Integration of a Two-Phase Partition Method into Proteomics Research on Rat Liver Plasma Membrane Proteins

To comprehensively identify proteins of the rat liver plasma membrane (PM), we have adopted a
proteomics strategy that utilizes sucrose density centrifugation in conjunction with aqueous two-phase
partition for plasma membrane isolation, followed by SDS-PAGE, mass spectrometry and bioinformatics.
Western blot analysis showed that this method results in highly purified plasma membrane fractions,
which is a key to successful plasma membrane proteomics. The PM proteins were separated by SDS-PAGE and digested with trypsin. Through nano-ESI−LC MS/MS analysis we identified 428 rat liver
membrane proteins, of which 304 had a gene ontology (GO) annotation indicating a cellular component,
and 204 (67%) of the latter were known integral membrane proteins or membrane-associated proteins.
In addition to proteins known to be associated with the plasma membrane, several hypothetical proteins
have also been identified. This study not only provides a tool to study plasma membrane proteins
with low levels of contamination, but also provides a data set for proteins of high to moderate abundance
in rat liver plasma membranes, thus allowing for more comprehensive characterization of membrane
proteins and a better understanding of membrane dynamics.
Keywords: rat liver • plasma membrane • plasma membrane proteins • two-phase partition • LC−MS/MS