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Amino Acids. 2012 May;42(5):1583-90. doi: 10.1007/s00726-011-0873-7. Epub 2011 Mar 11.

Operator- and software-related post-experimental variability and source of error in 2-DE analysis.

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Division of Metabolism, Department of Clinical and Experimental Medicine, University of Padua, via Giustiniani 2, 35128, Padua, Italy.


In the field of proteomics, several approaches have been developed for separating proteins and analyzing their differential relative abundance. One of the oldest, yet still widely used, is 2-DE. Despite the continuous advance of new methods, which are less demanding from a technical standpoint, 2-DE is still compelling and has a lot of potential for improvement. The overall variability which affects 2-DE includes biological, experimental, and post-experimental (software-related) variance. It is important to highlight how much of the total variability of this technique is due to post-experimental variability, which, so far, has been largely neglected. In this short review, we have focused on this topic and explained that post-experimental variability and source of error can be further divided into those which are software-dependent and those which are operator-dependent. We discuss these issues in detail, offering suggestions for reducing errors that may affect the quality of results, summarizing the advantages and drawbacks of each approach.

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