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.
- Q-PCR in Combination with ChIP Assays to Detect Changes in Chromatin Acetylation
- Analysis of Allele-Specific Gene Expression
- Isolation of Intracellular Protein DNA Complexes Using HaloCHIP, an Antibody-Free Alternative to Chromatin Immunoprecipitation
- Hematopoietic Stem and Progenitor Cells
- Evaluation of the Fate of rAAV Genomes Following In Vivo Administration
- Quantitative Measurement of mRNA Using the RNase Protection Assay
- Preparation of Human Chromosomal Painting Probes From Somatic Cell Hybrids
- Engineered Chromosomes in Transgenics
- Comparative Genomic Hybridization on BAC Arrays
- Protein Fractionation by Preparative Electrophoresis