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Protein identification pipeline for the homology-driven proteomics

JUNQUEIRA, Magno; SPIRIN, Victor; BALBUENA, Tiago Santana; THOMAS, Henrik; ADZHUBEI, Ivan; SUNYAEV, Shamil; SHEVCHENKO, Andrej
Fonte: ELSEVIER SCIENCE BV Publicador: ELSEVIER SCIENCE BV
Tipo: Artigo de Revista Científica
Português
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Homology-driven proteomics is a major tool to characterize proteomes of organisms with unsequenced genomes. This paper addresses practical aspects of automated homology-driven protein identifications by LC-MS/MS on a hybrid LTQ orbitrap mass spectrometer. All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download. (C) 2008 Elsevier B.V. All rights reserved.; U.S. National Institutes of Health (NIH); NIH NIGMS[1R01GM070986-01A1]

Análise proteômica das diversas fases de diferenciação osteoblástica de células-tronco mesenquimais de medula óssea; Proteomics analysis of the various stages of osteoblastic differentiation of mesenchymal stem cells from bone marrow

Paula, Leonardo Barcelos de
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 13/12/2010 Português
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O crescimento, desenvolvimento e manutenção do tecido ósseo são processos altamente regulados. Diversas proteínas como hormônios, fatores de crescimento e citocinas estão envolvidas nestes processos e exercem atividade direta sobre células osteoblástica e osteoclástica, atuando em sua diferenciação e ativação metabólica. O processo de regeneração óssea é iniciado por fatores estimuladores locais como as proteínas morfogenética óssea (BMP Bone Morphogenetic Proteins). As BMPs são um produto do metabolismo dos osteoblastos, odontoblastos e de várias células tumorais, sendo armazenadas na forma de concentrados no osso, dentina e em células neoplásicas do osteossarcoma e de certos tumores odontogênicos, tais como: fibroma cementificante, cementoblastoma benigno, dentinoma, fibroma odontogênico e odontoma. Esclarecer os mecanismos que controlam a remodelação óssea é uma questão bastante relevante. Nesse sentido, as células-tronco mesenquimais têm despertado grande interesse devido ao seu potencial envolvimento no processo de reparo tissular. A obtenção de osteoblastos funcionais a partir de células-tronco mesenquimais tem sido utilizada na engenharia de tecidos e terapia celular. Desse modo, no presente trabalho foi realizada uma análise proteômica das proteínas envolvidas nas diversas fases de diferenciação osteoblástica de células-tronco mesenquimais de medula óssea de rato Wistar e humana...

Ferramentas de bioinformática para proteômica; Bioinformatics tools for proteomics

Itaraju Junior Baracuhy Brum
Fonte: Biblioteca Digital da Unicamp Publicador: Biblioteca Digital da Unicamp
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 23/07/2007 Português
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A área de proteômica visa estudar um conjunto completo de proteínas expressas por um organismo ou tecido numa dada situação, através da identificação e quantificação. Apesar de limitações nas técnicas disponíveis, vem se aumentando o volume de informações oriundos desta área, situação que exige o emprego de ferramentas computacionais para permitir o uso eficiente de dados disponíveis, além de buscar-se novas formas de análise destes. Este projeto visa o desenvolvimento de ferramentas de bioinformática para aplicação em proteômica. Estas ferramentas abrangem as seguintes aplicações: Cálculo Teórico de Ponto Isoelétrico e Peso Molecular de seqüências de aminoácidos, eletroforese-bidimensional teórica, digestão teórica e simulação de eletroforese e identificação de peptídeos, ferramenta para análise de Vias Metabólicas a partir de dados de proteômica; The proteomics field aims to study sets of proteins expressed in a cell or tissue, according to a specific situation, through protein identification and quantification. Though technical limitations do exist, the amount of information derived from this field increases each day. And so, there is a need for employing computational tools that enable efficient analysis of data. This project aims developing bioinformatics tools for application in proteomics. The tools here presented comprehend the following tasks: theoretical computation of isoeletric point and molecular weight of aminoacid sequences...

Avaliação comparativa dos perfis proteômicos e metaloproteômicos de sementes de soja (Glycine max (L.) Merril) modificadas geneticamente; Comparative evaluation of proteomics and metalloproteomics profiles of sybean seeds (Glycine max (L.) Merril) genetically modified

Herbert de Sousa Barbosa
Fonte: Biblioteca Digital da Unicamp Publicador: Biblioteca Digital da Unicamp
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 21/03/2011 Português
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Este trabalho de pesquisa consiste na comparação entre dois tipos de sementes de soja [Glycine max (L.) Merrill], transgênica e não-transgênica, em termos proteômicos e metaloproteômicos, de modo a avaliar possíveis diferenças existentes entre as amostras (Ex. diferença de expressão protéica, concentração das espécies metálicas e não-metálicas ligadas às biomoléculas). Para isso, inicialmente, as biomoléculas foram extraídas usando um tampão extrator específico e, após o tratamento adequado da amostra, separadas por meio da técnica de eletroforese bidimensional em gel de poliacrilamida (2D-PAGE) e caracterizadas por meio de técnicas de espectrometria de massas (MALDI-QTOF e ESI-QTOF) e identificadas por meio de buscas em banco de dados relacionados utilizando o programa Mascot, a partir dos dados gerados pelo espectrômetro de massas. Sendo assim, foram identificadas um total de 192 proteínas, sendo 13 proteínas na faixa de pH de 3 a 10 e 179 na faixa de pH de 4 a 7, sendo que esta última faixa de pH mostrou melhor resolução dinâmica na separação das proteínas. A distribuição funcional das proteínas identificadas mostrou que a maior parte (49%) destas estão envolvidas em armazenamento de nutrientes e atividade proteolítica...

Candidate-based proteomics in the search for biomarkers of cardiovascular disease

Anderson, Leigh
Fonte: Blackwell Science Inc Publicador: Blackwell Science Inc
Tipo: Artigo de Revista Científica
Português
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The key concept of proteomics (looking at many proteins at once) opens new avenues in the search for clinically useful biomarkers of disease, treatment response and ageing. As the number of proteins that can be detected in plasma or serum (the primary clinical diagnostic samples) increases towards 1000, a paradoxical decline has occurred in the number of new protein markers approved for diagnostic use in clinical laboratories. This review explores the limitations of current proteomics protein discovery platforms, and proposes an alternative approach, applicable to a range of biological/physiological problems, in which quantitative mass spectrometric methods developed for analytical chemistry are employed to measure limited sets of candidate markers in large sets of clinical samples. A set of 177 candidate biomarker proteins with reported associations to cardiovascular disease and stroke are presented as a starting point for such a ‘directed proteomics’ approach.

Broad-based proteomic strategies: a practical guide to proteomics and functional screening

Graham, David RM; Elliott, Steven T; Van Eyk, Jennifer E
Fonte: Blackwell Science Inc Publicador: Blackwell Science Inc
Tipo: Artigo de Revista Científica
Português
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Proteomics, the study of the proteome (the collection of all the proteins expressed from the genome in all isoforms, polymorphisms and post-translational modifications), is a rapidly developing field in which there are numerous new and often expensive technologies, making it imperative to use the most appropriate technology for the biological system and hypothesis being addressed. This review provides some guidelines on approaching a broad-based proteomics project, including strategies on refining hypotheses, choosing models and proteomic approaches with an emphasis on aspects of sample complexity (including abundance and protein characteristics), and separation technologies and their respective strengths and weaknesses. Finally, issues related to quantification, mass spectrometry and informatics strategies are discussed. The goal of this review is therefore twofold: the first section provides a brief outline of proteomic technologies, specifically with respect to their applications to broad-based proteomic approaches, and the second part provides more details about the application of these technologies in typical scenarios dealing with physiological and pathological processes. Proteomics at its best is the integration of carefully planned research and complementary techniques with the advantages of powerful discovery technologies that has the potential to make substantial contributions to the understanding of disease and disease processes.

P191-M A Comparison of nLC-ESI-MS/MS and nLC-MALDI-MS/MS for GeLC-Based Protein Identification and iTRAQ-Based Shotgun Quantitative Proteomics

Yang, Y.; Zhang, S.; Howe, K.; Thannhauser, T. W.
Fonte: The Association of Biomolecular Resource Facilities Publicador: The Association of Biomolecular Resource Facilities
Tipo: Artigo de Revista Científica
Publicado em /02/2007 Português
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The use of nano-HPLC electrospray ionization multistage tandem mass spectrometry (nLC-ESI-MS/MS) in shotgun proteomics experiments and nano-liquid-chromatography tandem mass spectrometry (GeLC-MS/MS) analysis is well accepted and routinely available in most proteomics laboratories. The same can not be said for nLC-MALDI MS/MS, which has yet to experience such widespread acceptance. This is not totally surprising, given the inability to monitor the separation performance in real time and the time-consuming processes of off-line data analysis and interpretation that are associated with MALDI. This is unfortunate, as the MALDI technology offers several critical advantages over ESI that can be exploited to improve experimental outcomes. Here, we re-evaluate and demonstrate both the complementary nature of the two approaches and the synergism attainable through the employment of both ionization technologies to two common applications: protein identification in 1D gel bands and quantification of the dynamics of protein expression during ontogenesis.

P199-S Assessing Signal to Noise in Quantitative Proteomics

Friedman, D. B.; Whitwell, C. W.; Loyd, J. E.; Meyrick, B.
Fonte: The Association of Biomolecular Resource Facilities Publicador: The Association of Biomolecular Resource Facilities
Tipo: Artigo de Revista Científica
Publicado em /02/2007 Português
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The complex methodology used in many large-scale quantitative proteomics experiments often dictates an experimental design with small sample size and limited repetition. Variation in a complex dataset may hopefully arise from changes caused by the experimental perturbation, but could also arise due to technical noise (poor sample prep, run-to-run variation) and biological noise (normal differences between samples, especially present in clinical samples). Here, we apply principle component analysis (PCA) and unsupervised hierarchical clustering (HC) to the data generated from multi-variable difference gel electrophoresis (DIGE) experiments. This global perspective on multivariable datasets assesses whether the variation in the system describes the biological signal, rather than being derived from technical/biological noise whereby “significant” changes may arise stochastically. Although we use DIGE datasets as examples (due to the low technical noise), these issues are germane to all proteomics experimental platforms.

An Integrated Proteomics/Transcriptomics Approach Points to Oxygen as the Main Electron Sink for Methanol Metabolism in Methylotenera mobilis▿†

Beck, David A. C.; Hendrickson, Erik L.; Vorobev, Alexey; Wang, Tiansong; Lim, Sujung; Kalyuzhnaya, Marina G.; Lidstrom, Mary E.; Hackett, Murray; Chistoserdova, Ludmila
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /09/2011 Português
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Methylotenera species, unlike their close relatives in the genera Methylophilus, Methylobacillus, and Methylovorus, neither exhibit the activity of methanol dehydrogenase nor possess mxaFI genes encoding this enzyme, yet they are able to grow on methanol. In this work, we integrated a genome-wide proteomics approach, shotgun proteomics, and a genome-wide transcriptomics approach, shotgun transcriptome sequencing (RNA-seq), of Methylotenera mobilis JLW8 to identify genes and enzymes potentially involved in methanol oxidation, with special attention to alternative nitrogen sources, to address the question of whether nitrate could play a role as an electron acceptor in place of oxygen. Both proteomics and transcriptomics identified a limited number of genes and enzymes specifically responding to methanol. This set includes genes involved in oxidative stress response systems, a number of oxidoreductases, including XoxF-type alcohol dehydrogenases, a type II secretion system, and proteins without a predicted function. Nitrate stimulated expression of some genes in assimilatory nitrate reduction and denitrification pathways, while ammonium downregulated some of the nitrogen metabolism genes. However, none of these genes appeared to respond to methanol...

Opportunities and Challenges for Nutritional Proteomics in Cancer Prevention12

Romagnolo, Donato F.; Milner, John A.
Fonte: American Society for Nutrition Publicador: American Society for Nutrition
Tipo: Artigo de Revista Científica
Português
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Knowledge gaps persist about the efficacy of cancer prevention strategies based on dietary food components. Adaptations to nutrient supply are executed through tuning of multiple protein networks that include transcription factors, histones, modifying enzymes, translation factors, membrane and nuclear receptors, and secreted proteins. However, the simultaneous quantitative and qualitative measurement of all proteins that regulate cancer processes is not practical using traditional protein methodologies. Proteomics offers an attractive opportunity to fill this knowledge gap and unravel the effects of dietary components on protein networks that impinge on cancer. The articles presented in this supplement are from talks proffered in the “Nutrition Proteomics and Cancer Prevention” session at the American Institute for Cancer Research Annual Research Conference on Food, Nutrition, Physical Activity and Cancer held in Washington, DC on October 21 and 22, 2010. Recent advances in MS technologies suggest that studies in nutrition and cancer prevention may benefit from the adoption of proteomic tools to elucidate the impact on biological processes that govern the transition from normal to malignant phenotype; to identify protein changes that determine both positive and negative responses to food components; to assess how protein networks mediate dose-...

Proteomics profiles from mass spectrometry

Koch, I.; Hoffmann, P.; Marron, J.S.
Fonte: Institute of Mathematical Statistics Publicador: Institute of Mathematical Statistics
Tipo: Artigo de Revista Científica
Publicado em //2014 Português
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Proteomics is a rapidly growing research area within bioinformatics which focuses on quantification of peptide concentrations and on the identification of proteins and peptides. In quantitative proteomics the identification of biomarkers from peptide concentrations is important for diagnostic purposes and treatment of diseases. The goal of this paper is to facilitate research in this area, by providing a test bed for comparison of 1D curve registration methods. This is done in a novel way, by providing not only curves, but also an answer key as to how the peaks should align. In the following papers a number of approaches to this problem are given, and the answer key provides unusually useful insights into how the methods compare. For this reason, we consider proteomics mass spectrometry profiles which are part of a larger study into the identification of biomarkers in Acute Myeloid Leukaemia (AML). For these profiles large ion counts result in large peaks, but these peaks may occur at different retention times for different profiles. The first step in the quantification of peptides in proteomics profiles is the alignment of the 1D curves of total ion count (TIC). The paper includes a description of proteomics mass spectrometry profiling...

Understanding the apoptotic signaling pathways in breast cancer using microarrays, proteomics and bioinformatics.

Alanazi, Ibrahim Oqla
Fonte: Universidade de Adelaide Publicador: Universidade de Adelaide
Tipo: Tese de Doutorado
Publicado em //2014 Português
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Breast cancer is one of the most common causes of cancer death to women worldwide. In this study A431 cells, derived from epidermoid carcinoma, are used as a model to study breast cancer. This cell line over-expresses the Epidermal Growth Factor Receptor (EGFR/HER1) and when treated with a high dose of EGF will undergo apoptosis via the activation of EGFR/HER1 signaling. However, little work has been conducted to identify the underlying molecular mechanisms. The limited available data implicates components of the interferon response pathway as mediators of the apoptotic signal in cancer cells. The genetic network through which EGFR/HER1 can induce apoptosis is not known at the present time. With understanding of the genetic regulatory hierarchy and the molecular mechanisms linking EGFR/HER1 signaling and apoptosis, better drug targets that might regulate apoptosis in cancers that over express HERs can be identified. This thesis focuses on the hypothesis that an apoptosis specific signalling cascade can be triggered by HERs in A431cells. Activation of HER receptors has led us to identify downstream components by global analyses of gene expression and associated regulatory miRNAs and protein levels using microarray and proteomics platforms. A high dose of EGF leads to the induction of apoptosis in A431 cells by activating a number of pathways...

APP: an Automated Proteomics Pipeline for the analysis of mass spectrometry data based on multiple open access tools

Malm, E.K.; Srivastava, V.; Sundqvist, G.; Bulone, V.
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em //2014 Português
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BACKGROUND: Mass spectrometry analyses of complex protein samples yield large amounts of data and specific expertise is needed for data analysis, in addition to a dedicated computer infrastructure. Furthermore, the identification of proteins and their specific properties require the use of multiple independent bioinformatics tools and several database search algorithms to process the same datasets. In order to facilitate and increase the speed of data analysis, there is a need for an integrated platform that would allow a comprehensive profiling of thousands of peptides and proteins in a single process through the simultaneous exploitation of multiple complementary algorithms. RESULTS: We have established a new proteomics pipeline designated as APP that fulfills these objectives using a complete series of tools freely available from open sources. APP automates the processing of proteomics tasks such as peptide identification, validation and quantitation from LC-MS/MS data and allows easy integration of many separate proteomics tools. Distributed processing is at the core of APP, allowing the processing of very large datasets using any combination of Windows/Linux physical or virtual computing resources. CONCLUSIONS: APP provides distributed computing nodes that are simple to set up...

Plasma Proteome Analysis Using Peptide Group-Specific Immunoprecipitation "Triple X Proteomics"; Plasma Proteom Analyse mit peptidgruppenspezifischer Immunopräzipitation "Triple X Proteomics"

Schneider, Sonja
Fonte: Universidade de Tubinga Publicador: Universidade de Tubinga
Tipo: Dissertação
Português
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Blood plasma, the largest human proteome is readily accessible and can be minimalinvasively sampled making it a valuable source of potential biomarkers. However, its analysis is complicated by its complexity and the huge dynamic concentration range of its constituents. Automated assays were established using magnetic microspheres and customized group-specific triple X proteomics (TXP) antibodies. These antibodies are directed against short N- or C-terminal epitope motifs for the immunoprecipitation of signature peptides derived from groups of trypsin-digested plasma proteins. The introduction of these antibodies led to a very efficient enrichment of the targeted analytes and a reduction in sample complexity similar to the SISCAPA (Stable Isotope Standards and Capture by Anti-Peptide Antibodies) approach introduced by Anderson et al. (2004). The quantitative evaluation as targeted approach, via nano liquid chromatography multiple reaction monitoring and stable isotopes peptide standards revealed limits of detection of 21 ng/ml and limits of quantification of 189 ng/ml in a tryptic plasma digest assay. Two peptides with the same TXP tag were simultaneously captured with one TXP antibody in a multiplex dynamic range of about 7,000 (5 fmol peptide were still detectable in presence of 33.3 pmol matrix peptide). The qualitative evaluation as discovery approach...

Optimizing capillary electrophoresis for top-down proteomics of 30-80 kDa proteins.

Li, Yihan; Compton, Philip D.; Tran, John C.; Ntai, Ioanna; Kelleher, Neil L.
Fonte: Wiley VCH (Proteomics) Publicador: Wiley VCH (Proteomics)
Tipo: Relatório
Português
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The direct analysis of intact proteins via mass spectrometry offers compelling advantages in comparison to alternative methods due to the direct and unambiguous identification and characterization of protein sequences it provides. The inability to efficiently analyze proteins in the ???middle mass range???, defined here as proteins from 30-80 kDa, in a robust fashion has limited the adoption of these ???top-down??? methods. Largely a result of poor liquid chromatographic performance, the limitations in this mass range may be addressed by alternative separations that replace chromatography. Herein, the short migration times of capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) have been extended to size-sorted whole proteins in complex mixtures from Pseudomonas aeruginosa PA01. An electrokinetically pumped nanospray interface, a coated capillary and a stacking method for on-column sample concentration were developed to achieve high loading capacity and separation resolution. We achieved full width at half maximum of 8-16 seconds for model proteins up to 29 kDa and identified 30 proteins in the mass range of 30-80 kDa from Pseudomonas aeruginosa PA01 whole cell lysate. These results suggest that CZE-ESI-MS/MS is capable of identifying proteins in the middle mass range in top-down proteomics.; This work was supported by the National Institute of General Medical Sciences and National Institute of Drug Abuse of the National Institutes of Health under award numbers R01 GM067193 and DA018310...

Proteômica baseada em espectrometria de massas na descoberta de candidatos à biomarcadores em câncer e na identificação de novos alvos de ADAM17; Using mass spectrometry-based proteomics to discover cancer candidate biomarkers and to identify novel ADAM17 substrates

Rebeca Kawahara
Fonte: Biblioteca Digital da Unicamp Publicador: Biblioteca Digital da Unicamp
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 28/04/2015 Português
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A espectrometria de massas aplicada à análise proteômica permite a caracterização e quantificação em larga-escala de proteínas expressas em uma determinada condição ou sistema biológico. Na presente tese, mostramos por meio de diferentes abordagens a utilidade da espectrometria de massas (1) no estudo de proteínas secretadas ou clivadas da superfície (secretoma) por células tumorigênicas como fonte de biomarcadores em câncer (2) na validação de candidatos biomarcadores em saliva humana de pacientes com câncer oral e (3) no estudo de alvos de uma metaloprotease envolvida na progressão de câncer, a ADAM17 (A disintegrin and metalloproteinase 17). Os resultados gerados pela espectrometria de massas juntamente com ferramentas estatísticas e de bioinformática para visualização de dados em agrupamento, heatmaps, rede de interação proteína-proteína, enriquecimento de vias e processos biológicos indicaram proteínas específicas direcionadas à hipótese que puderam ser validadas por métodos complementares quantitativos e funcionais. No contexto de biomarcadores em câncer, um painel de marcadores foi indicado a partir da análise do secretoma de células de carcinoma, melanoma e não cancerosas. Dentre os candidatos em carcinoma...

Clinical proteomics stretch goals: EuPA 2012 roundtable report

O'Neil, S.E.; Palviainen, M.J.; Ten Have, S.; Penque, Deborah; Baker, M.S.
Fonte: Elsevier/ European Proteomics Association (EuPA) Publicador: Elsevier/ European Proteomics Association (EuPA)
Tipo: Artigo de Revista Científica
Publicado em 02/08/2013 Português
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The field of clinical proteomics is faced with multiple challenges which need to be overcome in order to improve our understanding of human diseases and provide management solutions. Researchers interested in clinical proteomics assembled for a roundtable discussion at the European Association for Proteomics (EuPA) conference held in Glasgow in July 2012, to discuss these challenges and highlight the key areas for successful clinical proteomic studies. This report shares topics of discussion and the resulting stretch goals of clinical proteomics for researchers to strive towards.

Proteins' promise - progress and challenges in ovarian cancer proteomics

Koehn, H.; Oehler, M.
Fonte: Royal Society of Medicine Press Ltd. Publicador: Royal Society of Medicine Press Ltd.
Tipo: Artigo de Revista Científica
Publicado em //2007 Português
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Ovarian cancer is the leading cause of gynaecological cancer death. The mortality rate of ovarian cancer could be greatly decreased if there were a screening test which was able to detect the disease at an early stage, resulting in an increased probability of cure. The most promising prospect for the early detection of ovarian cancer comes from the rapidly advancing field of clinical proteomics. An increasing number of reports on the potential clinical application of proteomics research for early detection as well as risk assessment and management of ovarian cancer are being published. Although the research is very promising, major technical challenges are still preventing new discoveries in ovarian cancer proteomics from being translated into clinical practice.; H Koehn and M K Oehler; Copyright © 2007 British Menopause Society

Molecular characterization of the contribution of autophagy to antigen presentation using quantitative proteomics

Bell, Christina
Fonte: Université de Montréal Publicador: Université de Montréal
Tipo: Thèse ou Mémoire numérique / Electronic Thesis or Dissertation
Português
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L’autophagie est une voie hautement conservée de dégradation lysosomale des constituants cellulaires qui est essentiel à l’homéostasie cellulaire et contribue à l’apprêtement et à la présentation des antigènes. Les rôles relativement récents de l'autophagie dans l'immunité innée et acquise sous-tendent de nouveaux paradigmes immunologiques pouvant faciliter le développement de nouvelles thérapies où la dérégulation de l’autophagie est associée à des maladies auto-immunes. Cependant, l'étude in vivo de la réponse autophagique est difficile en raison du nombre limité de méthodes d'analyse pouvant fournir une définition dynamique des protéines clés impliquées dans cette voie. En conséquence, nous avons développé un programme de recherche en protéomique intégrée afin d’identifier et de quantifier les proteines associées à l'autophagie et de déterminer les mécanismes moléculaires régissant les fonctions de l’autophagosome dans la présentation antigénique en utilisant une approche de biologie des systèmes. Pour étudier comment l'autophagie et la présentation antigénique sont activement régulés dans les macrophages, nous avons d'abord procédé à une étude protéomique à grande échelle sous différentes conditions connues pour stimuler l'autophagie...

ISPIDER Central: an integrated database web-server for proteomics.

Siepen, J.A.; Belhajjame, K.; Selley, J.N.; Embury, S.M.; Paton, N.W.; Goble, C.A.; Oliver, S.G.; Stevens, R.; Zamboulis, L.; Martin, Nigel
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Português
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Despite the growing volumes of proteomic data, integration of the underlying results remains problematic owing to differences in formats, data captured, protein accessions and services available from the individual repositories. To address this, we present the ISPIDER Central Proteomic Database search (http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl), an integration service offering novel search capabilities over leading, mature, proteomic repositories including PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas and the Global Proteome Machine. It enables users to search for proteins and peptides that have been characterised in mass spectrometry-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers/clients. In order to overcome limitations imposed by the great variability in protein accessions used by individual laboratories, the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service is used to resolve accessions from different sequence repositories. Custom-built clients allow users to view peptide/protein identifications in different contexts from multiple experiments and repositories, as well as integration with the Dasty2 client supporting any annotations available from Distributed Annotation System servers. Further information on the protein hits may also be added via external web services able to take a protein as input. This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics.