Shifting the Paradigm: Peptide-Centric Analysis of Systematically Sampled Mass Spectrometry Data

Abstract

In mass spectrometry-based shotgun proteomics, data-independent acquisition (DIA) is an emerging technique due to its systematic and unbiased sampling of precursor ions. However, current DIA methods often use wide precursor isolation windows, resulting in co-fragmentation and complex mixture spectra, posing various challenges in DIA data analysis. In this dissertation, I aim to shift the paradigm of data analysis in DIA tandem mass spectrometry with peptide-centric analysis. I first describe the analytical advantages of peptide-centric analysis over the conventional spectrum-centric analysis for DIA data analysis. Next, I describe a new tool I developed, named PECAN, that enables peptide-centric analysis for robust peptide detection for DIA data without a prerequisite library. I demonstrate rigorous validation of PECAN performance, including validation with synthesized analytical standards using an in vitro translation system. I further discuss the impact on the selectivity of DIA data to peptide detection. All DIA methods balance between acquisition parameters, such as precursor selectivity, fragmentation method, ion injection time/dwell time, and resolving power of MS/MS analysis. I discuss using PECAN detection as a quantitative metric to characterize the effects of these acquisition parameters in the context of DIA analysis. Along with two other applications, I demonstrate the versatility of PECAN and peptide-centric analysis of DIA data. Finally, I apply peptide-centric analysis to characterize the murine heart proteome with SS-31 treatment. Here, I first show improvement in cardiac function of SS-31-treated old mice. Next, I interrogate the mitochondrial and global proteome changes impacted by the SS-31 treatment in the murine heart proteome with DIA MS/MS and PECAN. I show the proteome dynamics of several pathways hypothesized to be involved with the SS-31 mechanisms, shedding light on the underlying mechanisms of the SS-31 cardiac protective effects.