Complementary proteomic analysis of protein complexes.
Proteomic characterization of protein complexes leverages the versatile platform of liquid chromatography-tandem mass spectrometry to elucidate molecular and cellular signaling processes underlying the dynamic regulation of macromolecular assemblies. Here, we describe a complementary proteomic approach optimized for immunoisolated protein complexes. As the relative complexity, abundance, and physiochemical properties of proteins can vary significantly between samples, we have provided (1) complementary sample preparation workflows, (2) detailed steps for HPLC and mass spectrometric method development, and (3) a bioinformatic workflow that provides confident peptide/protein identification paired with unbiased functional gene ontology analysis. This protocol can also be extended for characterization of larger complexity samples from whole cell or tissue Xenopus proteomes.
PubMed ID: 22956100
PMC ID: PMC3616387
Article link: Methods Mol Biol.
Grant support: R01 DE018825 NIDCR NIH HHS, R01 HL112618 NHLBI NIH HHS , R21 HD073044 NICHD NIH HHS