Detection and Quantification of Protein Spots by Pinnacle
Part of the
Methods in Molecular Biology
book series (MIMB, volume 1384)
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.
Key wordsAutomated methods Image processing Spot detection Wavelet denoising
Coefficient of determination
Percent coefficient of variation
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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