Detection and Quantification of Protein Spots by Pinnacle

  • Jeffrey S. MorrisEmail author
  • Howard B. Gutstein
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 words

Automated 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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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Department of BiostatisticsThe University of Texas MD Anderson Cancer CenterHoustonUSA
  2. 2.Anesthesiology and Perioperative MedicineThe University of Texas MD Anderson Cancer CenterHoustonUSA

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