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.