| 1. |
- Albar, JP, et al.
(författare)
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Promoting proteomics knowledge in Europe
- 2007
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Ingår i: Proteomics. - : Wiley. - 1615-9861 .- 1615-9853. ; 7:S1, s. 90-94
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Tidskriftsartikel (refereegranskat)abstract
- The early transition of knowledge from highly specialised and sophisticated proteomics research to a diverse community in need of know-how is a challenge that requires backing from advanced research centres and groups, and a coordinating body for the dissemination of this knowledge. The European Proteomics Association (EuPA) Education Committee signified this as a priority area when the EuPA was formed, and began its program to coordinate proteomics training and knowledge dissemination in 2006. This repor t serves as an update of our past activities and an announcement of upcoming events. Over the last year the EuPA Education Committee has coordinated or suppor ted dif ferent educational activities including basic and advanced courses, a summer school, workshops and tutorials. A new programme of basic courses dubbed Teaching the Teachers has been initiated. These courses reach a larger, Europe wide, audience in a short timeframe, thus improving the oppor tunities for trainees of elementary proteomics techniques. Another impor tant event has been the merger of the EuPA and HUPO (Human Proteome Organisation) Education Committees into a single one in order to combine ideas and ef for ts that will favour global education in proteomics.
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| 2. |
- Arrigoni, Giorgio, et al.
(författare)
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Chemical derivatization of phosphoserine and phosphothreonine containing peptides to increase sensitivity for MALDI-based analysis and for selectivity of MS/MS analysis
- 2006
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Ingår i: Proteomics. - : Wiley. - 1615-9861 .- 1615-9853. ; 6:3, s. 757-766
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Tidskriftsartikel (refereegranskat)abstract
- Protein phosphorylation is one of the most important and common ways of regulating protein function in cells. However, phosphopeptides are difficult to analyse, ionising poorly under standard MALDI conditions. Several methods have been developed to deal with the low sensitivity and specificity of phosphopeptide analysis. Here, we show an approach using a simple one-step beta-elimination/Michael addition reaction for the derivatization of phosphoserine and phosphothreonine. The substitution of the negatively charged phosphate group by a positively charged S-ethylpyridyl group greatly improves the ionisation of the modified peptides, especially in MALDI MS, increasing the sensitivity of the analysis. The modification allows the formation of a unique fragment ion at m/z 106 under mild collisional activation conditions, which can be used for parent (precursor) ion scanning in order to improve both the sensitivity and the selectivity of the analysis. The optimisation of the approach is described for a standard model peptide and protein and then applied to phosphorylation analysis in two biologically derived proteins purified from different experimental systems.
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| 3. |
- Berggård, Tord, et al.
(författare)
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Methods for the detection and analysis of protein-protein interactions
- 2007
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Ingår i: Proteomics. - : Wiley. - 1615-9861 .- 1615-9853. ; 7:16, s. 2833-2842
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Forskningsöversikt (refereegranskat)abstract
- A large number of methods have been developed over the years to study protein-protein interactions. Many of these techniques are now available to the nonspecialist researcher thanks to new affordable instruments and/or resource centres. A typical protein-protein interaction study usually starts with an initial screen for novel binding partners. We start this review by describing three techniques that can be used for this purpose: (i) affinity-tagged proteins (ii) the two-hybrid system and (iii) some quantitative proteomic techniques that can be used in combination with, e.g., affinity chromatography and coimmunoprecipitation for screening of protein-protein interactions. We then describe some public protein-protein interaction databases that can be searched to identify previously reported interactions for a given bait protein. Four strategies for validation of protein-protein interactions are presented: confocal microscopy for intracellular colocalization of proteins, coimmunoprecipitation, surface plasmon resonance (SPR) and spectroscopic studies. Throughout the review we focus particularly on the advantages and limitations of each method.
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| 4. |
- Berglund, Lisa, et al.
(författare)
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A whole-genome bioinformatics approach to selection of antigens for systematic antibody generation
- 2008
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 8:14, s. 2832-2839
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Tidskriftsartikel (refereegranskat)abstract
- Here, we present an antigen selection strategy based on a whole-genome bioinformatics approach, which is facilitated by an interactive visualization tool displaying protein features from both public resources and in-house generated data. The web-based bioinformatics platform has been designed for selection of multiple, non-overlapping recombinant protein epitope signature tags by display of predicted information relevant for antigens, including domain- and epitope sized sequence similarities to other proteins, transmembrane regions and signal peptides. The visualization tool also displays shared and exclusive protein regions for genes with multiple splice variants. A genome-wide analysis demonstrates that antigens for approximately 80% of the human protein-coding genes can be selected with this strategy.
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| 5. |
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| 6. |
- Björklund, Asa K, et al.
(författare)
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Quantitative assessment of the structural bias in protein-protein interaction assays.
- 2008
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 8:22, s. 4657-46667
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Tidskriftsartikel (refereegranskat)abstract
- With recent publications of several large-scale protein-protein interaction (PPI) studies, the realization of the full yeast interaction network is getting closer. Here, we have analysed several yeast protein interaction datasets to understand their strengths and weaknesses. In particular, we investigate the effect of experimental biases on some of the protein properties suggested to be enriched in highly connected proteins. Finally, we use support vector machines (SVM) to assess the contribution of these properties to protein interactivity. We find that protein abundance is the most important factor for detecting interactions in tandem affinity purifications (TAP), while it is of less importance for Yeast Two Hybrid (Y2H) screens. Consequently, sequence conservation and/or essentiality of hubs may be related to their high abundance. Further, proteins with disordered structure are over-represented in Y2H screens and in one, but not the other, large-scale TAP assay. Hence, disordered regions may be important both in transient interactions and interactions in complexes. Finally, a few domain families seem to be responsible for a large part of all interactions. Most importantly, we show that there are method-specific biases in PPI experiments. Thus, care should be taken before drawing strong conclusions based on a single dataset.
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| 7. |
- Caesar, Robert, 1973, et al.
(författare)
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Comparative proteomics of industrial lager yeast reveals differential expression of the cerevisiae and non-cerevisiae parts of their genomes
- 2007
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 7:22, s. 4135-4147
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Tidskriftsartikel (refereegranskat)abstract
- The proteomes of three industrial lager beer strains, CMBS33, OG2252 and A15, were analysed under standardised laboratory growth conditions. Protein spots in the 2-DE pattern of the lager strains were subjected to MS/MS to identify protein variants. We found the protein composition of the three lager strains to be qualitatively rather similar, while being substantially different from the Saccharomyces cerevisiae strain BY4742. Database searches using several fully sequenced genomes from the Saccharomyces genera indicated that the non-cerevisiae proteins in the 2-D pattern of lager strains were most closely related to S. bayanus. For many proteins the regulation of the bayanus-like protein and its cerevisiae counterpart varied in a strain-dependent manner, e.g. the bayanus-like form of Tdh3p was roughly eight-fold more abundant than the cerevisiae form in the OG2252 strain. We also found differential regulation of cerevisiae- and bayanus-like proteins during various stress conditions like low temperature growth, and adaptation to high temperatures or high salinity, e.g. for Arg1p, Sti1p and Pdc1p. Our data on the differential regulation of the two genomes in these hybrid strains may have important industrial implications for strain improvement and strain protection. © 2007 Wiley-VCH Verlag GmbH & Co. KGaA.
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| 8. |
- Dubrovska, Anna, et al.
(författare)
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Efficient enrichment of intact phosphorylated proteins by modified immobilized metal-affinity chromatography
- 2005
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 5:18, s. 4678-4683
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Tidskriftsartikel (refereegranskat)abstract
- Phosphoproteome studies are hampered by the lack of methods which allow a comprehensive and fast analysis of intact phosphoproteins. Here we describe an immobilized metal-affinity chromatography (IMAC)-based technique for the enrichment of phosphorylated proteins, which allows recovery of up to 90% of phosphoproteins. This technique is compatible with 2-DE and can be applied to cultured cells and tissues.
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| 9. |
- Duroux, Meg, et al.
(författare)
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Light-induced immobilization of biomolecules as an attractive alternative to micro-droplet dispensing-based arraying technologies
- 2008
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Ingår i: Proteomics. - : Wiley. - 1615-9861 .- 1615-9853. ; 7:19, s. 1113-1113
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Tidskriftsartikel (refereegranskat)abstract
- The present work shows how UV light-induced molecular immobilisation (LIMI) of biomolecules onto thiol reactive surfaces can be used to make biosensors, without the need for traditional microdispensing technologies. Using LIMI, arrays of biomolecules can be created with a high degree of reproducibility. This technology can be used to circumvent the need for often expensive nano/microdispensing technologies. The ultimate size of the immobilised spots is defined by the focal area of the UV beam, which for a diffraction-limited beam can be less than 1 m in diameter. LIMI has the added benefit that the immobilised molecules will be spatially oriented and covalently bound to the surface. The activity of the sensor molecules is retained. Antibody sensor arrays made using LIMI demonstrated successful antigen binding. In addition, the pattern of immobilised molecules on the surface is not restricted to conventional array formats. The ultimate consequence of the LIMI is that it is possible to write complex protein patterns using bitmaps at high resolution onto substrates. Thus, LIMI of biomolecules provides a new technological platform for biomolecular immobilisation and the potential for replacing present microdispensing arraying technologies.
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| 10. |
- Eisenacher, Martin, et al.
(författare)
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Getting a grip on proteomics data - Proteomics Data Collection (ProDaC)
- 2009
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Ingår i: Proteomics. - : Wiley. - 1615-9861 .- 1615-9853. ; 9:15, s. 3928-3933
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Tidskriftsartikel (refereegranskat)abstract
- In proteomics, rapid developments in instrumentation led to the acquisition of increasingly large data sets. Correspondingly, ProDaC was founded in 2006 as a Coordination Action project within the 6th European Union Framework Programme to support data sharing and community-wide data collection. The objectives of ProDaC were the development of documentation and storage standards, setup of a standardized data submission pipeline and collection of data. Ending in March 2009, ProDaC has delivered a comprehensive toolbox of standards and computer programs to achieve these goals.
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