Global protein quantification using neutron-encoded mass signatures and high-resolution mass spectrometry

The following chapters detail methodological and computational improvements to stable isotope labeling for mass spectrometry-based quantitative proteomics. The development of mass spectrometry for protein characterization and quantification is briefly reviewed in Chapter 1. Chapter 2 introduces the concept of neutron-encoded (NeuCode) mass signatures and demonstrates its potential for accurate and multiplexed protein quantification. The third chapter describes the design, synthesis, and use of new amino acid reagents that greatly expand the utility and scope of the NeuCode approach. In systematic and biological settings, NeuCode is benchmarked against current gold standard methods for quantitative accuracy and multiplexing. Chapter 4 examines the peculiar challenges associated with quantification of NeuCode features from high-resolution mass spectra and chronicles the computational algorithms developed to suit a variety of NeuCode labeling schemes. Conclusions and future directions inspired by the content of this thesis are discussed in Chapter 5.