Nonlinear Dynamics unfolds new proteomics strategy

By Dr Matt Wilkinson

- Last updated on GMT

A new range of software has been launched to provide researchers
with tools to analyse multiple proteomics techniques and yield more
complete data sets.

Three new Progenesis software offerings: SameSpots v2.0, LC-MS and Stats; were launched at the Association of Biomolecular Resource Facilities (ABRF 2007) conference in Tampa, Florida this week with the aim of streamlining the analysis of proteomics experiments while giving results with higher statistical significance.

The overlap between two of the most commonly used proteomics techniques, 2D gel electrophoresis (2D) and liquid chromatography mass spectrometry (LC-MS), can be as little as 10 per cent, according to research published by Katrin Marcus and co-workers in the Journal of Proteome Research.

By combining the two sets of data a far greater coverage of the proteome is achieved.

"So far proteomics has struggled to provide the results everyone believes that it should be capable of," said Will Dracup, CEO of Nonlinear Dynamics.

The company claims that the latest version of its Progenesis SameSpots allows the analysis of these 2D experiments with greater speed, objectivity and statistical power than previously possible.

During the separation and identification of the proteins using 2D or LC-MS there is the potential to lose proteins of potential interest, and Nonlinear Dynamics claim that many software packages, even older versions of their own software, can lose more data during the analysis step.

Dracup believes that this loss of data has been one of the stumbling blocks in proteomics research as a lot of data was being lost before the analysis.

"This has limited proteomics greatly; so far successes have often been down to exceptionally intelligent individuals that have been able to see past the problems," he said.

The company claims the software matches 100 per cent of the observed spots using an advanced image alignment technique that leads to a complete data set - increasing the statistical relevance of the experiment.

The Progenesis LC-MS analysis software uses the same alignment protocols as SameSpots to enhance the validity of data points while minimising the need for editing.

Interestingly, Dracup believes that many researchers assumed that LC-MS allowed them to see more than the 2D analysis could and that the experiments were covering the same proteins.

According to the company the straightforward 'visualise and validate' view allows users to objectively select differences based on statistical significances, leading to greater confidence in the results.

Progenesis Stats was designed to further interrogate the results obtained during the experiments and to allow correlation of those results while "solving the statistics headache for proteomics researchers by making powerful multivariate statistics techniques accessible to non-statisticians."

Finally, Dracup believes that one of the major problems faced in proteomics research today is the apparent lack of reproducibility between laboratories.

The company is currently involved in a project, led by Jan van Oostrum and Novartis, to investigate the reproducibility of studies from various laboratories.

The project will initially focus on 2D experiments as preliminary results have indicated that this appears to be the most reproducible of the techniques.

"People are seeing cross-lab reproducibility as a real issue that needs to be tackled," said Dracup.

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