In MALDI, for laser fluences below the saturation point the ion yield per shot follows a cubic dependence on the irradiated area, leading to a conclusion that smaller spots produce overall less ions and therefore are less viable. However, Qiao et al. showed that by decreasing the laser spot size it is possible to raise the saturation point, and thus increase the ion yield per unit area, also known as sensitivity. Here we explore laser spots below 10 micrometer diameter to determine whether they offer any practical advantage. We show that sensitivity is greater for a flat-top 3-4 micrometer spot than for a 10 micrometer spot. The sensitivity is greater for a Gaussian-like 3-5 micrometer spot than for flat-top 5-25 micrometer spots. We also report for the first time sensitivity versus theoretical fluence profile for a Gaussian-like beam focused to a spot of 3-5 micrometer.

A major driving force for development of new catalyst systems is the need for more efficient synthesis of chemical compounds essential to modern life. Catalysts having superior performance offer significant environmental and economic advantages, but their discovery is not trivial. Well-defined, homogeneous catalysts can offer unparalleled understanding of ligand effects, which proves invaluable in directing redesign strategies. This thesis work focuses on the design of ruthenium complexes for applications in dinitrogen activation and olefin metathesis. The complexes developed create new directions in small-molecule activation and asymmetric catalysis by late-metal complexes. Also examined are the dual challenges, ubiquitous in catalysis, of adequate interrogation of catalyst structure and performance. Insight into both is essential to enable correlation of ligand properties with catalyst activity and/or selectivity. Improved methods for accelerated assessment of catalyst performance are described, which expand high-throughput catalyst screening to encompass parallel acquisition of kinetic data. A final aspect focuses on direct examination of metal complexes, both as isolated species, and under catalytic conditions. Applications of charge-transfer MALDI mass spectrometry to structural elucidation in organometallic chemistry is described, and the technique is employed to gain insight into catalyst decomposition pathways under operating conditions.

Biomarker validation remains one of the most important constraints to development of new clinical diagnostic assays. To address this challenge, an immuno-mass spectrometric assay known as SISCAPA has been developed for quantitation of protein biomarkers in human blood. The SISCAPA assay overcomes the sensitivity barrier facing most mass spectrometric approaches by utilizing high affinity antibodies for enrichment of specific surrogate peptide analytes from complex mixtures such as trypsin-digested human plasma. However, several technological barriers remain before the SISCAPA technology gains widespread use for biomarker validation. Improvements are required in areas such as selection of high affinity anti-peptide antibodies, peptide detection sensitivity and increasing sample throughput to allow biomarker validation on large sample sets. The work presented in this dissertation describes the development of new methods for antibody selection and for high-throughput application of SISCAPA technology to biomarker measurement in human plasma. Specifically, two technological developments are described: 1) an assay called MiSCREEN was developed, which allows high-throughput screening of anti-peptide antibodies, enabling selection of high affinity reagents for de novo SISCAPA assays and 2) a liquid chromatography (LC)-free SISCAPA assay was developed that enables quantitation of surrogate peptides using both MALDI-TOF and RapidFire/MS platforms. Taken together, these technological advances provide a meaningful solution to the biomarker validation dilemma and allow a unified system for biomarker qualification, verification, validation and development of clinical assays for diagnosis and monitoring of a variety of diseases. To demonstrate the utility of the unified SISCAPA system for biomarker measurement, an assay was developed for protein C inhibitor (PCI) as a marker for prediction of biochemical recurrence in prostate cancer patients. The PCI-specific analyte was shown to predict biochemical recurrence of prostate cancer after radiation/hormone treatment. Early stage detection of recurrence was achieved, when compared to the ‘gold standard’ marker for prostate cancer, prostate specific antigen (PSA). Two-dimensional gel electrophoresis studies on PCI, revealed unique protein spots in a serum sample from a biochemically recurrent patient. Studying such alterations at the protein level may enable understanding of the molecular mechanisms by which PCI is involved in prostate cancer progression. / Graduate

The human brain (lat. cerebrum) is the most complex and heterogeneous organ in the human body. It is involved in a great number of body functions like movement, touch sensing, vision, hearing, smelling, hormone regulation and many more. In no other organ, the molecular communication mechanisms between different cells are so poorly understood. Due to the extensive diversity of processes that are controlled by the brain, diseases and injuries of the nervous system affect the human body significantly. Because of the immense complexity of the brain, the molecular mechanisms underlying the pathology of the diseases remain largely unknown. Hence, there is an urgent need for the development of new analytical strategies in order to investigate these conditions on a molecular level. Here, a central focus lies in the study of protein and peptide expression profiles, which can provide an insight in ongoing molecular mechanisms underlying the pathophysiology of the diseases. A powerful approach for studying proteins and peptide dynamics is mass spectrometry based proteomics, which is defined as the comprehensive study of all proteins expressed in a biological matrix at a certain point of time. The central objective of this thesis was to develop and employ different mass spectrometric techniques to study protein and peptide dynamics in the central nervous system in different neurological diseases. The individual studies comprise different aspects of proteome research. The first two studies included clinical proteomic applications for investigating protein dynamics in traumatic brain injury and amyotrophic lateral sclerosis. A further study was focused on method development for MS analysis of intact neural cells. The final three projects described in this thesis comprised MS based protein and peptide imaging in brain and spinal cord tissue samples. Here, the aim was to elucidate topological changes in protein expression in ALS as well as neuropeptide alterations in distinct brain structures in L-DOPA induced dyskinesia (LID) in Parkinson’s disease. / Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 713

Objectives: Intact cell peptidome profiling (ICPP) with MALDI-ToF Mass-Spectrometry holds promise as a non invasive method to detect head and neck squamous cell carcinoma (HNSCC) objectively, which may improve the early diagnosis of oral cancer tremendously. The present study was designed to discriminate between tumour samples and non-cancer controls (healthy mucosa and oral lesions) by analysing complete spectral patterns of intact cells using MALDI-ToF MS. Material and Methods: In the first step, a data base consisting of 26 patients suffering from HNSCC was established by taking brush biopsy samples of the diseased area and of the healthy buccal mucosa of the respective contralateral area. After performing MALDI-ToF MS on these samples, classification analysis was used as a basis for further classification of the blind study composed of additional 26 samples including HNSCC, oral lesions and healthy mucosa. Results: By analyzing spectral patterns of the blind study, all cancerous lesions were defined accurately. One incorrect evaluation (false positive) occurred in the lesion cohort, leading to a sensitivity of 100%, a specificity of 93% and an overall accuracy of 96.5%. Conclusion: ICPP using MALDI-ToF MS is able to distinguish between healthy and cancerous mucosa and between oral lesions and oral cancer with excellent sensitivity and specificity, which may lead to a more impartial early diagnosis of HNSCC.

Stuttgart, Univ., Diss., 2008.

The aim of the study was to evaluate the total viable count and detects each microorganism by the use of mass spectroscopy. In the period of June to December 2017 35 samples of pasteurized milk from two vending machines (Hodkovice, Suchdol) were tested. For comparison samples were divided to warmer season (June-Septemeber) and colder season (October-December) sampling. The total amount of microorganism was determined in each sample of milk and total viable count was estimated by the use of mass spectroscopy MALDI-TOF. The total viable count in the tested pasteurized milk were from 3,27 log KTJ/ml up to 7,35 log KTJ/ml. The mass spectroscopy detected 210 microorganisms belonging to 20 families of gram-positive and gram-negative bacteria and one species of eukaryot organism. The most often identified species belong the Enterobacteriaceae family.

Submitted by MARCEL PRATAVIEIRA null (marcelprata93@hotmail.com) on 2016-03-07T15:52:49Z No. of bitstreams: 1 Dissertação - Marcel Pratavieira - 2016.pdf: 8130455 bytes, checksum: a459e73ed4ef0757431f12802bc7f15b (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-03-07T19:51:13Z (GMT) No. of bitstreams: 1 pratavieira_m_me_rcla.pdf: 8130455 bytes, checksum: a459e73ed4ef0757431f12802bc7f15b (MD5) / Made available in DSpace on 2016-03-07T19:51:13Z (GMT). No. of bitstreams: 1 pratavieira_m_me_rcla.pdf: 8130455 bytes, checksum: a459e73ed4ef0757431f12802bc7f15b (MD5) Previous issue date: 2016-02-23 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / As abelhas têm sido utilizadas como modelos robustos e influentes para o estudo de memória e aprendizagem, contribuindo para o melhor entendimento das bases da cognição. Nesse contexto, diferentes metabólitos foram caracterizados por desempenharem funções distintas no processo de aprendizagem e formação de memória em insetos. Considerando que pouco se sabe sobre os metabólitos em relação ao desenvolvimento das habilidades cognitivas em A. mellifera, ou mesmo em relação aos comportamentos reflexos (condicionados e/ou não condicionados), o presente estudo teve como objetivo a análise metabolômica do cérebro de abelhas submetidas ao ensaio comportamental de reflexo de extensão de probóscide (REP). Para isto, foi padronizada a técnica de análise metabolômica com o uso do sistema LC-ESI- MS e MSn, construindo-se inicialmente uma biblioteca de compostos característicos de cérebro de abelhas (neurotransmissores, aminoácidos livres, poliaminas, nucleotídeos, nucleosídeos, ácidos orgânicos, etc). Nesta primeira abordagem, dentre os 112 compostos da biblioteca, 48 foram identificados e quantificados; alguns destes compostos foram únicos para o grupo controle (cadaverina, espermina, glicose, uracila e n-acetil-L-glutamato 5-semialdeido), enquanto que outros foram únicos para o grupo REP (fenilalanina, betaína, espermidina, serina e creatina). Dentre os compostos identificados em ambos os grupos, apenas 5 compostos apresentaram diferenças quantitativas estatisticamente significantes (arginina, asparagina, guanosina monofosfato, putrescina e 4-guanitinobutanoato). Visando o estudo dos perfis metabólicos regionais (em cada região do cérebro), foi também padronizado o protocolo experimental utilizando-se a estratégia MALDI Spectral Imaging e o desenvolvimento de um método semi-quantitativo de metabólitos. Esta estratégia permitiu o mapeamento e o estudo da distribuição espacial dos metabólitos identificados em cortes de cérebro de abelhas, bem como uma melhor compreensão da distribuição dessas moléculas nas diferentes estruturas do cérebro e sua correlação com o comportamento ensaiado. As duas estratégias aplicadas mostraram-se complementares e fundamentais para a compreensão da cognição em abelhas. De modo geral, o ensaio de REP parece estimular intensa atividade cerebral, alto gasto energético, intensa sinalização química e a ativação de algumas cascatas metabólicas específicas, tais como a rota metabólica da prolina e arginina. Nos indivíduos do grupo REP a arginina provavelmente foi catabolizada nas sínteses de creatina, 4-guanidinobutanoato, putrescina e espermidina. Esses processos bioquímicos provavelmente foram importantes para coordenar o reconhecimento da molécula de sacarose, e associar esse odor com um comportamento reflexo para a extensão da probóscide (estímulo não condicionado). / The honeybee Apis mellifera has long served as an invertebrate model organism for learning and memory research, contributing to a better understanding of cognition bases. In this context, different metabolites (especially neurotransmitters) were characterized by play distinct roles in learning process and in memory formation in insects. Whereas little is known about the metabolites in relation to the development of cognitive skills in A. mellifera, the present study aims to perform a metabolomic analysis of the honeybee brains submitted to the behavioral test of proboscis extension reflex (PER). For this, has been standardized a metabolomic analysis technique through the use of LC-ESI-MS and MSn system. Initially a low molecular weight compounds library was created, containing characteristic compounds of bee brain (neurotransmitters, free amino acids, polyamines, nucleotides, nucleosides, organic acids, etc.). In this first approach, from the library of 112 compounds, 48 compounds were identified and quantified; some of these compounds were only identified in the control group (cadaverine, spermine, glucose, uracil and N-acetyl-L-glutamate 5- semialdehyde), while others were only identified in PER group (phenylalanine, betaine, spermidine, serine and creatine). Among the compounds identified in both groups, only five compounds showed statistically significant differences in quantitative results (arginine, asparagine, guanosine monophosphate, putrescine and 4-guanidinebutanoate). In order to study the metabolic profiles by regions (within each brain region) it was also standardized an experimental protocol using a novel semi-quantitative method of MALDI Spectral Imaging strategy. This strategy allowed the study and the mapping of the spatial distribution of metabolites identified in honeybee brain sections, as well as a better understanding of the distribution of molecules in the different brain structures and their correlation with the behavior tested. Both strategies applied proved to be complementary and essential to the understanding of cognition in bees. Overall, in this study the PER test seems to stimulate intense brain activity, high energy expenditure, intense chemical signaling and activation of some specific metabolic pathways, such the arginine and proline metabolic pathway. In individuals of PER group arginine was probably catabolized in the synthesis of creatine, 4-guanidinobutanoato, putrescine and spermidine. This biochemical process were probably important to coordinate the recognition of sucrose molecule and associate this odor with a reflex behavior for the proboscis extension (unconditioned stimulus). / FAPESP: 2014/05376-1

abstract: Bacteria of the Legionella genus are a water-borne pathogen of increasing concern due to being responsible for more annual drinking water related disease outbreaks in the United States than all other microbes combined. Unfortunately, the development of public health policies concerning Legionella has impeded by several key factors, including a paucity of data on their interactions and growth requirements in water distribution networks, a poor understanding of potential transmission sources for legionellosis, and limitations in current methodology for the characterization of these pathogens. To address these issues, a variety of research approaches were taken. By measuring Legionella survival in tap water, association in pipe material biofilms, population dynamics in a model distribution system, and occurrence in drinking water distribution system biofilms, key aspects of Legionella ecology in drinking water systems were revealed. Through a series of experiments qualitatively and quantitatively examining the growth of Legionella via nutrients obtained from several water sources, environmental nutritional requirements and capability for growth in the absence of host organisms were demonstrated. An examination of automobile windshield washer fluid as a possible source of legionellosis transmission revealed Legionella survival in certain windshield washer fluids, growth within washer fluid reservoirs, high levels and frequency of contamination in washer fluid reservoirs, and the presence of viable cells in washer fluid spray, suggesting the potential for exposure to Legionella from this novel source. After performing a systematic and quantitative analysis of methodology optimization for the analysis of Legionella cells via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, several strains of this microbe isolated from separated and varied environmental water sampling sites were distinctly typed, demonstrating a potential application of this technology for the characterization of Legionella. The results from this study provide novel insight and methodology relevant to the development of programs for the monitoring and treatment of Legionella in drinking water systems. / Dissertation/Thesis / Doctoral Dissertation Microbiology 2014

Mon travail de thèse a consisté à poursuivre le développement et l’application des matrices bithiophéniques spécifique aux alcaloïdes. Après l’optimisation d’un protocole efficace d’analyse, adapté à l’objectif de l’étude, la mise au point d’une méthode de dosage des alcaloïdes par MALDI dans des extraits végétaux et sans prétraitement préalable a été étudiée. Cette méthode a pu être validée en étudiant des alcaloïdes existant dans différents extraits des plantes toxiques. Ensuite, la synthèse et l’évaluation de nouveaux composés bithiophéniques ont été présentés de manière à évaluer les facteurs favorisant l’interaction avec les alcaloïdes. Ultérieurement, cinq nouvelles matrices intéressantes furent l’objet d’une étude plus détaillée. Sur la base des résultats obtenus, le dérivé fluoré F T3 s’avère le plus efficace. ll présente une meilleure sélectivité que la matrice courante CHCA vis-à-vis des alcaloïdes et plus performant pour analyser les alcaloïdes dans différents mélanges complexes tels que des extraits bruts de plantes, des insectes, et des solutions bio-actives commerciales (médicament et répulsif). À la fin, ces sont regroupés les résultats de l’étude des paramètres thermodynamiques de la matrice MT3P, ce qui permettra de proposer des hypothèses expliquant la sélectivité de la matrice bithiophéniques fonctionnalisée pour les alcaloïdes. / My thesis work consisted of pursuing the development and application of bithiophenic maldi matrices specific for alkaloids. After optimization of an efficient analysis protocol adapted to the objective of the study, a method for the determination of alkaloids in vegetable extracts by MALDI was developed. This method was validated by studying many alkaloids existing in extracts of different toxic plants. Subsequently, synthesis and evaluation of novel bithiophenic compounds were presented in order to evaluate the factors favoring the interaction with alkaloids. Then, five matrices among the molecules tested and having produced interesting results are chosen and were the subject of a more detailed study. On the basis of the results obtained, the fluorinated derivative PFPT3P proves to be the most effective molecules. It has a better selectivity with respect to alkaloids than the current matrix HCCA and performs better to analyze these metabolites in different complex mixtures such as crude extracts of plants,insects and commercial bioactive solutions (drug and repellent). At the end, the results of the study of the thermodynamic parameters of MT3P matrix are grouped. This will make possible to propose hypotheses explaining the selectivity of the functionalized bithiophene matrices for alkaloids.