Development
2. Methodology
ProteoSuite is being developed in the Java programming language to support cross-platform use. The code is released under the Apache License 2.0 allowing the community the reusability of components. At present, input files are based on the HUPO-PSI standard files mzML (raw data) and mzIdentML (identification data). The current version of ProteoSuite uses the jmzML API for raw data, jmzIdentML API for identifications and jmzQuantML API for quantitation outputs. Additionally, the jfreeChart library is used for charts.
Source code and a beta version can be accessed and downloaded at http://code.google.com/p/proteo-suite/.
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ProteoSuite employs the Agile software development as the standard methodology. This approach will benefit the management of the project, improve the technical quality and usability of the software produced.
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The following figure shows an update of the plugins implemented in xTracker which is used for the quantitation process. The figure is updated each time a new plugin is available and tested.
Last update: 30 April 2013.
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The following table represents a summary of the different tasks that are being covered in this development. This table is updated on regular basis to report the current status.
| Task | Leader | Start | Status | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| I Experimental methods | |||||||||||||
| 1 - MS1 label-based techniques | |||||||||||||
| 1.1 Metabolic labelling | |||||||||||||
| 1.1.1 SILAC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL | 01/12/2011 | Ongoing | ||||||||||
| 1.1.2 15N . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | Cranfield | 02/04/2012 | Ongoing | ||||||||||
| 1.2 Standards for absolute quantitation | |||||||||||||
| 1.2.1 AQUA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| 1.2.2 QConCat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| 1.3 Accurate feature detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| 1.4 Peptide to protein inference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL | 01/04/2013 | Ongoing | ||||||||||
| 2 - Label free by MS1 intensity | |||||||||||||
| 2.1 RT aligment algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL | 01/04/2013 | Ongoing | ||||||||||
| 3 - Spectral counting | |||||||||||||
| 3.1 Basic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| 3.2 emPAI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | Cranfield | 19/10/2012 | Beta version available | ||||||||||
| 3.3 APEX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| 3.4 QSpec . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| 4 - MS2 Tag based methods | |||||||||||||
| 4.1 iTRAQ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | Cranfield | 02/04/2012 | Beta version available | ||||||||||
| 4.2 TMT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | Cranfield | 02/04/2012 | Beta version available | ||||||||||
| 5 - SRM / MRM based . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| 6 - Other experimental methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| II Statistical analysis methods | |||||||||||||
| 7 - Normalisation methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| 8 - Interface for R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| 9 - Software Benchmarking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| III Graphical interface | |||||||||||||
| 10 - Interface for parameters capture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL | 19/03/2012 | Beta version available | ||||||||||
| 11 - 1D spectrum view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL | 01/02/2011 | Beta version available | ||||||||||
| 12 - 1D chromatogram view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL | 01/03/2011 | Beta version available | ||||||||||
| 13 - 2D Map viewer raw data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL | 01/04/2011 | Beta version available | ||||||||||
| 14 - 2D Map viewer for quant data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL | ||||||||||||
| 15 - Outputs | |||||||||||||
| 15.1 Tabular formats (CSV , Excel, etc) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL | 01/04/2013 | Beta version available | ||||||||||
| 15.2 mzQuantML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL/Cranfield | 16/11/2012 | Beta version available | ||||||||||
| 15.3 Import / Export to PRIDE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL | ||||||||||||
| IV Identification data | |||||||||||||
| 16 - Multiple search engine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL | ||||||||||||
| 17 - Protein inference algorithms | |||||||||||||
| 17.1 GAPP's APS scoring . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| 17.2 OMSSA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| 17.3 X!Tandem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| 17.4 Inspect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | TBA | ||||||||||||
| 17.5 MSGF+ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL/UCSD | 01/04/2013 | Beta version available | ||||||||||
| V Standards | |||||||||||||
| 18 - Import / export mzML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL | 01/02/2011 | Beta version available | ||||||||||
| 19 - Import / export mzIdentML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL | 16/11/2012 | Beta version available | ||||||||||
| 20 - Import / export mzQuantML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | UoL | 16/11/2012 | Beta version available | ||||||||||
TBA=To be assigned. Last update: 30 April 2013
If you want to contribute to this project please do not hesitate to contact us.
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