Swedish group evaluate Progenesis SameSpots and report the benefits of this fourth generation 2D gel analysis software
(Newcastle upon Tyne, UK) Nonlinear Dynamics Ltd, the world leading developer of analysis solutions for proteomics and biomarker discovery, saw its Progenesis SameSpots software rigorously evaluated by Swedish researchers and results published in the Journal of Proteome Research. The publication concluded that "SameSpots represents improvements both in reproducibility and objectivity in relation to previous generations of 2-DE analysis software 1."
The researchers from the Karolinska Institute, Karolinska Biomics Center and Karolinska University Hospital (Stockholm, Sweden) compared analysis results from a lab researcher, new to the software, and an expert user from Nonlinear Dynamics. The less-experienced user achieved the same or better statistical power as the expert user when they compared multivariate and univariate statistical analysis results respectively.
The team also investigated the affect of two key steps in 2D gel data analysis, background subtraction and normalization, on variance in the analysis. The publication summarised that "Overall, normalisation method of choice had a much larger impact on the variance than had the experience of the user 1". However, results showed that the default options provided in Progenesis SameSpots introduced the least amount of variation compared to methods found in other software.
By reducing variance in 2D gel analysis and running the significant number of replicates for your experiment design you improve the statistical power, which improves your ability to detect true positives i.e. the real and important results.
The publication helps to validate the approach and specific algorithms unique to Progenesis SameSpots. These were developed by Nonlinear specifically to make protein expression analysis faster and more objective with increased statistical power, regardless of your experience.
1 Silva E, O’Gorman M, Becker S, Auer G, Eklund A, Grunewald J, Wheelock AM, J. Proteome Res., 2010, 9 (3), pp 1522–1532.
