Development

1. Implementation

2. Methodology

3. Development pipeline

4. Development timeline

 

 

1. Implementation

 

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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2. Methodology

 

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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3. Development pipeline

 

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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4. Development Timeline

 

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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Copyright © ProteoSuite 2011-2013   Project Funded by the British Biotechnology and Biological Sciences Research Council, under the Bioinformatics and Biological Resources Scheme:
http://www.bbsrc.ac.uk/funding/opportunities/2009/bioinformatics-biological-resources-fund.aspx