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List of Developments
In the following we list all developments in relation to ProDaC; it is the intention to list not only finalized projects and tools but ONGOING to enable mutual support and to avoid doubled efforts.
| SHORT description (see comments column for more) |
Reference (if already exists) |
web link |
Comments | |
|---|---|---|---|---|
| mzML semantic validator | validator code for mzML | https://psidev.svn.sourceforge.net/svnroot/psidev/psi/mzml/validator/ | ||
| ProDaC Online Validator | web-based implementation of the mzML semantic validator | Eisenacher M, Hardt T, Hamacher M, Martens L, Häkkinen J, Levander F, Apweiler R, Meyer HE, Stephan C (2008) Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea. Proteomics 2008 8(7):1326-30 (PubMed) |
http://eddie.thep.lu.se/prodac_validator/validator.pl | |
| PRIDE Converter |
Converts MS data into valid PRIDE XML. Wizard-like graphical user interface, and access to the Ontology Lookup Service (OLS). | http://code.google.com/p/pride-converter/ | Formats supported (excerpt): ms_lims, Mascot Generic Files, Mascot Dat Files, X!Tandem, Spectrum Mill... See home page for the list of currently supported MS formats. | |
| PRIDE Wizard |
Converts MS data and Mascot results into PRIDE XML
format. |
Siepen JA, Swainston N, Jones AR, Hart SR, Hermjakob H, Jones P, Hubbard SJ. An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ, Proteome Science 2007;5:4 (PubMed) | http://www.mcisb.org/resources/PrideWizard/index.html | Currently supports iTRAQ and future extensions are planned for SILAC data. |
| ProCon | Java stand-alone tool for conversion of Proteomics formats (see comments for details) | http://www.medizinisches-proteom-center.de/software |
conversion of ProteinScape results to PRIDE XML (ready); Sequest results to AnalysisXML (in progress) | |
| MascotDatFile | Java parser for Mascot result files |
Helsens K, Martens L, Gevaert K, Vandekerckhove J, MascotDatfile,
an open-source library to fully parse and analyze Mascot MS/MS search
results, Proteomics 2007; 7(3):364-6 (PubMed, Wiley) |
http://genesis.ugent.be/MascotDatfile/ |
|
| PSI list of tools reading / writing mzML | "Current and future support for mzML" | http://psidev.info/index.php?q=node/257 | ||
| PIKE - Protein Information and Knowledge Extractor | Retrieves biological information from several databases at once, regarding to a set of proteins. | http://proteo.cnb.csic.es:8080/pike/ | Supports PRIDE xml files as input and also as output. | |
| MIAPE Generator tool |
Helps to generate MIAPE GE, GI, MS and MSI compliant reports |
http://www.proteored.org/acceso.asp |
You have to create a free user account in order to access the tool. Import and export of standard XML data formats (in progress) |
|
| OMSSA Parser |
An open-source library to parse and extract data from OMSSA MS/MS search results |
http://code.google.com/p/omssa-parser |
Java parser for OMSSA result files |