The Proteome Imaging group, 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
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 SA ( GeneBio)
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 / MelanieSoftware Package for 2-D Gel Electrophoresis computer analysis.
MSightLiquid chromatography and mass spectrometry imaging.
Partners and Collaborations:
- ImageMaster / Melanie is distributed by GE Healthcare, under the ImageMaster 2D Platinum brand name.
- MSight was involved in bio-, nano, and information-related technologies European project Loccandia, for more details about Loccandia project see:
- Appel RD, Palagi PM, Walther D, Vargas JR, Sanchez JC,
Ravier F, Pasquali C, Hochstrasser DF. Melanie II a
third-generation software package for analysis of two-dimensional
electrophoresis images: I. Features and user interface. Electrophoresis
1997; 18: 2724-2734. [PubMed]
- P.M. Palagi , D. Walther, M. Quadroni, S. Catherinet, J. Burgess, C.G. Zimmermann-Ivol, J.C. Sanchez, P.A. Binz, D.F. Hochstrasser and R.D. Appel,
MSight:An image analysis software for liquid chromatography-mass spectrometry.
Proteomics 2005; 5: 2381-2384. [PubMed]
- P.M. Palagi, and F. Lisacek,
Analytical bioinformatics for proteomics, in Bioinformatics: A Swiss Perspective
R.D. Appel and E. Feytmans, Editors. 2009, World Scientific: Singapore. [Book chapter]
- R.D. Appel, J.R. Vargas, P.M. Palagi, D. Walther and D.F. Hochstrasser,
Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms
Electrophoresis 1997; 18: 2735-2748. [PubMed]
- P.M. Palagi, M. Müller, D. Walther and F. Lisacek,
LC/MS Data Processing for Label-Free Quantitative Analysis
Data Mining in Proteomics Methods in Molecular Biology, 2011, Volume 696, Part 5, 369-377. [PubMed]
- D. Walther, G. Bouchet, S. Catherinet, S. Pelhatre, M. Tuloup, P. M. Palagi and R. D. Appel,
Melanie: analysis of proteomics data with ImageMaster and MSight
in 7th Siena Meeting From Genome To Proteome-Back to the future. [pdf].
- D. Walther, M. Quadroni, S. Catherinet, D.F. Hochstrasser, P. M. Palagi and R. D. Appel,
MSight: an LC-MS image analysis software
in 13th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) [pdf].
- A. W. Dowsey, Jane A. English, F. Lisacek, J.S. Morris, G. Yang and M. J. Dunn,
Image analysis tools and emerging algorithms for expression proteomics
in Proteomics, 2010. 10: p. 4226?4257.[Abstract]
LC/MS Data Processing for Label-Free Quantitative Analysis Data Mining
in Proteomics Methods in Molecular Biology, 2011, Volume 696, Part 5, p. 369-377. [Book chapter]