Shotgun proteomics on tissue specimens extracted with Acid guanidinium-thiocyanate-phenol-chloroform

Protein-containing organic fractions of acid guanidinium thiocyanate-phenol-chloroform-extracted tissues are an interesting source of proteins as this method is widely used for RNA extraction for gene expression analysis. However, due to difficulties in redissolving pelleted proteins from the organic phase, protein analysis has only been limitedly reported. Current shotgun mass spectrometry-based methods, however, require minute amounts of sample, and methods have been developed that allow SDS to be removed from an extraction buffer prior to protein digestion. The limited volume of starting material needed for shotgun proteomics facilitates redissolving proteins in SDS-containing buffers, allowing proteins to be readily extracted. Here we describe a protocol for an SDS-DTT-based extraction of proteins from the organic fraction of acid guanidinium-thiocyanate-phenol-chloroform-extracted tissues that remain after RNA isolation for shotgun MS analysis.