Proteomic Analysis of Biological Systems

Mass spectrometry-based proteomics have become critical for our understanding of biological systems. This technique allows for quantitative measurements of biomolecules that are altered between different sample states and types. The studies in this thesis describe comparisons between normal and cancerous tissues, normal and disease blood samples, and genetically manipulated cell lines. Further studies analyze various sample preparation and separation techniques to increase the information garnered from biological samples.

Transcript data was collected using quantitative real-time PCR (qRT-PCR), while protein level data was collected by bottom-up proteomic strategies using ultra-performance liquid chromatography or capillary zone electrophoresis coupled to an ESI-Orbitrap mass spectrometer. Targeted multiple reaction monitoring (MRM) experiments were performed on an ESI-triple quadrupole mass spectrometer. Data analysis was performed using a number of mass spectrometry software platforms, including Proteome Discoverer 1.4, MaxQuant statistical software, Perseus, R, and Proteosign, an online statistical analysis platform.