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Bochum-Hordel, Germany

Meckel H.,Ruhr University Bochum | Stephan C.,Ruhr University Bochum | Stephan C.,Universitatsstrasse 136 | Bunse C.,Ruhr University Bochum | And 5 more authors.
Biochimica et Biophysica Acta - Proteins and Proteomics

Proteomics methods, especially high-throughput mass spectrometry analysis have been continually developed and improved over the years. The analysis of complex biological samples produces large volumes of raw data. Data storage and recovery management pose substantial challenges to biomedical or proteomic facilities regarding backup and archiving concepts as well as hardware requirements. In this article we describe differences between the terms backup and archive with regard to manual and automatic approaches. We also introduce different storage concepts and technologies from transportable media to professional solutions such as redundant array of independent disks (RAID) systems, network attached storages (NAS) and storage area network (SAN). Moreover, we present a software solution, which we developed for the purpose of long-term preservation of large mass spectrometry raw data files on an object storage device (OSD) archiving system. Finally, advantages, disadvantages, and experiences from routine operations of the presented concepts and technologies are evaluated and discussed. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. © 2013 The Authors. Published by Elsevier B.V. All rights reserved. Source

Hofmann T.M.,Cologne University of Applied Sciences | Mudimu O.A.,Cologne University of Applied Sciences | Brauner F.,Cologne University of Applied Sciences | Strauss A.,Universitatsstrasse 136

In case of an acute disorder of the lung, for the patient every second counts. The artificial maintenance of gas exchange and blood circulation is state-of-the-art of science and technology in the stationary field during surgery and chronic diseases. However, there are no suitable systems for emergency rescue. Therefore, a system that suits the requirements of a modern emergency medical service in weight and compactness is developed. Two rotor bearing systems for blood pumps were tested for water and pork blood and compared by means of pump performance charts. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

Mayer G.,Ruhr University Bochum | Montecchi-Palazzi L.,EMBL EBI | Ovelleiro D.,EMBL EBI | Jones A.R.,University of Liverpool | And 13 more authors.

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. © The Author(s) 2013. Published by Oxford University Press. Source

Riebe O.,HygCen Germany GmbH | Riebe O.,Universitatsstrasse 136 | Beilenhoff U.,DEGEA Deutsche Gesellschaft fur Endoskopie Assistenzpersonal E. V. | Von Rheinbaben F.,HygCen Germany GmbH | And 5 more authors.
Hygiene + Medizin

Background: The difficulty and complexity of reprocessing of flexible endoscopes have been known for more than 20 years and have been already discussed after publication of the HYGEA study in 2002. More than ten years later, we now have re-evaluated this investigation using a comparable methodology. Method: The quality of the reprocessing procedure of colonoscopes, gastroscopes and duodenoscopes was tested under routine conditions in 16 endoscopy hospital facilities as well as in seven practices. In our investigation we included different types of endoscopes from different manufacturers as well as the associated water bottle systems and the air/water and suction valves. In addition, data about the performance of the reprocessing procedure were collected using a questionnaire. Results: Of 30 biopsy channels of the endoscopes tested, eight sampled by taking swabs and seven sampled by investigating the rinse fluid (in total 13 of 30 tested endoscopes) showed bacterial contamination at low levels (< 10 Colony Forming Units (CFU) per endoscope). In addition five of 30 water samples drawn from rinsing water of the optical rinsing systems and six of 30 samples of the rinsing bottles showed weak microbial contaminations (> 1 CFU per ml or per tube). The tube of one optical rinsing system had a bacterial load of 52 CFU per ml. Although unacceptable results were not observed for the endoscopes themselves, the air/water and suction valves were often found to be microbially contaminated. Samples taken from the valves showed contamination in case of 24 air/water valves and 24 suction valves, five of them having mor e than 100 CFU per valve. Conclusion: The results presented here of the endoscope tests (reprocessing with washer-disinfectors (WD) and validated processes) and the flushing bottles of the optics tests show that lessons were learned from the HYGEA study and improvements in everyday endoscopy facilities have been achieved. However, the consistent annual average complaint rates of about 4 % as part of the quality review for colonoscopies conducted by the German Associations of Statutory Health Insurance Physicians BfArMshould prompt further efforts in endoscope reprocessing. Source

Mayer G.,Ruhr University Bochum | Stephan C.,Ruhr University Bochum | Stephan C.,Universitatsstrasse 136 | Meyer H.E.,Ruhr University Bochum | And 4 more authors.
Journal of Proteomics

With the growing amount of experimental data produced in proteomics experiments and the requirements/recommendations of journals in the proteomics field to publicly make available data described in papers, a need for long-term storage of proteomics data in public repositories arises. For such an upload one needs proteomics data in a standardized format. Therefore, it is desirable, that the proprietary vendor's software will integrate in the future such an export functionality using the standard formats for proteomics results defined by the HUPO-PSI group. Currently not all search engines and analysis tools support these standard formats. In the meantime there is a need to provide user-friendly free-to-use conversion tools that can convert the data into such standard formats in order to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. ProCon is such a conversion tool written in Java for conversion of proteomics identification data into standard formats mzIdentML and Pride XML. It allows the conversion of Sequest™/Comet .out files, of search results from the popular and often used ProteomeDiscoverer® 1.x (x. =. versions 1.1 to1.4) software and search results stored in the LIMS systems ProteinScape® 1.3 and 2.1 into mzIdentML and PRIDE XML.This article is part of a Special Issue entitled: Computational Proteomics. © 2015. Source

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