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Proteome Research (proteome + research)
Selected AbstractsThe 6th East Midlands Proteomics Workshop supported by the BSPR and BMSS 14 November 2007, Nottingham, UKPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 9 2008Robert Layfield Dr. Abstract Now in its 6th year, the East Midlands Proteomics workshop held in November 2007 brought together over 200 scientists with a common interest in proteomic techniques and their application to complex biological and biomedical problems. For the first time, this meeting was jointly supported by the British Society for Proteome Research (BSPR) and British Mass Spectrometry Society (BMSS). [source] BSPR/EBI 2007 meeting report , Integrative Proteomics: From Molecules to Systems July 25,27, 2007 Wellcome Trust Conference Centre, Hinxton, UKPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 2 2008Pamela Donoghue Abstract This report reviews the joint British Society for Proteome Research (BSPR) and European Bioinformatics Institute (EBI) 2007 meeting, ,Integrative Proteomics: From Molecules to Systems' which took place at the Wellcome Trust Conference Centre, Hinxton, UK, from 25th to 27th July. The aim of this year's meeting was to explore how the integration of ,omic' technologies can lead to a comprehensive understanding of cellular organization, differentiation and signalling. Studies investigating protein,protein interactions and trafficking illustrated how the combination of proteomics and bioinformatics is allowing systems biology to develop as a discipline in its own right. [source] Sugarcane proteomics: Establishment of a protein extraction method for 2-DE in stalk tissues and initiation of sugarcane proteome reference mapELECTROPHORESIS, Issue 12 2010Ramesh Sundar Amalraj Abstract Sugarcane is an important commercial crop cultivated for its stalks and sugar is a prized commodity essential in human nutrition. Proteomics of sugarcane is in its infancy, especially when dealing with the stalk tissues, where there is no study to date. A systematic proteome analysis of stalk tissue yet remains to be investigated in sugarcane, wherein the stalk tissue is well known for its rigidity, fibrous nature, and the presence of oxidative enzymes, phenolic compounds and extreme levels of carbohydrates, thus making the protein extraction complicated. Here, we evaluated five different protein extraction methods in sugarcane stalk tissues. These methods are as follows: direct extraction using lysis buffer (LB), TCA/acetone precipitation followed by solubilization in LB, LB containing thiourea (LBT), and LBT containing tris, and phenol extraction. Both quantitative and qualitative protein analyses were performed for each method. 2-DE analysis of extracted total proteins revealed distinct differences in protein patterns among the methods, which might be due to their physicochemical limitations. Based on the 2-D gel protein profiles, TCA/acetone precipitation-LBT and phenol extraction methods showed good results. The phenol method showed a shift in pI values of proteins on 2-D gel, which was mostly overcome by the use of 2-D cleanup kit after protein extraction. Among all the methods tested, 2-D cleanup-phenol method was found to be the most suitable for producing high number of good-quality spots and reproducibility. In total, 30 and 12 protein spots commonly present in LB, LBT and phenol methods, and LBT method were selected and subjected to eLD -IT-TOF-MS/MS and nESI-LC-MS/MS analyses, respectively, and a reference map has been established for sugarcane stalk tissue proteome. A total of 36 nonredundant proteins were identified. This is a very first basic study on sugarcane stalk proteome analysis and will promote the unexplored areas of sugarcane proteome research. [source] High MS-compatibility of silver nitrate-stained protein spots from 2-DE gels using ZipPlates and AnchorChips for successful protein identificationELECTROPHORESIS, Issue 10 2007Grit Nebrich Abstract The availability of easy-to-handle, sensitive, and cost-effective protein staining protocols for 2-DE, in conjunction with a high compatibility for subsequent MS analysis, is still a prerequisite for successful proteome research. In this article we describe a quick and easy-to-use methodological protocol based on sensitive, homogeneous, and MS-compatible silver nitrate protein staining, in combination with an in-gel digestion, employing the Millipore 96-well ZipPlate system for peptide preparation. The improved quality and MS compatibility of the generated protein digests, as compared to the otherwise weakly MS-compatible silver nitrate staining, were evaluated on real tissue samples by analyzing 192 Coomassie-stained protein spots against their counterparts from a silver-stained 2-DE gel. Furthermore, the applicability of the experimental setup was evaluated and demonstrated by the analysis of a large-scale MALDI-TOF MS experiment, in which we analyzed an additional ,1000 protein spots from 2-DE gels from mouse liver and mouse brain tissue. [source] Identification of Modified Proteins by Mass SpectrometryIUBMB LIFE, Issue 2 2002Albert Sickmann Abstract Because it is obvious that high-throughput genomics do not lead to a molecular description or even a prediction of protein function, modern techniques for protein analysis become increasingly more important. Sequence analysis of proteins and peptides is not limited to the elucidation of the primary structure of a protein. The analysis of posttranslational modifications is an important task of protein chemistry in proteome research. Increased sensitivity in mass spectrometry as a result of more efficient ionization techniques and better detection systems has allowed the stepwise reduction of protein quantity for analysis. Protein spots of 2D-PAGE separated samples are now sufficient for an unequivocal identification of a protein by mass spectrometry. In addition to protein identification, a closer look at posttranslational modifications is now also possible. It is assumed that modifications such as phosphorylation or glycosylation exist on every second protein and that they are important for the protein function. [source] On-plate-selective enrichment of glycopeptides using boronic acid-modified gold nanoparticles for direct MALDI-QIT-TOF MS analysisPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 22 2009Jia Tang Abstract In this study, an on-plate-selective enrichment method is developed for fast and efficient glycopeptide investigation. Gold nanoparticles were first spotted and sintered on a stainless-steel plate, then modified with 4-mercaptophenylboronic acid to provide porous substrate with large specific surface and dual functions. These spots were used to selectively capture glycopeptides from peptide mixtures and the captured target peptides could be analyzed by MALDI-MS simply by deposition of 2,5-dihydroxybenzoic acid matrix. Horseradish peroxidase was employed as a standard glycoprotein to investigate the enrichment efficiency. In this way, the enrichment, washing and detection steps can all be fulfilled on a single MALDI target plate. The relatively small sample amount needed, low detection limit and rapid selective enrichment have made this on-plate strategy promising for online enrichment of glycopeptides, which could be applied in high-throughput proteome research. [source] Protein labeling by iTRAQ: A new tool for quantitative mass spectrometry in proteome researchPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 3 2007Sebastian Wiese Abstract A novel, MS-based approach for the relative quantification of proteins, relying on the derivatization of primary amino groups in intact proteins using isobaric tag for relative and absolute quantitation (iTRAQ) is presented. Due to the isobaric mass design of the iTRAQ reagents, differentially labeled proteins do not differ in mass; accordingly, their corresponding proteolytic peptides appear as single peaks in MS scans. Because quantitative information is provided by isotope-encoded reporter ions that can only be observed in MS/MS spectra, we analyzed the fragmentation behavior of ESI and MALDI ions of peptides generated from iTRAQ-labeled proteins using a TOF/TOF and/or a QTOF instrument. We observed efficient liberation of reporter ions for singly protonated peptides at low-energy collision conditions. In contrast, increased collision energies were required to liberate the iTRAQ label from lysine side chains of doubly charged peptides and, thus, to observe reporter ions suitable for relative quantification of proteins with high accuracy. We then developed a quantitative strategy that comprises labeling of intact proteins by iTRAQ followed by gel electrophoresis and peptide MS/MS analyses. As proof of principle, mixtures of five different proteins in various concentration ratios were quantified, demonstrating the general applicability of the approach presented here to quantitative MS-based proteomics. [source] Proteomics in rheumatology: The beginning of a fairy tale?PROTEOMICS - CLINICAL APPLICATIONS, Issue 3 2008Stijn Lambrecht Abstract One of the major challenges in proteome research is to translate its applications to the setting of human diseases. Proteomics in rheumatology is an area with marked potential including applications ranging from diagnostics, over therapeutic monitoring to discovery of new potential therapeutic targets. Biomarkers will be essential to discriminate between clinical similar rheumatic diseases, to monitor disease-states or to install the best appropriate therapy. Especially in the field of rheumatology, analysis of specific genes and/or their expression products by pharmacogenetics/-genomics or pharmacoproteomics could be necessary to enable an effective, patient-tailored therapy. In rheumatology, direct examination of proteins may be of utmost importance, as it is already known that PTMs, such as citrullination of proteins or peptides, may be involved in certain rheumatic diseases. The discovery and validation of antibodies directed against citrullinated proteins/peptides in rheumatic diseases using proteome analysis approaches has been described. Gel-free methods, SELDI-approaches and classic 2-DE approaches have been deployed on body fluids as well as on target tissues in different rheumatic diseases. Proteomics in rheumatology is on the rise and pilot studies have indicated that the application of proteomics-based technologies in rheumatic diseases appears to be an exciting example of translational research. [source] Exploring the proteome of meningococcal outer membrane vesicle vaccinesPROTEOMICS - CLINICAL APPLICATIONS, Issue 9 2007Jun X. Wheeler Dr. Abstract Neisseria meningitidis, one of the principal causes of bacterial meningitis and septicemia, continues to present a challenge for vaccine developers. While significant progress has been made in the development and implementation of conjugate vaccines, which are based on the capsular polysaccharide of the organism, this approach has failed to produce a vaccine against organisms expressing a serogroup B capsule. The completion of the first meningococcal genome sequences in 2000 provided new ways of meeting this challenge. One approach has been to learn more about meningococcal biology and pathogenesis through exploring its proteome. This article reviews the results of ten recent studies of the meningococcal proteome and compares the different methodologies employed. Not surprisingly, given the renewed impetus to develop a comprehensive vaccine and the continuing clinical development of outer membrane vesicle vaccines, many of these studies focus on the proteome of the outer membrane fraction. As in other areas of proteome research, the direct comparison of data from different studies is hampered by the lack of standardization of separation technologies and data formats. Nevertheless, proteomic analysis, especially when combined with detailed knowledge of meningococcal population structures, represents a powerful tool in the development of vaccines against this important pathogen. [source] | ||||||||||