Constructing a System for Quantitative Proteomics Based on Mass Spectrometry Techniques: A Data Analysis Challenge

• Activity Number: 88
• Type: Contributed
• Date/Time: Monday, August 9, 2004 : 8:30 AM to 10:20 AM
• Sponsor: Biopharmaceutical Section
• Author(s): Matthew Westlake*+ and Georgiy Bobashev and Benjamin J. Cargile and James L. Stephenson, Jr.
• Companies: RTI International and RTI International and RTI International and RTI International
• Keywords: spectrometry ; quantitative proteomics

Abstract

Measuring the differential expression of genes through mass spectrometry based techniques is a way to perform quantitative proteomics. In a typical experiment an isotopic tag is used to differentiate two samples whose protein content is extracted, possibly separated into discrete groups by electrophoresis or other methods, and the results are subjected to mass spectrometry analysis. The researcher is presented with a large number of spectra to compare. These spectra often contain noise and the identification of families of peaks representing peptides can be tedious and difficult, especially as the size of the proteome increases. Matching these peak families to proteins and comparing spectra is another challenge. The growth of mass-spectrometry-based techniques for measuring gene expression has prompted a need for tools to analyze the results. We present an approach developed to address these issues and automate the comparison process. Our process includes methods to separate signal from noise, identify peaks and peak families, identify shifts in peak location, identify incomplete peptide separation in adjacent spectra, and bring the results together for sample comparison.