Download or read book New Tools for Enhanced Proteome Characterization written by Rachel M. Miller (Ph.D.) and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are the key biological actors within cells, driving many biological processes integral for both healthy and diseased states. Understanding the depth of complexity represented within the proteome is crucial to our scientific understandingof cellular biology and to provide disease specific insights for clinical applications. Mass spectrometry-based proteomics is the premier method for proteome analysis, with the ability to both identify and quantify proteins. Although proteomics continues to grow as a robust field of bioanalytical chemistry, advances are still necessary to enable a more comprehensive view of the proteome. In this thesis, several new tools for the improvement of proteome characterization are described, seeking to not only increase the depth of proteome characterization, but also the precision of the results obtained. In Chapter 1, an overview of mass spectrometry-based proteomics is provided including specific background information for the different areas of proteomic analysis addressed in the chapters of this thesis. Chapter 2 introduces multi-protease protein inference and illustrates advantages of utilizing peptides from multiple proteolytic digests for protein inference. Chapter 3 describes an in silico digestion software tool called ProteaseGuru, designed to aid in the consideration of alternative proteases for bottom-up experiments. Chapter 4 establishes a software pipeline for the generation of sample-specific databases from PacBio long-read sequencing data. Chapter 5 describes the discovery and validation of dehydroamino acid residues within the HIV-1 virus. These uncommon post-translational modifications (PTMs) were initially discovered using global PTM discovery (GPTMD), and then subsequently validated using a chemical labeling strategy. All the works described throughout this thesis are summarized and future directions for the improvement of proteome characterization are outlined in Chapter 6.