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Projects lead by the PRIMA group |
Proteome Imaging
The Proteome Imaging (PRIMA) axis is one of the three principle research axes of the Proteome Informatics Group (PIG). It has been performing research and development of image processing and analysis software since 1984. The two-dimensional gel electrophoresis (2-DE) images are an important basis for quantitative analysis and comparative proteomics. Detecting protein expression changes associated with diseases and treatments, among many other applications, has been a major incentive to the development of specialized software systems for 2-DE image analysis, such as Melanie, the software developed by the PIG. Melanie has been constantly updated and enhanced based on feedback from specialised users. Currently, Melanie is jointly distributed by GE Healthcare, under the ImageMaster 2D Platinum brand name, and by Geneva Bioinformatics (GeneBio) SA under its original name. Melanie's algorithms and interface were then adapted to the visualisation and analysis of LC-MS datasets through the MSight software. Specific algorithms to the LC-MS data analysis, such as detection or matching, had to be carried out, while the general framework and all the visualisation and manipulation tools, as well as the data and statistical analysis modules could be re-used as such. This expertise shows that a general software framework, such as the Melanie platform, can be developed that may then lead to software packages for various proteomics techniques where visualisation and analysis of correlated data are necessary. Developing proteome imaging tools is our leitmotiv.Tools developed by the group:
- ImageMaster / Melanie - Software Package for 2-D PAGE computer analysis
- MSight - Liquid chromatography and mass spectrometry imaging
Publications:
- Palagi P.M., Walther D., Quadroni M., Catherinet S., Burgess J., Zimmermann-Ivol C.G., Sanchez J.C., Binz P.A., Hochstrasser D.F., Appel R.D. MSight: An image analysis software for liquid chromatography-mass spectrometry. Proteomics 2005; 5: 2381-2384. [PubMed]
- Palagi, P.M. and Lisacek, F., Analytical bioinformatics for proteomics, in Bioinformatics: A Swiss Perspective, Appel, R.D. and Feytmans, E., Editors. 2009, World Scientific: Singapore. [Book chapter]
- Appel R.D., Vargas J.R., Palagi P.M., Walther D., Hochstrasser D.F. Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms. Electrophoresis 1997; 18: 2735-2748. [PubMed]
People working at PRIMA:
Last modified 21/Jan/2010 by PAP