Nuclear matrix contains novel WD-repeat and disordered-region-rich proteins

To find novel proteins predicted to participate in the formation of nuclear bodies, nuclear speckles, and nuclear macro-protein complexes, we applied proteome analysis to a HeLa cell nuclear matrix fraction. Proteins in the fraction were separated by SDS-PAGE, digested with trypsin, and analyzed by nanoflow liquid chromatography-iontrap-tandem mass spectrometry. Three hundred and thirty three proteins including 39 novel ones were identified. Seven WD-repeat proteins and 16 disordered region-rich proteins, which act frequently as scaffolding proteins for macro-protein complexes, were found amongst the novel proteins.