Developing Targeted Protein Measurement for Label-Free Multiple Reaction Monitoring

• Activity Number: 281
• Type: Topic Contributed
• Date/Time: Tuesday, August 3, 2010 : 8:30 AM to 10:20 AM
• Sponsor: Section on Statistical Learning and Data Mining
• Author(s): Dean Billheimer*+
• Companies: The University of Arizona
• Keywords: proteomics ; multiple reaction monitoring ; biomarker verification ; label-free quantitation ; analytical sensitivity ; stable-isotope dilution

Abstract

Liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM-MS) provides a powerful tool for targeted protein quantitation. The most common implementation of LC-MRM-MS uses stable isotope dilution (SID), in which synthetic, isotopically labeled peptides serve as internal standards for all target peptides. Implementation of the SID-based approach is limited by the cost of acquiring standards, particularly when application to biomarker verification may require configuration of dozens to hundreds of assays. I evaluate performance of SID together with alternative methods that do not require isotopically labeled version of target peptides. I develop a measure of technical merit for comparing measurement methods, and show its extension to the multivariate calibration setting for MRM.