Shifting the Paradigm: Peptide-Centric Analysis of Systematically Sampled Mass Spectrometry Data
Year: 2016
Type: dissertation
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 iv 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-31treated 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.
Author: Ying S. Ting
Language: English
Subfield: Spectroscopy
Field: Chemistry
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W2591664289