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 Pinnacle_V1.2.6_v.zip  18487 KB This software was developed by Dr. Jeffrey S. Morris, and the GUI was developed by Ebiotics
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This computer program provides a basis for processing 2-D gel electrophoresis images to detect and quantify proteins from a set of gel images. The method was first introduced in Morris, Clark and Gutstein, Bioinformatics 24: 529-536, 2008, and a published comparison with Progenesis SameSpots was published in Morris, Clark, Wei, and Gutstein Journal of Proteome Research 9(1): 595-604, 2010. There is a US Patent for these software and underlying algorithms (Morris JS and Gutstein H, inventors: Method and Computer-Program Product for Detecting and Quantifying Protein Spots, Patent Number US 8,031,925, Issue Date 10/4/2011).

We have another document (available here) detailing the software and its use on this site that you can read before installing and using the software.


  • The Pinnacle software is a standalone Windows package with a graphical user interface, so a Windows-based system is needed to use the software. It should work with Windows 7. Other Windows versions may be compatible but this has not been tested.

  • Administrative permissions may be required to install Pinnacle depending on the chosen installation location.

  • The software requires the gel images be stored as 16-bit .tif files. All gel images for a common analysis should be stored in a common directory.

  • VERY IMPORTANT: Pinnacle is designed to work with gel images that have already been registered or warped to each other so that the spots are reasonably well aligned on the separate gel images. There is no such registration package included with Pinnacle, so the user must use another package to do the registration and warping, save the warped/aligned images as 16-bit .tif files, and then use these for the Pinnacle analysis. Various commercial and non-commercial methods are available for performing this registration; some are automated algorithms while others require manual intervention. We use RAIN (Dowsey, Dunn, and Yang Bioinformatics 24: 950-957, 2008).

  • Do NOT edit the .tif images in Photoshop or any other imaging processing software, as this could alter the quantitative information in the gel image and affect accuracy.

  • When scanning the gels, avoid saturation of the gel images – Pinnacle works best when gels have little to no saturation.

  • Pinnacle is intended to be used on an entire set of gel images, and should not be applied to individual images.