CORE: Mass Spectrometry Proteomics Shared Resource (Omics Group) PROJECT SUMMARY Since the inaugural of the P30 CCSG, the Proteomics Shared Resource (PSR) has undergone major expansion and corresponding restructuring of operations. Notably, the mass spectrometry branch of the PSR was separated from the antibody-based and reverse phase protein array (RPPA) platforms to streamline management of the growing instrument capacity and diversification of the offered methodologies that are mass spectrometry driven. The newly organized Mass Spectrometry (MS) Proteomics Shared Resource now operates state-of-the-art ABSCIEX 5600 and Thermo Fisher instruments, including Thermo Orbitrap Elite. Collectively, support from the Dan L. Duncan Cancer Center, Institution and CPRIT (Cancer Prevention & Research Institute of Texas) is also committed to the acquisition of two more such instruments. Concurrent to these substantial improvements in technologies and sequencing capacity, we have strived to make major technological developments in mass spectrometry, protein biochemistry, and informatics techniques. In the last four years, we have collected extensive immunoprecipitation/MS data and protein profiling from cancer cell lines and specimens. Using these primary data sets we developed protein interaction algorithms that established a very robust reference resource for the human protein complex interaction networks. We have also transformed protein profiling capacity with new protocols enabling routine and rapid identification and quantification of limited-sample size proteomes in depths of over 7,000 gene products. We have also developed a new generation of DNA-based affinity reagents, including transcription factor profiling ?catTFRE? bait, to study dynamics of transcriptional activation in response to cellular states, physiological signaling and pharmaceutical drugs. Finally, a highly customized database and software system was built to facilitate storage, management, and, perhaps more importantly, interpretation of MS results. Proteome profiling, transcription factor profiling, and large-scale post translational modification profiling all together constitute a comprehensive suite of assays for discovery of potential biomarkers in cancers. The MS Proteomics Shared Resource is now ready to apply this comprehensive set of proteomics assays towards project missions of the Cancer Center at BCM.