identified more than 12,000 proteins with enrichments of soluble proteins and potential cerebrospinal fluid markers. This mild extraction has enriched membrane, cytoplasmic, and secreted proteins from tissue samples and should be used as a general method for increased success in the mass spectrometry-based proteomic discovery of circulating biomarkers.