| 11. |
- Eisenacher, Martin, et al.
(författare)
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Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands
- 2009
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Ingår i: Proteomics. - : Wiley. - 1615-9861 .- 1615-9853. ; 9:2, s. 218-222
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Tidskriftsartikel (refereegranskat)abstract
- ProDaC (Proteomics Data Collection), a Coordination Action within the 6th EU framework programme, was created to support the collection, distribution and public availability of data from proteomics experiments. Within the consortium standards are created and maintained enabling an extensive data collection within the proteomics community. Important elements of ProDaC are workshops held twice a year to allow communication between the ProDaC partners and to report the ongoing progress. The most recent assembly was the 4th ProDaC workshop on August 15th, 2008, in Amsterdam, The Netherlands. It took place directly before the 7th HUPO Annual World Congress (Human Proteome Organisation). Work package coordinators and partners presented the progress achieved since the last meeting. Additionally, an EU official presented funding opportunities for proteomics in the next EU framework programme and five external speakers presented talks about their work in relation to ProDaC.
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| 12. |
- Eisenacher, Martin, et al.
(författare)
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Proteomics Data Collection-5th ProDaC Workshop
- 2009
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Ingår i: Proteomics. - : Wiley. - 1615-9861 .- 1615-9853. ; 9:14, s. 3626-3629
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Tidskriftsartikel (refereegranskat)abstract
- The Proteomics Data Collection (ProDaC) consortium, a "Coordination Action" funded by the 6th EU Framework Programme, started in October 2006. Its aim was to facilitate the collection and distribution of proteomics data and the public availability of data sets from proteomics experiments. Within the consortium standard formats are created and tools are developed to allow extensive data collection within the proteomics community. An important part of ProDaC is the organization of workshops twice a year to inform about the consortium's progress and to stimulate communication between the ProDaC partners and between partners and interested members of the proteomics community. ProDaC ends on March 31, 2009. The most recent (and final) workshop was the 5th ProDaC workshop held on March 4, 2009 in Kolympari, Crete, Greece. The progress since the last meeting and an overall summary was presented by the work package coordinators and partners. Four external speakers presented talks about their work in relation to ProDaC.
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| 13. |
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| 14. |
- Mayer, Gerhard, et al.
(författare)
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The HUPO proteomics standards initiative-mass spectrometry controlled vocabulary
- 2013
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Ingår i: Database: the journal of biological databases and curation. - : Oxford University Press (OUP). - 1758-0463. ; , s. 009-009
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Tidskriftsartikel (refereegranskat)abstract
- Controlled vocabularies (CVs), i.e. a collection of predefined terms describing a modeling domain, used for the semantic annotation of data, and ontologies are used in structured data formats and databases to avoid inconsistencies in annotation, to have a unique (and preferably short) accession number and to give researchers and computer algorithms the possibility for more expressive semantic annotation of data. The Human Proteome Organization (HUPO)-Proteomics Standards Initiative (PSI) makes extensive use of ontologies/CVs in their data formats. The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. Owing to the range of topics covered by the CV, collaborative development across several PSI working groups, including proteomics research groups, instrument manufacturers and software vendors, was necessary. In this article, we describe the overall structure of the CV, the process by which it has been developed and is maintained and the dependencies on other ontologies.
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| 15. |
- Schroetter, Andreas, et al.
(författare)
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Key players in neurodegenerative disorders in focus - New insights into the proteomic profile of Alzheimer's disease, schizophrenia, ALS, and multiple sclerosis24th HUPO BPP Workshop : September 29, 2015, Vancouver, Canada
- 2016
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Ingår i: Proteomics. - : Wiley-Blackwell Publishing Inc.. - 1615-9853 .- 1615-9861. ; 16:7, s. 1047-1050
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Tidskriftsartikel (refereegranskat)abstract
- The HUPO Brain Proteome Project (HUPO BPP) held its 24th workshop in Vancouver, Canada, September 29, 2015. The focus of the autumn workshop was on new insights into the proteomic profile of Alzheimer's disease, schizophrenia, ALS and multiple sclerosis.
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| 16. |
- Spitzer, Philipp, et al.
(författare)
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cNEUPRO: Novel Biomarkers for Neurodegenerative Diseases.
- 2010
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Ingår i: International journal of Alzheimer's disease. - : Hindawi Limited. - 2090-0252. ; 2010
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Forskningsöversikt (refereegranskat)abstract
- "clinical NEUroPROteomics of neurodegenerative diseases" (cNEUPRO) is a Specific Targeted Research Project (STREP) within the sixth framework program of the European Commission dedicated to the search for novel biomarker candidates for Alzheimer's disease and other neurodegenerative diseases. The ultimate goal of cNEUPRO is to identify one or more valid biomarker(s) in blood and CSF applicable to support the early and differential diagnosis of dementia disorders. The consortium covers all steps required for the discovery of novel biomarker candidates such as acquisition of high quality CSF and blood samples from relevant patient groups and controls, analysis of body fluids by various methods, and finally assay development and assay validation. Here we report the standardized procedures for diagnosis and preanalytical sample-handling within the project, as well as the status of the ongoing research activities and some first results.
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| 17. |
- Walz, Anke, et al.
(författare)
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Identification of glycoprotein receptors within the human salivary proteome for the lectin-like BabA and SabA adhesins of Helicobacter pylori by fluorescence-based 2-D bacterial overlay
- 2009
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 9:6, s. 1582-1592
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Tidskriftsartikel (refereegranskat)abstract
- Because gastric infection by Helicobacter pylori takes place via the oral route, possible interactions of this bacterium with human salivary proteins could occur. By using modified 1- and 2-D bacterial overlay, binding of H. pylori adhesins BabA and SabA to the whole range of salivary proteins was explored. Bound salivary receptor molecules were identified by MALDI-MS and by comparison to previously established proteome maps of whole and glandular salivas. By use of adhesin-deficient mutants, binding of H. pylori to MUC7 and gp-340 could be linked to the SabA and BabA adhesins, respectively, whereas binding to MUC5B was associated with both adhesins. Binding of H. pylori to the proline-rich glycoprotein was newly detected and assigned to BabA adhesin whereas the SabA adhesin was found to mediate binding to newly detected receptor molecules, including carbonic anhydrase VI, secretory component, heavy chain of secretory IgA1, parotid secretory protein and zinc-alpha(2)-glycoprotein. Some of these salivary glycoproteins are known to act as scavenger molecules or are involved in innate immunity whereas others might come to modify the pathogenetic properties of this organism. In general, this 2-D bacterial overlay technique represents a useful supplement in adhesion studies of bacteria with complex protein mixtures.
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