Abstract
Accurate spot detection and quantification is a challenging task that must be performed effectively in order to properly extract the proteomic information from two-dimensional (2-D) gel electrophoresis images. In Morris et al., Bioinformatics 24:529–536, 2008, we introduced Pinnacle, an automatic, fast, effective noncommercial package for spot detection and quantification for 2-D gel images, and subsequently we have developed a freely available gui-based interface for applying the method to a set of gels. In this chapter, we overview Pinnacle, and in a step-by-step manner we describe how to use the software to obtain spot lists and quantifications, to be used for comparative proteomic analysis.
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Abbreviations
- 2-D:
-
Two-dimensional
- R 2 :
-
Coefficient of determination
- %CV:
-
Percent coefficient of variation
References
Morris JS, Clark BN, Gutstein HB (2008) Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data. Bioinformatics 24:529–536
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Dowsey AW, Dunn MJ, Yang GZ (2008) Automated image alignment for 2-D gel electrophoresis in a high-throughput proteomics pipeline. Bioinformatics 24:950–957
Acknowledgements
This work was supported by grants from the National Cancer Institute (CA107304, CA160736) and from the National Institute on Drug Abuse (DA18310) and the National Institute on Alcohol Abuse and Alcoholism (AA16157).
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Morris, J.S., Gutstein, H.B. (2016). Detection and Quantification of Protein Spots by Pinnacle . In: Marengo, E., Robotti, E. (eds) 2-D PAGE Map Analysis. Methods in Molecular Biology, vol 1384. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3255-9_11
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DOI: https://doi.org/10.1007/978-1-4939-3255-9_11
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-3254-2
Online ISBN: 978-1-4939-3255-9
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