Book Description

This dissertation presents research focusing on the development of new instrumentation and methodology to leverage ion-ion reactions for proteomic analyses. Electron transfer dissociation (ETD) technologies have proven a valuable alternative to collision-based fragmentation methods for sequencing peptides and proteins to advance global proteome characterization. Chapter 1 outlines the core concepts central to mass spectrometry (MS)-based proteomics, in addition to the basic principles of ETD and various strategies to improve its efficacy - including the technology that is the focus of this work, i.e., activated ion ETD (AI-ETD). Chapter 2 describes the first application of AI-ETD to intact proteins, which are more chemically complex and, thus, more difficult to sequence, than their peptide counterparts. Chapter 3 discusses a new strategy to improve signalto- noise in ETD spectra, which is especially beneficial for intact protein analysis and which has been incorporated into the newest generation of commercially available quadrupole-Orbitrap-linear ion trap hybrid MS systems. AI-ETD capabilities were also recently implemented on this stateof- the-art MS system (Chapter 4), and the ability to perform AI-ETD on this instrument enables comprehensive sequence coverage of moderately-sized intact proteins (Chapter 5), significantly improves proteoform characterization in large-scale analyses of complex mixtures of intact proteins (Chapter 6), and also enhances characterization of larger intact proteins (Chapter 7). Furthermore, AI-ETD improves characterization of post-translational modifications. Chapter 8 demonstrates the utility of AI-ETD for phosphosite localization in phosphopeptides and intact phosphoproteins, and Chapter 9 presents the largest glycoproteomic study to date by using AI-ETD to interrogate intact N-glycopeptides. Beyond positive-mode analyses of peptide and protein cations, ion-ion reactions also bring unique benefits to negative-mode analyses of precursor anions, where collision-based dissociation fails to consistently produce sequence-informative fragments. Chapter 10 describes implementation of negative ETD (NETD) and activated ion NETD (AI-NETD) and their application to whole-proteome sequencing in the negative mode, and Chapter 11 presents a modified search algorithm to improve interpretation of large-scale NETD and AI-NETD data. Conclusions and future directions of these projects are discussed in Chapter 12.