Improved image analysis in proteomics research
2D gel electrophoresis (2DGE), is not only time consuming but can
often miss 'hits' and give false positives. But it doesn't have to
be that way, according to Swedish company Ludesi.
Speaking at the AngloNordic Biotech Conference IV, held in London last week, Ludesi CEO Ola Forsstrom-Olsson believes his company has developed a solution to these problems so that its pay-per-image service can free up scientists' time and give better, more reproducible results. Although 2D electrophoresis is not a new technology - it's use dates back to the 70's - it is still one of the most useful when trying to decipher the complex make-up of mixtures of biomolecules. However, automatic image analysis is flawed, while manual analysis is time consuming and requires significant training. Proteomics scientists organise their digital image files using Ludesi's software to enable them to tailor the analysis to what they need. The Swedish company then carry out the work and the results can be downloaded and visualised using the Ludesi software client. Forsstrom-Olsson explained to DrugResearcher.com that the whole process is faster than if they did the analysis themselves, taking days instead of weeks for a typical project. He continued: "Another of the major problems [with 2DGE image analysis] is that there is a lot of lab to lab variability because there are no strict protocols of how to do the analysis across the industry." However, the team at Ludesi employ protocols across their analysis leading to what Forsstrom-Olsson asserts is the "industry's highest level of accuracy." This accuracy is also possible because, typically, analysis software has to be a trade off between ease-of-use and accuracy. This isn't necessary when the analysis is done by Ludesi, as only the visualisation software needs to be easy to use. Quality control is carried out at each stage of images analysis: protein spot detection, spot segmentation, matching, quantification and normalisation. This can reduce error propagation and therefore the quality of subsequent results. Indeed, Ludesi claims that: "the final outcome of experiments will typically show a two- to threefold increase in the number of statistically significant changes in expression levels compared to competitors," and a large decrease in the number of false positives. In an independent study run by Steven Elliott and his colleagues at Johns Hopkins University, US, images were sent to Ludesi and the results compared to automatic and manual analysis of three of Ludesi's software rivals: GE Healthcare's Decyder 5.01, and two products from Nonlinear Dynamics in Progenesis v2005 and PG240 with SameSpots. In fact, the analysis using the latter software was carried out by Nonlinear scientists themselves. Elliott concluded that: "Ludesi provided the highest overall correctness for the serum gels analysed, based on spot detection matching and segmentation. This will improve the ability of the 2D gel platform to track protein changes." The team also said that manual editing of Progenesis analyses was necessary when looking at complex 2D gels as it improved the quality of analysis. They also said that "complex serum gels with different concentrations and spot constellations make a Progenesis SameSpots alignment difficult". The service is also being used by researchers at the National Institutes of Health, DSM Nutritional Products and Mitsubishi Pharmaceuticals, among others. Forsstrom-Olsson said that he is planning to expand the company's services into other areas of proteomics data analysis with some initial projects already under way - although he wouldn't divulge details at this time.
