High reproducibility of large-gel two-dimensional electrophoresis.

Abstract	Two-dimensional gel electrophoresis (2-DE) facilitates the separation of thousands of proteins from highly complex protein mixtures and has become a central method in proteomics in recent years. In the present study, we examined the technical variability of large 2-DE gels with respect to sample preparation, electrophoresis procedure, data acquisition, and biological variation by analyzing a disease (Huntington's disease) and control state with a commercially available software package, PROTEOMWEAVER trade mark. Scatter plots and correlation coefficients were obtained to quantify both technical and biological variation. Even 2-DE gels run separately in both dimensions yielded correlation coefficients around 0.88 and deviations from the mean close to 20% for low-intensity spots. This indicates a high technical reproducibility of the 2-DE procedure developed in our laboratory. Variability within a biological condition was low and comparable to technical variation (at least 0.87). Two-dimensional (2-D) gels obtained from samples of different biological conditions (health vs. disease) achieved a variability similar to intracondition and technical variability. These findings highlight the importance of multiple gel and spot-by-spot comparisons to identify biological significant changes. Minor errors introduced by technical and biological variation allow a comparison of all gels within a study which facilitates the tackling of complex biological problems.
Authors	Kiran Kumar Challapalli, Claus Zabel, Johannes Schuchhardt, Angela M Kaindl, Joachim Klose, Hanspeter Herzel
Journal	Electrophoresis (Electrophoresis) Vol. 25 Issue 17 Pg. 3040-7 (Sep 2004) ISSN: 0173-0835 [Print] Germany
PMID	15349946 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
Chemical References	Htt protein, mouse Huntingtin Protein Nerve Tissue Proteins Nuclear Proteins Proteome
Topics	Animals Brain Chemistry Electrophoresis, Gel, Two-Dimensional (methods) Huntingtin Protein Huntington Disease (genetics) Male Mice Mice, Inbred C57BL Mice, Inbred CBA Mice, Transgenic Nerve Tissue Proteins (genetics, isolation & purification) Nuclear Proteins (genetics) Proteome Reproducibility of Results Software

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