This dissertation details innovations in mass spectrometry-based instrumentation that expand our ability to survey biopolymers, including proteins, peptides, and oligonucleotides, with increased sensitivity, speed, and depth. Chapter 1 provides an overview of mass spectrometry instrumentation at the leading edge of proteomics and for nucleic acid analysis. In Chapter 2, the optical-fiber enabled coupling of a mass spectrometer to an infrared laser improves proteomic characterization. For Chapter 3, electron transfer dissociation-based proteomics is investigated and inefficiencies of related ion-ion reactions are characterized. Chapter 4 introduces a novel nucleic acid sequencing technology with activated ion-negative electron transfer dissociation to profile RNA molecules and their modifications. In Chapter 5, tandem mass spectrometry comprehensively characterizes heavily-modified RNA therapeutics. Chapter 6 focuses on a proteome-wide analysis of the bacterial post-translational modification O-mycoloylation. In Chapter 7, a novel tandem mass spectrometry strategy, termed activated ion-tandem mass tags, is revealed, boosting quantitative reporter ion generation. Chapter 8 expands upon AI-TMT for quantitative single-cell proteomics, realizing sensitivity gains which drive a greater dynamic range of quantification. In Chapter 9, a novel mass spectrometer enables the one hour human proteome and we explore one minute proteome analyses, pushing the limits of high-throughput proteome analysis. Chapter 10 discusses emergent proteomic techniques and suggests future directions of the field.

The characterization of synthetic polymers and complex oligomeric mixtures by a combination of different mass spectrometry (MS) techniques is the main topic of this dissertation. Ion mobility (IM) separation and/or tandem mass spectrometry (MS2) were interfaced with single stage mass spectrometry for the fast, complete, precise and accurate characterization of different polymers, biopolymers, and biodegradation products. Additionally, the development of a mass spectrometry protocol for the quantitation of proteins adsorbed on different polymer surfaces was accomplished in this dissertation. Over the passed years, synthetic routes for the creation of PEGs have been modified by the elimination of organic catalysts and solvents and the application of green chemistry for the generation of new polymers. In Chapter 4 of this dissertation, MS and MS2 were employed, as the main analytical techniques, for the structural elucidation of enzyme-catalyzed, functionalized PEG and tetraethylene glycol (TEG) biomaterials. The samples analyzed were synthesized by two different processes, transesterification and Michael addition reactions, both of them using CALB as the catalyst. In Chapter 5 of this dissertation, polylactide was degraded using Proteinase K and its biodegradation products were analyzed by MS and MS2. Elucidation of its degradation products is important to the biomedical community; knowledge of these products helps to see any toxicity problems with the use of this polymer. The MS and MS2 results showed that the degradation products are short polylactide chains, down to the monomer. No other, potentially dangerous organics were detected. In the following chapter of this dissertation (Chapter 6), the adsorption of three model proteins onto two different surfaces was evaluated over a pH range. The results were explained on terms of polymer chemistry, surface morphology, proteins' isoelectricpoints and molecular dimensions. Finally, Chapter 7 reports how derivatization, degradation, or chromatographic separation can be avoided for the analysis of complex systems, if multidimensional mass spectrometry methods combining ion mobility separation and different ionization techniques are employed. Using this new approach complex poly([alpha]-peptoid) samples were characterized. The results showed that the main product in the system contained the N-heterocyclic carbene (NHC) moiety that served as ring-opening polymerization catalyst. Furthermore, it was demonstrated that elimination of the NHC segment leads to cyclic poly([alpha]-peptoid)s that have very similar conformations with comparably sized polypeptides.

Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry Detailed resource presenting the capabilities of MALDI mass spectrometry (MS) to industrially and environmentally significant areas in the biosciences Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry fulfills a need to bring the key analytical technique of MALDI mass spectrometric analysis into routine practice by specialists and non-specialists, and technicians. It informs and educates established researchers on the development of techniques as applied to industrially significant areas within the biosciences. Throughout the text, the reader is presented with recognized and emerging techniques of this powerful and continually advancing field of analytical science to key areas of importance. While many scientific papers are reporting new applications of MS-based analysis in specific foci, this book is unique in that it draws together an incredibly diverse range of applications that are pushing the boundaries of MS across the broad field of biosciences. Contributed to by recognized experts in the field of MALDI MS who have been key players in promoting the advancement and dissemination of authoritative information in this field, Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry covers sample topics such as: Oil microbiology, marine and freshwater ecosystems, agricultural and food microbiology, and industrial waste microbiology Bioremediation and landfill sites microbiology, microbiology of inhospitable sites (e.g. Arctic and Antarctic, and alkaline and acidic sites, and hot temperatures) Veterinary, poultry and animals, viral applications of MS, and antibiotic resistance using tandem MS methods Recent developments which are set to transform the use of MS from its success in clinical microbiology to a wide range of commercial and environmental uses Bridging the gap between measurement and key applications, this text is an ideal resource for industrial and environmental analytical scientists, including technologists in the food industry, pharmaceuticals, and agriculture, as well as biomedical scientists, researchers, clinicians and academics and scientists in bio-resource centers.

Tandem Mass Spectrometry - Molecular Characterization presents a comprehensive coverage of theory, instrumentation and description of experimental strategies and MS/MS data interpretation for the structural characterization of relevant molecular compounds. The areas covered include the analysis of drugs, metabolites, carbohydrates and protein post-translational modifications. The book series in Tandem Mass Spectrometry serves multiple groups of audiences; professional (academic and industry), graduate students and general readers interested in the use of modern mass spectrometry in solving critical questions of chemical and biological sciences.

Second Edition provides up-to-the-minute discussions on the application of mass spectrometry to the biological sciences. Shows how and why experiments are performed and furnishes details to facilitate duplication of results.

Leading practitioners describe in detail advanced methods of mass spectrometry used in structural characterization of biomacromolecules of both natural and recombinant origin. They demonstrate by example how these methodologies can solve a wide array of real-world problems in protein biochemistry, immunology, and glycobiology, as well as for human bacterial pathogens, lipids, and nucleic acids. The book offers a unique opportunity to learn these techniques that are revolutionizing the field. Its authoritative assessment in the context of how to solve important and challenging problems in bioscience and medicine ensures a competitive advantage for today's researchers.