Statistical Analysis of Proteomics Mass Spectrometry Data in a Ubiquitin Substrate Profiling

• Activity Number: 510
• Type: Contributed
• Date/Time: Wednesday, August 1, 2012 : 10:30 AM to 12:20 PM
• Sponsor: Biometrics Section
• Author(s): Qinghua Song*+ and Anita Izrael-Tomasevic and Eugene Varfolomeev and Daisy Bustos and Corey P. Bakalarski and Domagoj Vucic and Donald Kirkpatrick and William Forrest
• Companies: Genentech and Genentech and Genentech and Genentech and Genentech and Genentech and Genentech and Genentech
• Keywords: Ubiquitination ; mass spectrometry (MS) ; mixed-effect models ; label-free proteomics

Abstract

Ubiquitination is a Post-Translational protein Modification (PTM) procedure that plays important roles in apoptosis, or programmed cell death. The Inhibitor of APoptosis (IAP) proteins are crucial for the regulation of apoptosis in the sense that the ring finger dependent E3 activities of some of the IAPs can catalyze auto-ubiquitination. It had been demonstrated that small-molecule IAP antagonists induced dramatic auto-ubiquitination activity and rapid proteasomal degradation of c-IAPs. When cancer cells are treated with chemotherapeutic drugs, changes can be observed in ubiquitination of certain substrates. Recently, mass spectrometry (MS) technologies have been implemented to identify and quantify PTMs including modification of cellular proteins by ubiquitin. Our study performed global ubiquitin substrate profiling using mass spectrometry in IAP antagonist sensitive and resistant cell lines in order to get further understanding of the mechanisms of IAP antagonist induced cell death. Graphical analysis and mixed-effect models were applied to label-free proteomics MS data to identify the proteins differentially ubiquitinated in response to IAP antagonist-Gemcitibine combinat