ProteinScape
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Proteomics Data Analysis & Management nnovation with Integrity Mass Spectrometry

ProteinScape - a Virtual Environment To overcome the growing complexity of proteomics experiments, Brukers bioinformatics platform, ProteinScape™, collects all your data and arranges it in a way that reflects the way you work. Customizable tables and viewers present the information such that the advanced data mining features help you get the maximum out of your data and sophisticated reports help you efficiently communicate your findings. ProteinScape is the key to running successful proteomics projects. % Project NavicjatoiM^_ The project navigation tree logically reflects the experiment...

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Proteomics Data Handling Made ProteinScape viewers enable fast and interactive evaluation and validation of proteomics data. Real-time updating of the linked displays speeds browsing and information management. Selection of viewers for protein identification E3 g>|lSKH33-4 FOP 1 ATp synthase submit alpJia pt SeteOor EntJ>es Store* Pephfes 5C dMSWtppin] ftsnk Investigation of identification results (in the Peptide and protein perspective), here from a 1D gel workflow with Navigation Tree, gel image, protein and peptide table. Sequence Viewer, Survey viewer and spectrum.

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Powerful Tools for Protein Analysis ProteinScape uses Mascot as search engine (other engines are supported via mzIdentML) together with expert algoritms that increase the quality and reliability of protein identifications. Compiling protein lists for improved search results The ProteinExtractor compiles multiple peptide lists from a number of different techniques and instruments, significantly improving overall search results and increasing confidence in identifications. Decoy validation approaches ProteinScape supports decoy-database approaches to generate protein lists based on defined...

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Biological knowledge at your Once a protein is identified, ProteinScape automatically assembles information such as taxonomy, GO terms, and structure files from external databases. display highlights identified regions and modifications and a gene ontology overview gives information on protein Extracting Knowledge through Data Mining Managing the huge amount of data generated in proteomics projects can be a daunting task. Efficient tools are required to quickly and precisely extract information from the mass of available data. ProteinScape uses queries to search defined data subsets for...

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Integrated Search Engine for Glycans One of the most important classes glycosylation. Glycans are very difficult to investigate manually so ProteinScape provides the following analysis and automation tools: ■ the search engine GlycoQuest ■ Glycan search result tables ■ Spectrum Viewer for glycan annotation ■ Glycan Structure Editor GlycoQuest is a built-in glycan search engine supporting several kinds of ■ Released glycans, free or reduced ■ Glycan moieties of glycopeptides As with protein database searches, search parameters like glycan composition range, mass tolerances, databases, etc....

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Glycopeptide Analysis even more challenging than the ana- lysis of single glycans since additional steps like detection of glycopeptide MS/ MS spectra in LC-MS/MS data and the determination of the peptide masses are required. ProteinScape meets these challenges in a unique way. Its effective combination of spectra classification masses of the peptide and glycan moi- eties and our integrated search engine makes it a must-have tool for the analysis Glycopeptide analysis tools: glycopeptide spectra ■ Combined glycopeptide table ■ SpectrumViewer with glycan and peptide fragment annotation...

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Technical Specifications Client/Server based architecture Interactive viewers Database management User management with read/write access administration Project-oriented data management Database structure reflecting laboratory workflow, including separation protocols, free text notes etc. ProteinScape Server with a central server and five or more clients ProteinScape Workstation, with the whole system installed on a single PC Gel viewer LC-MS survey viewer Spectrum viewer Protein sequence viewer 3D protein structure viewer Glycan structure viewer Quantitation statistics viewer Venn diagram...

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