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PriDE is a thin and high-performance Java O/R mapper for relational databases. It does not follow any persistence management standards like JDO or EJB-CMP but relies on common design patterns and is production-proved in both J2SE and J2EE environments.
PRIDE Tool Suite is a collection of tools and libraries to handle Mass Spectrometry (MS) related data. These tools can visualize and perform quality assessment of your MS dataset as well as accessing all the experiments in PRIDE public database. These libraries are a host of programmable APIs which allows you to build highly customized proteomics applications.
The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data. It has been developed to provide the proteomics community with a public repository for protein and peptide identifications together with the evidence supporting these identifications. The original motivation behind its development was to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE,
jmzReader - Easily Accessing Peak List FilesGeneralThe jmzReader library is a collection of Java APIs to parse the most commonly used MS peak list formats. Currently, the library contains parsers for dta mgf ms2 mzData mzXML pkl mzML PRIDE XML All parsers are optimized to be used in conjunction with mzIdentML (see link in the left panel). Based on a custom build class to efficiently parse text files line by line all parsers can handle arbitrary large files in minimal memory, allowing easy and ef
This project is aimed at providing a web-based interface to creating a user-defined, processed protein sequence database based on the UniProtKB protein sequence databases SwissProt and TrEMBL. The live web page can be found at http://www.ebi.ac.uk/pride/dod. The project was supported by the BBSRC Tools and Resources grant 'Database on Demand' (BB/F016255/1).
XTandem ParserNews What is XTandem Parser? Libraries Maven Dependency Converting XTandem Files to PRIDE XML Result Analysis Screenshots XTandem Parser Publications: Muth et al: Proteomics 2010 Apr;10(7):1522-4. If you use XTandem Parser as part of a paper, please include the reference above. SearchGUI: To run X!Tandem searches we recommend the use of SearchGUI. PeptideShaker: To visualize and analyze X!Tandem results we recommend the use of PeptideShaker. NewsApril 28 2012: XTandem Parser v1.4 i
PRIDE ConverterNews About PRIDE Converter Getting PRIDE Converter Requirements Downloading Troubleshooting Upgrading How to Submit Data to PRIDE How to Reference PRIDE Submissions Getting Help Source Code Screenshots PRIDE Converter Publications: Barsnes et al: Nat Biotechnol. 2009 Jul;27(7):598-9. Barsnes et al: Methods Mol Biol. 2011;694:237-53. If you publish your data as part of a paper, please include the first reference above. See the How to Reference PRIDE Submissions section. NewsJanuary