Methods Of Protein Sample Preparation Using Digital Microfluidics And Gas Phase Techniques With Detection By Mass Spectrometry

Biological samples are complicated, having many different components at a wide variety of concentrations. Some means to simplify these samples while leaving the discrete components unaltered is required. Small structural differences can render a protein unusable role. Mass spectrometry is a valuable tool to characterize proteins but the number of components in these samples present a challenge for accurate detection. Sample preparation and separation methods are effective tools to alleviate this challenge In this dissertation, I present methods for simplifying protein samples for analyze with mass spectrometry using liquid and gas phase methods. In the first chapter, I review some sample preparation options. In Chapter 2, I present a microscale method for high abundance protein depletion using digital microfluidics and functionalized magnetic particles. This is a fast, effective, and multiplexed method for reducing the interference caused from proteins like serum albumin and immunoglobulins resulting in a 4-fold improvement in signal to noise for a low abundant protein. Chapter 3 extends this methodology by employing the same fluid and particle handling technique to immunoprecipitation. This chapter introduces the use of a pre-concentration method called pre-concentration using liquid intake by paper (P-CLIP), a promising 'world-to-chip' interface for many digital microfluidic applications. In Chapter 4, gas-phase vapours are used to simplify analysis of peptides by electrospray mass spectrometry. Acetonitrile vapour suppresses in-source fragmentation of fragile ions by clustering with fragile ions resulting in improved limits of detection. Chapter 5 presents a union of liquid chromatography and differential mobility spectrometry for characterization of biopharmaceutical proteins. This new combination, called DMS-SWATH, increases MS/MS sequence coverage for proteins and alleviates problems found in traditional analysis by mass spectrometry and differential mobility spectrometry. Overall this work presents important steps forward in miniaturizing and ameliorating the use of mass spectrometry for the characterization of proteins.