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No description available.

No description available.

A Matrix-assisted Laser Desorption/Ionization (MALDI) – Ion Mobility (IM) – Surface-induced Dissociation (SID) – Time-of-Flight (TOF) instrument with three different collision source configurations was developed in order to improve the SID performance in high throughput peptide sequencing. The first version of the instrument was equipped with an angle resolved SID source in order to maximize the collection efficiency of the SID scattering ions. An orthogonal TOF was also implemented as the second MS stage in this instrument to increase mass resolution. The second version of the instrument was developed towards simplifying the coupled configuration of the IM, SID and TOF components by using a combined SID/TOF source with a confinement ring electrode as the collision target. The fragmentation efficiency of SID in this configuration was increased up to 50% due to the surface normal impact angle used as compared with the results from a previous experiment using 45 degree impact angle. The third version of the instrument was equipped with a dual-source/dual-detector TOF to facilitate high throughput tandem analysis of peptides through simultaneous separation, fragmentation and mass analysis, while retaining precursor ion identity in the same experimental sequence. A series of small organic molecules, model peptides and tryptic peptides from a protein digest were analyzed to demonstrate the utility of these new designs for enhanced SID performance and peptide sequencing capability. Finally, a new mobility drift cell using a periodic focusing mechanism has been designed and fabricated to replace the previous uniform field drift cell. Improvement in ion transmission has been observed in the periodic focusing drift cell instrument without sacrificing the mobility resolution.

A Matrix-assisted Laser Desorption/Ionization (MALDI) – Ion Mobility (IM) – Surface-induced Dissociation (SID) – Time-of-Flight (TOF) instrument with three different collision source configurations was developed in order to improve the SID performance in high throughput peptide sequencing. The first version of the instrument was equipped with an angle resolved SID source in order to maximize the collection efficiency of the SID scattering ions. An orthogonal TOF was also implemented as the second MS stage in this instrument to increase mass resolution. The second version of the instrument was developed towards simplifying the coupled configuration of the IM, SID and TOF components by using a combined SID/TOF source with a confinement ring electrode as the collision target. The fragmentation efficiency of SID in this configuration was increased up to 50% due to the surface normal impact angle used as compared with the results from a previous experiment using 45 degree impact angle. The third version of the instrument was equipped with a dual-source/dual-detector TOF to facilitate high throughput tandem analysis of peptides through simultaneous separation, fragmentation and mass analysis, while retaining precursor ion identity in the same experimental sequence. A series of small organic molecules, model peptides and tryptic peptides from a protein digest were analyzed to demonstrate the utility of these new designs for enhanced SID performance and peptide sequencing capability. Finally, a new mobility drift cell using a periodic focusing mechanism has been designed and fabricated to replace the previous uniform field drift cell. Improvement in ion transmission has been observed in the periodic focusing drift cell instrument without sacrificing the mobility resolution.

This study focuses on the application of 193-nm excimer laser (ArF) photodissociation to tandem time-of-flight mass spectrometry. In particular, it focuses on identifying the optimal experimental conditions for peptide sequencing and applying the technology to interesting systems. The early focus is on optimizing the sample preparation conditions that define the initial internal energy state of MALDI-produced ions. Subsequent chapters investigate the effect of changing photodissociation laser conditions and define conditions under which the information content of the spectrum is maximized. Later chapters compare the photodissociation experiment to technologies that represent the current state of the art in tandem mass spectrometry, illustrating both the advantages and shortcoming of photodissociation TOF methodology. Finally, we apply photodissociation to the study of interesting systems of biological relevance, including (1) peptides derived from enzymatic digestion, (2) post-translationally modified peptides, and (3) peptide-transition metal ion complexes. In the final chapter we consider the analytical implications of the work as a whole and comment on the analytical viability of the methodology and look forward to new directions for the experiments.

This study focuses on the application of 193-nm excimer laser (ArF) photodissociation to tandem time-of-flight mass spectrometry. In particular, it focuses on identifying the optimal experimental conditions for peptide sequencing and applying the technology to interesting systems. The early focus is on optimizing the sample preparation conditions that define the initial internal energy state of MALDI-produced ions. Subsequent chapters investigate the effect of changing photodissociation laser conditions and define conditions under which the information content of the spectrum is maximized. Later chapters compare the photodissociation experiment to technologies that represent the current state of the art in tandem mass spectrometry, illustrating both the advantages and shortcoming of photodissociation TOF methodology. Finally, we apply photodissociation to the study of interesting systems of biological relevance, including (1) peptides derived from enzymatic digestion, (2) post-translationally modified peptides, and (3) peptide-transition metal ion complexes. In the final chapter we consider the analytical implications of the work as a whole and comment on the analytical viability of the methodology and look forward to new directions for the experiments.

The utilization of click chemistry to perform inter- and intramolecular ligation on DNA has become ubiquitous in the literature. Advances in copper (I) stabilizing ligands that prevent DNA degradation via redox pathways have provided nucleic acid researchers access to the efficiency and quantitative nature of the click reaction. The majority of ligation procedures in the literature are performed in solution after DNA assembly and modification with alkyne reporter groups. However, without specialty alkyne reagents that can be sequentially and selectively deprotected, the solution phase method requires that the click reaction be performed on all DNA-attached alkynes simultaneously. Therefore, the variability of the azide reagent is limited to a singular R group. However, performing the click reaction on DNA during synthetic elongation (immediately after each alkyne installation) allows for the possibility of performing multiple click reactions with variable azide reagents. Unfortunately, most solid phase click procedures require long reaction times or the utilization of microwave irradiation to accelerate the reaction. The development of methods for the ligation of azides to alkynes without the use of microwave irradiation on solid phase is potentially very useful. Herein, we report a simple, efficient, and robust solid phase synthetic method for the ligation of azido-diamondoids to the alkyne-modified phosphate backbone of DNA with click chemistry using [Cu(CH₃CN)₄]PF₆ without stabilizing ligand. Interestingly, it was found that as the size of diamondoid increased, a corresponding increase in melting temperature of hybridized duplexes was observed. The developed method has the potential to complement existing DNA ligation procedures for applications in biotechnology and diagnostics. Interest in peptides incorporating boronic acid moieties is increasing due to their potential as therapeutics/diagnostics for a variety of diseases such as cancer. The utility of peptide boronic acids may be expanded with access to vast libraries that can be deconvoluted rapidly and economically. Unfortunately, current detection protocols using mass spectrometry are laborious and confounded by boronic acid trimerization, which requires time consuming analysis of dehydration products. These issues are exacerbated when the peptide sequence is unknown, as with de novo sequencing, and especially when multiple boronic acid moieties are present. Thus, a rapid, reliable and simple method for peptide identification is of utmost importance. Herein, we report the identification and sequencing of linear and branched peptide boronic acids containing up to five boronic acid groups by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Protocols for preparation of pinacol boronic esters were adapted for efficient MALDI analysis of peptides. Additionally, a novel peptide boronic acid detection strategy was developed in which 2,5-dihydroxybenzoic acid (DHB) served as both matrix and derivatizing agent in a convenient, in situ, on-plate esterification. Finally, we demonstrate that DHB-modified peptide boronic acids from a single bead can be analyzed by MALDI-MSMS analysis, validating our approach for the identification and sequencing of branched peptide boronic acid libraries. It is well known that RNA ligands incorporating basic and intercalating moieties display high RNA affinity. Unfortunately, these ligands are also often plagued by promiscuous binding to off-target substrates. Due to the potential utility of RNA ligands in biology and medicine, it is imperative to elucidate RNA binders which display high specificity as well as affinity. Boronic acid peptides promise unique RNA binding motifs through the interaction between the empty p-orbital of boron and the 2'-hydroxyl group of RNA. Herein, we describe the incorporation of lysine and phenylalanine boronic acid analogues into a branched peptide combinatorial library in an effort to impart increased selectivity towards the HIV-1 Rev Response Element (RRE). We were able to easily select and deconvolute 6 resulting "hit" peptides from 65,536 unique library members by high throughput screening and de novo sequencing. Although we were unable to evaluate peptide selectivity towards RRE due to general insolubility in aqueous media, we demonstrated the efficient deconvolution of a branched peptide library that incorporates boronic acids. / Ph. D.

Spiders produce multiple types of silk that exhibit diverse mechanical properties and biological functions. Most molecular studies of spider silk have focused on fibroins from dragline silk and capture silk, two important silk types involved in the survival of the spider. In this study we have focused on the characterization of egg case silk, a third silk fiber produced by the black widow spider, Latrodectus hesperus , whose DNA coding sequences have not been reported. Based upon solubility differences in 8 M guanidine hydrochloride, it is demonstrated by sodium dodecyl sulfate polyacrylamide gel electrophoresis and silver staining that the egg case silk is relatively complex at the molecular level, containing a large number of proteins with differing molecular weights. Protein components of egg case silk with a size about 100 kDa were obtained by a solubilization time course study, which indicates these proteins are likely to be embedded in the silk filament. Peptides in these 100 kDa proteins were released by tryptic in-gel and in-solution digestion. The peptides were sequenced using a MALDI tandem TOF mass spectrometer. Some of the de novo sequences were confirmed using a linear ion trap mass spectrometer equipped with a nanospray ion source. Combining the peptide sequences obtained, reverse genetics was employed to trace silk genes encoding proteins containing these de novo peptides. Three silk protein coding sequences were successfully discovered, which encode silk proteins named 3B, T1 and ECSP-1, respectively. 3B and T1 show the standard fibroin protein pattern. Amino acid repeat patterns were observed in these two silk clones. But the amino acid compositions of 3B and T1 show differences with the total amino acid composition of egg case silk, and also, the peptide sequences cannot be found in the primary amino acid sequences of 3B and T1. ECSP-1 protein represents one of the egg case silk proteins with a size of about 100 kDa. A number of peptide sequences obtained by mass spectrometric de novo sequencing were successfully located in ECSP-1's primary amino acid sequence. Sequence analysis demonstrates ECSP-1 represents a new class of silk proteins, with fibroin-like properties. The expression pattern of ecsp-1 is largely restricted to the tubuliform gland inside of the L. hesperus spider, with lower levels detected in the major and minor ampullate glands, which also confirms the identity of ECSP-1. It is also demonstrated that ECSP-1 assembles into higher aggregate structures through the formation of disulfide bonds. Peptide sequences from silk proteins from the Tarantula spider Grammostola rosea were also obtained. These sequences will be beneficial in obtaining genes encoding the silk from this spider species.

Este projeto teve como objetivo principal realizar um estudo proteômico diferencial aplicado às amostras de casca do caule de plantas cítricas sadias e infectadas pela morte súbita dos citros. Subsequentemente, a identificação de proteínas diferentemente expressas será de grande importância, uma vez que estas poderão servir não somente como candidatos a biomarcadores para a doenças, mas também auxiliarão no melhor compreensão da doença. À partir dos géis bidimensionais obtidos para amostras de porta-enxerto (limão cravo e limão volkameriano) e copa (laranja valência) foi possível verificar que existem dois conjuntos de proteínas sensivelmente sub-expressas em plantas doentes. Um desses conjuntos, constituído por 13 spots, apresenta valores de pI entre 4,5 e 5,2 e MM aproximadamente igual a 30 kDa. No outro conjunto, esse composto por 9 spots, valores de pI variando entre 6,1 e 9,6 e MM em torno de 20 kDa são observados. Por meio das técnicas de MALDI-TOF-TOF e LC-ESI-MS/MS, inúmeros spots foram inequivocamente identificados, incluindo os spots correspondentes às regiões diferentemente expressas. Os 13 spots correspondentes a região com valores de pI entre 4,5 e 5,2 e MM ~ 30 kDa foram todos identificados como sendo constituídos por três isoformas de quitinases. Por outro lado, os spots referentes a região com pI entre 6,1 e 9,6 e MM ~ 20 kDa foram identificados como proteína putativa similar a miraculina 2. A justificativa para o fato de diversos spots terem recebido a mesma identificação é atribuída às inúmeras e diferentes modificações pós-traducionais, comumente verificadas em plantas. Entretando, o aspecto mais relevante relacionado a essas identificações é o fato de que ambas as proteínas são conhecidas marcadoras de resistência de defesa em plantas e assim sendo, a priori, espera-se-ia que estivessem sendo super expressas em plantas doentes. Porém, um comportamento inverso foi verificado, o que reforça as evidências de que as quitinases não agem apenas como marcadores de defesa em plantas, possuindo assim outras funções. Além disso, no total, outras 19 proteínas puderam ser identificadas. / The main goal of this project was to perform a differential proteomic analysis of bark tissues of healthy and CSD (citrus sudden death)- affected citrus plants. Subsequently, the identification of differently expressed proteins will be of great importance since they can be used not only as biomarkers for CSD but also as basic information for improving the knowledge about the disease. According to the 2D gels, obtained for bark tissues of both rootstock (rangpur lime and volkamerian lemon) and scion samples, there are two sets of proteins remarkably under expressed in CSD-affected samples. One of these sets is composed by 13 proteins, which presents MW around 30 kDa and pI ranging from 4.5 to 5.2. The other set includes 9 proteins with pI ranging from 6.1 to 9.6 and MW around 20 kDa. By using two mass spectrometry approaches (MALDI-TOF-TOF and LC-ESI-MS/MS), several proteins have been unequivocally identified, including the differentially expressed ones. Thirteen spots have been identified as a mixture of three chitinase isoforms. These spots are relative to the region with pI ranging from 4.5 to 5.2 and MW ~ 30 kDa. On the other hand, the 9 spots referent to the region with MW ~ 20 kDa and pI between 6.1 and 9.6 were identified as putative miraculin-like 2 protein. Several spots have been identified as the same protein most probably due to the occurrence of different post-translational modifications. The most valuable point regarding the identity of these proteins is the fact that they are well-known plant pathogen-related proteins and then they should be over expressed in affected plants. However, the opposite behavior was verified, which may indicate that chitinases and putative miraculin-like 2 protein perform unknown functions, besides the established ones. In addition, other 19 constitutive proteins have been identified.