Mass spectrometry (MS) is used in peptidomics to find novel endogenous peptides that may lead to the discovery of new biomarkers. Identifying endogenous peptides from MS is a time-consuming and challenging task; storing identified peptides in a database and comparing them against unknown peptides from other MS runs avoids re-doing identification. MS produce large amounts of data, making interpretation difficult. A platform for helping the identification of endogenous peptides was developed in this project, including a library application for storing peptide data. Machine learning methods were also used to try to find patterns in peptide abundance that could be correlated to a specific sample or treatment type, which can help focus the identification work on peptides of high interest.

<p>The sequencing of genomes has caused a growing demand for functional analysis of gene products. This research field named proteomics is derived from the term proteome, which by analogy to genome is defined as all proteins expressed by a cell or a tissue. Proteomics is however methodologically restricted to the analysis of proteins with higher molecular weights. The development of a technology which includes peptides with low molecular weight and small proteins is needed, since peptides play a central role in many biological processes. </p><p>To study endogenous peptides and hormones, the peptidome, an improved method comprising rapid deactivation in combination with nano-flow liquid chromatography (LC) and mass spectrometry (MS) was developed. The method has been used to investigate endogenous peptides in brains of mouse and rat. Several novel peptides have been discovered together with known neuropeptides. </p><p>To elucidate the <i>post mortem</i> time influence on peptides and proteins, a time course study was performed using peptidomics and proteomics technologies. Already after three minutes a substantial amount of protein fragments emerged in the peptidomics study and some endogenous peptides were drastically reduced with increasing <i>post mortem</i> time. Of about 1500 proteins investigated, 53 were found to be significantly changed at 10 minutes <i>post mortem</i> as compared to control. Moreover, using western blot the level of MAPK phosphorylation was shown to decrease by 95% in the 10 minutes <i>post mortem </i>sample. </p><p>A database, SwePep (a repository of endogenous peptides, hormones and small proteins), was constructed to facilitate identification using MS. The database also contains additional information concerning the peptides such as physical properties. A method for analysis of LC-MS data, including scanning for, and further profiling of, biologically significant peptides was developed. We show that peptides present in different amounts in groups of samples can be automatically detected.</p><p>The peptidome approach was used to investigate levels of peptides in two animal models of Parkinson’s disease. PEP-19, was found to be significantly decreased in the striatum of MPTP lesioned parkinsonian mice. The localization and expression was further investigated by imaging MALDI MS and by <i>in situ</i> hybridization. The brain peptidome of reserpine treated mice was investigated and displayed a number of significantly altered peptides. This thesis demonstrates that the peptidomics approach allows for the study of complex biochemical processes.</p>

The sequencing of genomes has caused a growing demand for functional analysis of gene products. This research field named proteomics is derived from the term proteome, which by analogy to genome is defined as all proteins expressed by a cell or a tissue. Proteomics is however methodologically restricted to the analysis of proteins with higher molecular weights. The development of a technology which includes peptides with low molecular weight and small proteins is needed, since peptides play a central role in many biological processes. To study endogenous peptides and hormones, the peptidome, an improved method comprising rapid deactivation in combination with nano-flow liquid chromatography (LC) and mass spectrometry (MS) was developed. The method has been used to investigate endogenous peptides in brains of mouse and rat. Several novel peptides have been discovered together with known neuropeptides. To elucidate the post mortem time influence on peptides and proteins, a time course study was performed using peptidomics and proteomics technologies. Already after three minutes a substantial amount of protein fragments emerged in the peptidomics study and some endogenous peptides were drastically reduced with increasing post mortem time. Of about 1500 proteins investigated, 53 were found to be significantly changed at 10 minutes post mortem as compared to control. Moreover, using western blot the level of MAPK phosphorylation was shown to decrease by 95% in the 10 minutes post mortem sample. A database, SwePep (a repository of endogenous peptides, hormones and small proteins), was constructed to facilitate identification using MS. The database also contains additional information concerning the peptides such as physical properties. A method for analysis of LC-MS data, including scanning for, and further profiling of, biologically significant peptides was developed. We show that peptides present in different amounts in groups of samples can be automatically detected. The peptidome approach was used to investigate levels of peptides in two animal models of Parkinson’s disease. PEP-19, was found to be significantly decreased in the striatum of MPTP lesioned parkinsonian mice. The localization and expression was further investigated by imaging MALDI MS and by in situ hybridization. The brain peptidome of reserpine treated mice was investigated and displayed a number of significantly altered peptides. This thesis demonstrates that the peptidomics approach allows for the study of complex biochemical processes.

The aim of the research was to find new potential biomarkers of preterm premature rupture of membranes. The amniotic fluid and fetal membranes peptidic composition was analyzed using a fully automated 2D liquid chromatographic system coupled to mass spectrometry. A comparison of peptidomes of amniotic fluid and amniochorionic membranes with preterm premature rupture and term intact membranes was performed. Ten proteins from amniotic fluid were identified as potential biomarkers for PPROM. The created map of amniotic fluid peptides and proteins depending on the gestational age is important for proteomics-based identification of biomarkers for fetal abnormalities and other pregnancy complications. / Mokslinio darbo metu siekta nustatyti potencialius priešlaikinio neišnešioto vaisiaus dangalų plyšimo biožymenis. Panaudojant dvidimensinę skysčių chromatografiją bei masių spektrometriją išanalizuota vaisiaus vandenų ir dangalų peptidinė sudėtis. Ištirti ir palyginti amniochorioninės membranos ir vaisiaus vandenų peptidai bei su jais siejami baltymai, kai prieš laiką plyšta neišnešioto vaisiaus dangalai arba vaisius išnešiojamas iki numatyto gimdymo termino ir dangalai išlieka sveiki. Išanalizavus skirtumus, nustatyti nauji galimi priešlaikinio neišnešioto vaisiaus dangalų plyšimo biožymenys.

O gênero Bothrops apresenta ampla distribuição pelo território brasileiro, sendo a espécie B. jararaca seu representante de maior importância médica na região sudeste. Análises genéticas e filogeográficas descrevem a existência de um grupo monofilético, denominado grupo Jararaca, que inclui, além da espécie B. jararaca, as espécies insulares B. alcatraz e B. insularis. A proximidade evolutiva entre estas espécies, cujo desenvolvimento se iniciou no Pleistoceno, e suas diferenças quanto à dieta, levantam subsídios para o entendimento de seus venenos e suas atividades biológicas. O objetivo deste estudo foi a caracterização dos componentes do veneno de B. alcatraz por diferentes metodologias analíticas com a finalidade de aprofundar o conhecimento sobre os venenos do gênero Bothrops e sobre a evolução dos venenos das espécies do grupo Jararaca. As abordagens analíticas utilizadas foram a avaliação do proteoma dos venenos do grupo Jararaca por eletroforese e identificação de proteínas por digestão com tripsina e análise por cromatografia líquida acoplada à espectrometria de massas (LC-MS/MS), análise do N-terminoma e do peptidoma do veneno de B. alcatraz por LC-MS/MS e análise da glicosilação dos venenos do grupo Jararaca pelo tratamento com glicosidases, cromatografia de afinidade à lectinas (concanavalin A, ConA; wheat germ agglutinin, WGA; peanut agglutininin, PNA) e caracterização do N-glicoma por MSn. Os perfis eletroforéticos unidimensionais, obtidos com e sem redução das proteínas, mostraram que o veneno de B. alcatraz difere dos venenos de B. jararaca (adultos e filhotes) e do veneno de B. insularis (adultos). O perfil eletroforético bidimensional do veneno de B. alcatraz corroborou estas diferenças e revelou que a coleta do veneno na presença ou ausência de inibidores de proteinases tem influência no número de spots visualizados. Os resultados da análise dos proteomas dos venenos do grupo Jararaca mostraram que não há diferenças qualitativas significantes entre eles, e que os três apresentam um padrão similar de distribuição das classes de toxinas. A análise quantitativa label free dos proteomas revelou algumas diferenças, indicando que o veneno de B. alcatraz apresenta maior conteúdo de metaloproteinses e fosfolipases A2, que os venenos de B. jararaca e B. insularis. A identificação do peptidoma do veneno de B. alcatraz mostrou diversas formas de peptídeos potenciadores de bradicinina, além de produtos de degradação de diferentes classes de toxinas. A avaliação da glicosilação das proteínas dos três venenos revelou que após a remoção das cadeias de N-glicanos e O-glicanos os perfis eletroforéticos se mostram mais parecidos. A identificação das proteínas do veneno de B. alcatraz que mostraram afinidade pelas lectinas revelou que a ConA interagiu com um número maior de componentes, seguida por WGA e PNA. As análises qualitativa e quantitativa do N-glicoma dos venenos do grupo Jararaca mostrou que os três venenos compartilham as mesmas estruturas de N-glicanos e em abundância relativa similar. Em conjunto, os resultados deste estudo indicaram que no grupo Jararaca, os proteomas dos venenos das espécies B. jararaca e B. insularis apresentam similaridade entre si, e se diferem do veneno de B. alcatraz, principalmente com relação ao grau de glicosilação de suas proteínas. / The Brothrops genus is largely distributed on the Brazilian territory, and B. jararaca is the species of most medical importance in the Southeastern region. Genetic and phylogeographic analyses describe the existence of a monophyletic group, named Jararaca group, which is composed of B. jararaca and of the insular species B. alcatraz and B. insularis. The close evolutionary relationship between these species, which started in the Pleistocene era, and their diet-related differences, are important aspects for the understanding of their venoms and biological activities. The aim of this study was to characterize the venom of B. alcatraz by different analytical methodologies, in order to advance the knowledge on the venoms of Bothrops genus and on the evolution of the venoms of species of the Jararaca group. The analytical approaches used in this study included the charactrization of the proteomes of the venoms of the Jararaca group by electrophoresis and protein identification by trypsin digestion and analysis by liquid chromatography coupled to mass spectrometry (LC-MS/MS), N-terminomic and peptidomic analyses of the venom of B. alcatraz by LC-MS/MS and glycosylation analyses of the venoms of the Jararaca group by treatment with glycosidases, affinity chromatography to lectins (concanavalin A, Con A; wheat germ agglutinin, WGA; peanut agglutininin, PNA) and characterization of the N-glicomes by MSn. The one-dimensional electrophoretic profiles were evaluated under reducing and non-reducing conditions and showed that the venom of B. alcatraz differs from B. jararaca (newborn and adult) and B. insularis (adult) venoms. The two-dimensional electrophoretic profile of B. alcatraz venom corroborated these differences and revealed that the milking of the venom in the presence or in the absence of proteinase inhibitors influences the number of spots visualized on the gel. The results of the analysis of venom proteomes of the Jararaca group showed no significant qualitative differences between them; moreover, the three venoms showed a similar pattern of distribution of toxins classes. However, the label free quantitative analysis of these proteomes revealed some differences, and indicated that the venom of B. alcatraz has a higher content metaloproteinses and phospholipase A2 than B. jararaca and B. insularis venoms. The identification of B. alcatraz venom peptidome showed various forms of bradykinin-potentiating peptides, as well as products of the degradation of different toxins classes. The assessment of the glycosylation level of proteins of the three venoms showed that after removal of N-glycan and O-glycan chains their electrophoretic profiles become more similar. The identification of B. alcatraz venom proteins that showed affinity for lectins indicated that ConA interacted with a larger number of components, followed by WGA and PNA. The qualitative and quantitative analysis of the N-glicome of the venoms of the Jararaca group showed that they share the same N-glycan structures, which were also found in similar relative abundance. Taken together, the results of this study indicate that in the Jararaca group, the venom proteomes of B. jararaca and B. insularis show similarity to each other and differ from the venom of B. alcatraz, especially with respect to the degree of protein glycosylation.

Made available in DSpace on 2014-06-11T19:30:55Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-02-25Bitstream added on 2014-06-13T18:41:08Z : No. of bitstreams: 1 baptistasaidemberg_nb_dr_rcla.pdf: 2299823 bytes, checksum: f0d4fcfb7ac2f2634065f5dff821690c (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Os peptídeos possuem um papel essencial para as funções fisiológicas de animais, plantas e de alguns microrganismos, e frequêntemente apresentam-se como candidatos a novas drogas na sua forma natural, servindo como modelos para o “desenho” de peptídeos modificados, para uma obtenção de perfis farmacológicos melhores. Neste contexto, os venenos das vespas sociais são interessantes sob o ponto de vista da pesquisa, uma vez que são ricos em peptídeos policatiônicos envolvidos com processos inflamatórios (lise de membranas, Desgranulação de mastócitos, quimiotaxia, entre outros processos), além de efeitos antibióticos contra bactérias Gram-positivas e Gram-negativas. Com base nisso, o objetivo deste trabalho foi realizar uma bioprospecção dos diferentes componentes peptídicos presentes nos venenos das vespas sociais Agelaia pallipes pallipes e Agelaia vicina, através da identificação e da caracterização estrutural e funcional dos componentes peptídicos mais abundantes destes venenos. Para isso, os venenos das vespas supracitadas foram extraidos em acetonitrila, fracionados por cromatografia de fase reversa e analisado por espectrometria de massas (ESI-MS e ESI-MSn). Todos os peptídeos caracterizados foram sintetizados manualmente por estratégia Fmoc, para a realização de ensaios farmacológicos e fisiológicos. Além de abrir novas vertentes de estudos estruturais e funcionais, o presente projeto alcançou os objetivos inicialmente almejados, identificando e caracterizando estruturalmente doze peptídeos presentes nos venenos das duas espécies de vespas. As denominações e atividades biológicas dessas moléculas foram: Protonectina apresentou-se lítico para hemáceas, degranulador de leucócitos quimiotático, induziu o fenômeno de hiperalgesia e foi edematogênico; o peptídeo Protonectina (1-4)-OH apresentou-se hemolítico para eritrócitos e desgranulador... / Peptides have an important role on physiologic functions of animals, plants and microorganisms. These natural peptides frequently are candidates for new drugs natural, and are used as models for the construction of modificated peptides in order to improve their pharmacological activities. From academic point of view, social wasp venoms are interesting once they are rich in policationic and polifunctional peptides that are involved with inflammatory processes (membrane lyses, mast cell degranulation, chemotaxis, and other processes), antimicrobial effects against Gram-positive and Gram-negative bacterias. Therefore, the main objective of this study was to bioprospect a diversity of peptidic compounds from the venoms of the neotropical social wasps Agelaia pallipes pallipes and Agelaia vicina through peptidomic analysis, identifying and characterizing these molecules structurally and functionally. For that, the venom from both wasps was extracted in MeCN 50% (v/v), analyzed and sequenced by ESI-MS, ESI-MSn. All characterized peptides were manually synthesized by Fmoc strategy and used for pharmacological and phisiological activities. This work has reached the initially poposed objectives by the indentification and functional characterization of twelve peptides from the social wasps venoms studied. Of these identified molecules, nine were isolated from the social wasp A. p. pallipes venom (Protonectin (1-4)-OH, Protonectin (1-5)-OH, Protonectin (1-6)-OH, Protonectin (7-12); Agelaia MP-I, Agelaia MP-II, Pallipin-I, Pallipin-II, and Pallipin-III), and from the venom of the social wasp A. vicina, four peptides were characterized (Protonectin (7-9)-OH, Protonectin, Protonectin (1-6), and Agelaia MP-I). These results show that the venom of both wasps are very similar to each other, probably due to the kinship of such species. Functionally, the peptide protonectin is lytic to erythrocytes... (Complete abstract click electronic access below)

Orientador: Mario Sergio Palma / Banca: Luiz Alberto Beraldo de Moraes / Banca: Dulce Helena Siqueira Silva / Banca: Everardo Magalhães Carneiro / Banca: Yara Cury / Resumo: Os peptídeos possuem um papel essencial para as funções fisiológicas de animais, plantas e de alguns microrganismos, e frequêntemente apresentam-se como candidatos a novas drogas na sua forma natural, servindo como modelos para o "desenho" de peptídeos modificados, para uma obtenção de perfis farmacológicos melhores. Neste contexto, os venenos das vespas sociais são interessantes sob o ponto de vista da pesquisa, uma vez que são ricos em peptídeos policatiônicos envolvidos com processos inflamatórios (lise de membranas, Desgranulação de mastócitos, quimiotaxia, entre outros processos), além de efeitos antibióticos contra bactérias Gram-positivas e Gram-negativas. Com base nisso, o objetivo deste trabalho foi realizar uma bioprospecção dos diferentes componentes peptídicos presentes nos venenos das vespas sociais Agelaia pallipes pallipes e Agelaia vicina, através da identificação e da caracterização estrutural e funcional dos componentes peptídicos mais abundantes destes venenos. Para isso, os venenos das vespas supracitadas foram extraidos em acetonitrila, fracionados por cromatografia de fase reversa e analisado por espectrometria de massas (ESI-MS e ESI-MSn). Todos os peptídeos caracterizados foram sintetizados manualmente por estratégia Fmoc, para a realização de ensaios farmacológicos e fisiológicos. Além de abrir novas vertentes de estudos estruturais e funcionais, o presente projeto alcançou os objetivos inicialmente almejados, identificando e caracterizando estruturalmente doze peptídeos presentes nos venenos das duas espécies de vespas. As denominações e atividades biológicas dessas moléculas foram: Protonectina apresentou-se lítico para hemáceas, degranulador de leucócitos quimiotático, induziu o fenômeno de hiperalgesia e foi edematogênico; o peptídeo Protonectina (1-4)-OH apresentou-se hemolítico para eritrócitos e desgranulador... (resumo completo, clicar acesso eletrônico abaixo) / Abstract: Peptides have an important role on physiologic functions of animals, plants and microorganisms. These natural peptides frequently are candidates for new drugs natural, and are used as models for the construction of modificated peptides in order to improve their pharmacological activities. From academic point of view, social wasp venoms are interesting once they are rich in policationic and polifunctional peptides that are involved with inflammatory processes (membrane lyses, mast cell degranulation, chemotaxis, and other processes), antimicrobial effects against Gram-positive and Gram-negative bacterias. Therefore, the main objective of this study was to bioprospect a diversity of peptidic compounds from the venoms of the neotropical social wasps Agelaia pallipes pallipes and Agelaia vicina through peptidomic analysis, identifying and characterizing these molecules structurally and functionally. For that, the venom from both wasps was extracted in MeCN 50% (v/v), analyzed and sequenced by ESI-MS, ESI-MSn. All characterized peptides were manually synthesized by Fmoc strategy and used for pharmacological and phisiological activities. This work has reached the initially poposed objectives by the indentification and functional characterization of twelve peptides from the social wasps venoms studied. Of these identified molecules, nine were isolated from the social wasp A. p. pallipes venom (Protonectin (1-4)-OH, Protonectin (1-5)-OH, Protonectin (1-6)-OH, Protonectin (7-12); Agelaia MP-I, Agelaia MP-II, Pallipin-I, Pallipin-II, and Pallipin-III), and from the venom of the social wasp A. vicina, four peptides were characterized (Protonectin (7-9)-OH, Protonectin, Protonectin (1-6), and Agelaia MP-I). These results show that the venom of both wasps are very similar to each other, probably due to the kinship of such species. Functionally, the peptide protonectin is lytic to erythrocytes... (Complete abstract click electronic access below) / Doutor

Biological functions within cells and organisms are mainly carried out by the translational products; proteins and peptides. The analysis and characterization of these biomolecules are of great importance for the progress in disease research and biomarker and drug discovery. The term peptidomics was introduced to describe the comprehensive analysis of peptides (e.g. neuropeptides) in biological tissues. In this thesis, a peptidomics approach using nanoflow liquid chromatography coupled to electrospray mass spectrometry (MS) has been developed for detection, identification, and quantification of neuropeptides in different disease models. A thoroughly controlled sample preparation technique and targeted neuropeptide sequence collections have been used to improve sample quality and to increase the number of identified neuropeptides. In particular, neuropeptide changes in experimental models of Parkinson’s disease (PD), with or without L-DOPA treatment, and the effect of antidepressant treatment on neuropeptide expression have been investigated. Several novel, potentially bioactive, neuropeptides have been identified and a number of peptides derived from precursors such as secretogranin-1, preproenkephalin-B, and somatostatin have been found differentially expressed. Some of them represent novel findings, not previously associated with PD or treatment with antidepressants. In addition, MALDI imaging MS (IMS), a technology that permits detection and spatial distribution determination of endogenous compounds and/or administered drugs directly on tissue sections, has been used in both small protein and drug applications. MALDI IMS on tissue samples from experimental models of PD revealed differential expression patterns of two small proteins involved in calcium regulation, PEP-19 and FKBP-12. Biomolecular interaction analysis was performed on FKBP-12 using surface plasmon resonance together with MS and several potential binding partners were identified. In a second approach, MALDI IMS was used to study the distribution of the anticholinergic bronchodilator tiotropium in rat lung following inhalation of the drug. The distribution of the drug was monitored in both MS and MS/MS mode and the levels where linearly quantifiable in the range of 80 fmol – 5 pmol. Conclusively, in this thesis mass spectrometry based technologies have successfully been developed to detect, identify, and characterize small proteins, peptides, and drugs in various tissue samples.

Biological function is mainly carried out by a dynamic population of proteins which may be used as markers for disease diagnosis, prognosis, and as a guide for effective treatment. In analogy to genomics, the study of proteins is called proteomics and it is generally performed by two-dimensional gel electrophoresis and mass spectrometric methods. However, gel based proteomics is methodologically restricted from the low mass region which includes important endogenous peptides. Furthermore, the study of endogenous peptides, peptidomics, is compromised by protein fragments produced post mortem during conventional sample handling. In this thesis nanoflow liquid chromatography and mass spectrometry have been used together with improved methods for sample preparation to semi-quantitatively monitor peptides in brain tissue. The proteolysis of proteins and rise of fragments in the low mass region was studied in a time-course study up to ten minutes, where a potential marker for sample quality was found. When rapidly denatured brain tissue was analyzed, the methods enabled detection of hundreds of peptides and identifications of several endogenous peptides not previously described in the literature. The identification process of endogenous peptides has been improved by creating small targeted sequence collections from existing databases. In applications of the MPTP model for Parkinson’s disease the protein and peptide expressions were compared to controls. Several proteins were significantly changed belonging to groups of mitochondrial, cytoskeletal, and vesicle associated proteins. In the peptidomic study, the levels of the small protein PEP-19 was found to be significantly decreased in the striatum of MPTP administered animals. Using imaging mass spectrometry the spatial distribution of PEP-19 was found to be predominant in the striatum and the levels were concordantly decreased in the parkinsonian tissue as verified by immunoblotting.

Bioactive peptides constitute a major class of signaling molecules in animals and have been shown to play a role in diverse physiological processes, including hypertension, appetite and sleep. As a result, knowing the identity of these molecules and understanding the mechanisms by which they are regulated has basic and medical significance. In this dissertation, I describe the development and application of novel methods for discovering bioactive peptides and the molecular pathways that control their activity. Recent analyses of mammalian RNAs have revealed the translation of numerous short open reading frames (sORFs). However, it is unknown whether these translation events produce stable polypeptide products that persist in the cell at functionally relevant concentrations. In Chapter 1, I describe a study in which we used a novel mass spectrometry-based strategy to directly detect sORF-encoded polypeptides (SEPs) in human cells. This analysis identified 115 novel SEPs, which is the largest number of mammalian SEPs discovered in a single study by more than a factor of 25. We observed widespread translation of SEPs from non-canonical RNA contexts, including polycistronic mRNAs and sORFs defined by non-AUG start codons. We also found that SEPs possess properties characteristic of functional proteins, such as stable expression, high cellular copy numbers, post-translational modifications, sub-cellular localization, the ability to participate in specific protein-protein interactions and the ability to influence gene expression. Taken together, these findings provide the strongest evidence to date that coding sORFs constitute a significant human gene class. In chapter 3, I describe a study in which we combine quantitative in vivo peptidomics, classical biochemical experiments and pharmacological studies in animal models to elucidate the metabolism of the neuropeptide substance P in the spinal cord. We identified two physiological substance P metabolites: the N- terminal fragments SP(1-9) and SP(1-7). Focusing our efforts on the SP(1-9)- producing pathway, we determined that an activity sensitive to the inhibitor GM6001 is the dominant SP(1-9)-generating activity in the spinal cord. We also show that GM6001 treatment causes a nearly three-fold increase in endogenous substance P levels in the spinal cords of mice, highlighting the functional relevance of the pathway blocked by this inhibitor.