Proteome Imaging

The Proteome Imaging team, 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 SIB Swiss Institute of Bioinformatics.

Melanie has been constantly updated and enhanced based on feedback from specialized users. Currently, Melanie is jointly distributed by Swiss Institute of Bioinformatics and by Cytiva (formerly GE Healthcare Life Sciences). Melanie's algorithms and interface were then adapted to the visualization 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 visualization 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 visualization and analysis of correlated data are necessary. Developing proteome imaging tools is our leitmotiv.

Tools developed by the team:

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. Muller, 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:

  • Sayeed, Maheen & Beckett, P. & Voordijk, Sonja & Hirano, Joe & Zang, Y. & Chimento, David & Abarca Heidemann, Karin. (2017). Enhanced HCP Coverage Analysis utilizing Multiplexed 2D Electrophoresis [pdf]
  • Voordijk, Sonja & Sayeed, Maheen & Bouchet, Gerard & Catherinet, Sebastien & Walther, Daniel & Beckett, Phil & Xenarios, Ioannis & Hirano, Joe & Abarca Heidemann, Karin. (2017) Robust HCP Coverage Analysis with Dedicated Melanie Software [pdf]
  • 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:

  • Proteomics analysis revealed the presence of inflammatory and oxidative stress markers in the plasma of migraine patients during the pain period in Brain Research, Volume 1797, 15 December 2022 [Article]
  • Comparison of the proteome patterns of adipose-derived stem cells with those treated with selegiline using a two dimensional gel electrophoresis analysis in Biotechnic & Histochemistry, Volume 95, 2020 - Issue 3 [Article]
  • Differential expression of porcine testis proteins during postnatal development in Animal Reproduction Science, Volume 123, Issues 3–4, February 2011, Pages 221-233 [Article]
  • Exploiting the potential of 2D DIGE and 2DE immunoblotting for comparative analysis of crude extract of Trichinella britovi and Trichinella spiralis muscle larvae proteomes in Veterinary Parasitology, Volume 289, January 2021. [Article]
  • 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]
  • Development of high-performance two-dimensional gel electrophoresis for human hair shaft proteome in Plos One. [Article]
  • Endometriosis Peritoneal Fluid Factors Involved in the Alteration of Decidualization Process in Biotechnology & Biotechnological Equipment. [Article]
  • Differential in Gel Electrophoresis (DIGE) Comparative Proteomic Analysis of Macrophages Cell Cultures in Response to Perthamide C Treatment in Marine Drugs. [Article]
  • Sheikhi R, Amin M, Hamidinia M, Assarehzadegan M A, Rostami S, et al. Comparative Proteomics Analysis of Two Strains of Neisseria meningitidis Serogroup B and Neisseria lactamica in Journal of Microbiology. [Article]
  • Proteomic study of pig's spleen in Journal of Food Sciences. [Article]
  • Divergent selection for residual feed intake affects the transcriptomic and proteomic profiles of pig skeletal muscle in Journal of Animal Science. [Article]
  • A study on Nim expression in Bacteroides fragilis in Microbiology [Article]
  • The proteomics approach to find biomarkers in gastric cancer. in Journal of Korean Medical Science. [Article]
  • Production of Paralytic Shellfish Toxins (PSTs) in Toxic Alexandrium catenella is Intertwined with Photosynthesis and Energy Production. in Toxins. [Article]
  • Glycosylated VCAM-1 isoforms revealed in 2D western blots of HUVECs treated with tumoral soluble factors of breast cancer cells in BMC Chemical Biology. [Article]
  • Effects of T-2 toxin on the muscle proteins of shrimp (Litopenaeus vannamei) � a proteomics study in Journal of the Science of Food and Agriculture. [Article]
  • A comparative proteomic study identified LRPPRC and MCM7 as putative actors in imatinib mesylate cross-resistance in Lucena cell line in Proteome Science. [Article]
  • Annotated Differentially Expressed Salivary Proteins of Susceptible and Insecticide-Resistant Mosquitoes of Anopheles stephensi in PLOS ONE. [Article]
  • Comparison of the Proteome Profiling of Iranian isolates of Leishmania tropica, L. major and L. infantum by Two-Dimensional Electrophoresis (2-DE) and Mass-spectrometry in Iranian Journal of Parasitology. [Article]
  • Psoriasin (S100A7) is a major Escherichia coli-cidal factor of the female genital tract in mucosal immunology. [Article]
  • Proteomic identification of fucosylated haptoglobin alpha isoforms in ascitic fluids and its localization in ovarian carcinoma tissues from Mexican patients in Journal of Ovarian Research. [Article]
  • Data in support of comparative physiology and proteomic analysis of two wheat genotypes contrasting in drought tolerance in Journal Data in Brief. [Article]
  • Information quality in proteomics in Brief Bioinform. [Article]
  • Minimization of side reactions during Lys Tag derivatization of C-terminal lysine peptides in Analytica Chimica Acta [Article]

Videos:

  • Melanie 9 Coverage Principles [View]
  • Melanie 9 Expression short presentation [View]
Proteome Imaging - Clinical Bioinformatics Group - SIB Swiss Institute of Bioinformatics