Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data

Bioinformatics
Jeffrey S MorrisHoward B Gutstein

Abstract

One of the key limitations for proteomic studies using 2-dimensional gel electrophoresis (2DE) is the lack of rapid, robust and reproducible methods for detecting, matching and quantifying protein spots. The most commonly used approaches involve first detecting spots and drawing spot boundaries on individual gels, then matching spots across gels and finally quantifying each spot by calculating normalized spot volumes. This approach is time consuming, error-prone and frequently requires extensive manual editing, which can unintentionally introduce bias into the results. We introduce a new method for spot detection and quantification called Pinnacle that is automatic, quick, sensitive and specific and yields spot quantifications that are reliable and precise. This method incorporates a spot definition that is based on simple, straightforward criteria rather than complex arbitrary definitions, and results in no missing data. Using dilution series for validation, we demonstrate Pinnacle outperformed two well-established 2DE analysis packages, proving to be more accurate and yielding smaller coefficiant of variations (CVs). More accurate quantifications may lead to increased power for detecting differentially expressed spots, an ide...Continue Reading

References

Mar 1, 1997·Electrophoresis·L Anderson, J Seilhamer
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Aug 26, 2006·Anesthesia and Analgesia·Jijun J XuHoward B Gutstein

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Citations

Dec 4, 2010·Bioinformatics·António dos AnjosHamid R Shahbazkia
Nov 10, 2011·BMC Bioinformatics·Feng Li, Françoise Seillier-Moiseiwitsch
Jul 10, 2013·Biomedical Engineering Online·Robert KoprowskiMirosław Kwaśniewski
Aug 19, 2011·Computational Statistics & Data Analysis·Feng LiValeriy R Korostyshevskiy
Nov 18, 2014·Proteomics. Clinical Applications·Georgia ArentzPeter Hoffmann
Nov 13, 2008·Proteomics·Olivier Langella, Michel Zivy
Nov 4, 2010·Proteomics·Andrew W DowseyMichael J Dunn
Apr 19, 2011·Proteomics·Panagiotis Tsakanikas, Elias S Manolakos
Jan 10, 2014·IEEE Journal of Biomedical and Health Informatics·Eirini KostopoulouDimitris Maroulis
Jul 15, 2015·Computer Methods and Programs in Biomedicine·E KostopoulouD Maroulis
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
Feb 14, 2008·Mass Spectrometry Reviews·Howard B GutsteinJonathan V Sweedler
Jan 1, 2010·The Annals of Applied Statistics·Yuliya V KarpievitchAlan R Dabney

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