Proteome Imaging

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 Swiss-Prot Group.

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 / Melanie
Software Package for 2-D Gel Electrophoresis computer analysis.
MSight
Liquid chromatography and mass spectrometry imaging.

Partners and Collaborations:

Publications:

  • 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]

Posters:

  • 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].

References:

  • 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]
Proteome Imaging - Swiss-Prot Group - SIB Swiss Institute of Bioinformatics