Evaluating the performance of new approaches to spot quantification and differential expression in 2-dimensional gel electrophoresis studies.

Journal of Proteome Research
Jeffrey S MorrisHoward B Gutstein

Abstract

Spot detection and quantification for 2-DE are challenging and important tasks to fully extract the proteomic information from these data. Traditional analytical methods have significant weaknesses, including spot mismatching and missing data, which require time-consuming manual editing to correct, dramatically decreasing throughput and compromising the objectivity and reproducibility of the analysis. To address this issue, we developed Pinnacle, a novel, quick, automatic, noncommercial method that borrows strength across gels in spot detection and has been shown to yield more precise spot quantifications than traditional methods. New commercial software, notably SameSpots, has also recently been developed as an improvement over traditional workflows. In this paper, we briefly describe Pinnacle and compare its performance to SameSpots in spot detection, spot quantification precision, and differential expression. Our analysis is performed in a rigorous fashion that, unlike other comparisons in the literature, summarizes performance across all spots detected on the gels, and we manually optimize SameSpots results while simply running Pinnacle with standard settings and no manual editing. While both methods showed marked improveme...Continue Reading

References

Jul 27, 2004·Proteomics·Krzysztof KaczmarekBernard G M Vandeginste
Mar 6, 2007·Journal of Chromatography. a·M DaszykowskiB Walczak
Oct 19, 2007·Expert Review of Proteomics·Howard B Gutstein, Jeffrey S Morris
Feb 14, 2008·Mass Spectrometry Reviews·Howard B GutsteinJonathan V Sweedler
Feb 20, 2008·Proteomics·Brittan N Clark, Howard B Gutstein

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Citations

Nov 18, 2014·Proteomics. Clinical Applications·Georgia ArentzPeter Hoffmann
Nov 4, 2010·Proteomics·Andrew W DowseyMichael J Dunn
Apr 19, 2011·Proteomics·Panagiotis Tsakanikas, Elias S Manolakos
Jun 23, 2011·Analytical Chemistry·Ai-Ying NieFu-Chu He
Nov 16, 2011·Journal of Bioinformatics and Computational Biology·Yukun Wu, Le Zhang
Mar 10, 2017·IEEE Transactions on Nanobioscience·Michal Marczyk
Nov 14, 2017·Statistical Modelling·Jeffrey S Morris, Veerabhadran Baladandayuthapani
May 29, 2016·Applied and Environmental Microbiology·Song HuangGwénaël Jan
Dec 3, 2020·Journal of Proteomics·Sau-Yee KokMeilina Ong-Abdullah

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