Analysis of Data from Proteomics Study Utilizing SILAC (Stable Isotopic Labeling of Amino Acids in Cell Culture)

• Activity Number: 582
• Type: Contributed
• Date/Time: Wednesday, August 4, 2010 : 2:00 PM to 3:50 PM
• Sponsor: Biometrics Section
• Author(s): Qinghua Song*+ and Daniel Spellman and Ronald Miller and Andy Liaw
• Companies: Merck & Co., Inc. and Merck & Co., Inc. and Merck & Co., Inc. and Merck & Co., Inc.
• Keywords: Mass Spectrometry ; SILAC ; Proteomics

Abstract

SILAC is a mass spectrometry-based technique developed for detection and quantification of relative protein abundance between two samples, by supplementing one of the samples with growth medium containing a 'light' (normal) amino acid and the other containing a 'heavy' (stable-isotope labeled) amino acid. Heavy and light samples are mixed, processed and analyzed in a single mass spectrometry experiment. Pairs of peptides with different stable-isotope composition can be differentiated owing to their mass difference by investigating the ratio of peak intensities. We present step-by-step statistical analysis of the data from a SILAC Proteomics study including data preprocessing, correction factor estimation, and decision threshold optimization. Our approach led to significant reduction in the false positive rate comparing with the currently used methodology.