Copyright by Michelle Renee Robinson 2016 The Dissertation Committee for Michelle Renee Robinson Certifies that this is the approved version of the following dissertation: Advancement of Photodissociation Mass Spectrometry Methods for the Analysis of Protein Post-translational Modifications Committee: Jennifer S. Brodbelt, Supervisor Richard M. Crooks Kevin N. Dalby Lauren J. Webb Yan Jessie Zhang Advancement of Photodissociation Mass Spectrometry Methods for the Analysis of Protein Post-translational Modifications by Michelle Renee Robinson, B.S. Dissertation Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy The University of Texas at Austin May, 2016 Dedication For my parents Jim and Joanne Acknowledgements To start I would like to acknowledge my advisor, Jennifer Brodbelt, for giving me the opportunity to earn my PhD in your lab. I feel fortunate to have had access to state of the art instrumentation and to have been granted freedom in pursuing my research interests. Your willingness to initiate correspondence with other experts in the field on my behalf helped me overcome many road blocks in my research and gave me access to several interesting collaborations. In particular, I am indebted to Professor Joshua Coon and his graduate student Catie Minogue for hosting me at the University of Wisconsin and providing hands on training for IMAC phosphopeptide enrichment. Also to Daniel Boutz, who showed me the process of cell culture and helped to grow enough HeLa to last through my many initial attempts at phosphoproteomics. The data analysis to determine phosphate retention was greatly aided by code written by Joyce Ho. Thanks for letting me distract you from your own dissertation. Thank you to Dr. Kevin Dalby and his graduate student Juliana Taliaferro for donating HCC70 cell lysates and to Dr. Jessie Zhang and her graduate student Josh Mayfield for providing CTD samples. To both groups, thank you for lending your expertise regarding protein phosphorylation and for providing interesting applications for my work. Thank you to my labmates in the Brodbelt group over the years, especially Victoria Cotham and Dustin Klein. I hope you know how much your friendship has helped me during these last six years. Thanks for always coming through with useful suggestions and never letting me get too down on myself at times when research was slow to progress. v I have also been blessed with an incredible support system of friends outside of the lab. Special thanks to my roommates over the years including Jenny Knipe, Amanda Paine, and Rachel James for standing in as my Austin family. Thanks for the fun times and memories. Finally I am so grateful to my family for all their love and endless support during my time in graduate school. You gave me the push that I needed to embark on my Austin adventure and have been instrumental in my success ever since. Mom, Dad, Chris, and Shannon, I could not have done this without you. vi Advancement of Photodissociation Mass Spectrometry Methods for the Analysis of Protein Post-translation Modifications Michelle Renee Robinson, Ph.D. The University of Texas at Austin, 2016 Supervisor: Jennifer S. Brodbelt Post-translational modifications (PTMs) are important for regulating protein structure and function. Despite significant progress for PTM analysis using liquid chromatography tandem mass spectrometry (LC-MS/MS), opportunities for new method development remain. The research presented in this dissertation promotes 193 nm ultraviolet photodissociation (UVPD) as an alternative activation technique for PTM analysis with specific utility for phosphorylated and sulfated peptides. A novel de novo sequencing method with applications for unbiased PTM discovery was developed utilizing Lys-N proteolysis, N-terminal imidazolinylation, and UVPD to direct fragmentation for the formation of N-terminal ions. The N-terminal a, b, and c ions generated by UVPD were differentiated from one another by characteristic mass shifts. Sets of triplet peaks were used to distinguish N-terminal ions from confounding C-terminal ions and improve the accuracy of de novo sequencing. UVPD was evaluated for the analysis of phosphopeptide cations and anions. Negative mode analysis was advantageous for the detection of casein peptides in high phosphorylation states, while positive mode proved more robust for global phosphoproteomic analysis of HeLa and HCC70 cell lysates. Compared to collisional vii activation, the depth of coverage was lower using UVPD yet more extensive fragmentation and improved phosphate retention on products ions was achieved. Phosphorylation mapping by LC-UVPD-MS was carried out in the C-terminal domain (CTD) of RNA polymerase II as a function of kinase treatment, ERK2 or TFIIH, and organism, yeast or fruit fly. Single phosphorylations on Ser2 or Ser5 in the consensus heptad, YSPTSPS, were observed across all experimental conditions. Analysis of the non-consensus fruit fly CTD revealed the significance of Tyr1 and Pro residues in the +1 position relative to Ser for phosphorylation to occur. For sulfated peptides, negative mode UVPD yielded a and x ions that largely retained the labile sulfate modification which facilitated peptide sequencing and PTM localization. With appropriate MS/MS tools established, the next step towards global sulfoproteomics was the development of enrichment methods. Weak anion exchange (WAX) was applied for this purpose. Following carbamylation to neutralize primary amines which otherwise repel the anion exchanger; improved WAX retention was observed for sulfopeptides relative to a complex mixture of unmodified bovine serum albumin peptides. viii Table of Contents Chapter 1: Introduction ............................................................................................1 1.1 Introduction ............................................................................................1 1.2 Bottom-up/shotgun Proteomics .............................................................2 1.2.1 Modification Specific Proteomics.................................................4 1.2.2 De novo Sequencing .....................................................................5 1.3 Tandem Mass Spectrometry Nomenclature ...........................................6 1.3.1 Collision Induced Dissociation .....................................................9 1.3.2 Ultraviolet Photodissociation at 193 nm .....................................10 1.5 References ............................................................................................15 Chapter 2: Experimental Methods .........................................................................20 2.1 Mass Spectrometry...............................................................................20 2.1.1 Thermo Fisher Scientific LTQ XL Linear Ion Trap ...................21 2.1.2 Thermo Fisher Scientific Velos Pro Dual Linear Ion Trap.........21 2.1.3 Oribtrap Elite Mass Spectrometer ...............................................21 2.1.4 Orbitrap Fusion Tribrid Mass Spectrometer ...............................22 2.2 Liquid Chromatography .......................................................................22 2.2.1 Dionex Ultimate 3000 .................................................................22 2.2.1.1 Positive Mode LC-MS/MS Analysis ...........................23 2.2.1.2 Negative Mode LC-MS/MS Analysis ..........................24 2.3 Ion Activation ......................................................................................25 2.3.1 Collisional Activation .................................................................26 2.3.1 Photodissociation at 193 nm .......................................................26 2.4 Chemicals .............................................................................................27 2.5 Sample Preparation ..............................................................................27 2.5.1 Cell Culture .................................................................................27 2.5.2 Protein Processing .......................................................................28 2.5.3 Peptide Derivatization .................................................................29 2.6 Enrichment ...........................................................................................30 ix 2.6.1 Immobilized Metal Affinity Chromatography ............................30 2.6.2 Hydroxyapatite ............................................................................30 2.6.3 Weak Anion Exchange ...............................................................31 2.7 Automated Peptide Sequencing ...........................................................31 2.7.1 PEAKS ........................................................................................32 2.7.2 Proteome Discoverer ...................................................................32 2.7.3 MassMatrix .................................................................................33 2.8 References ............................................................................................35 Chapter 3: 193 nm Ultraviolet Photodissociation of Imidazolinylated Lys-N Peptides for De Novo Sequencing ...............................................................................36 3.1 Overview ..............................................................................................36 3.2 Introduction ..........................................................................................37