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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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1
Division of Metabolism, Department of Clinical and Experimental Medicine, University of Padua, via Giustiniani 2, 35128, Padua, Italy. millionirenato@gmail.com

Abstract

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.

PMID:
21394601
DOI:
10.1007/s00726-011-0873-7
[Indexed for MEDLINE]
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