Detection and Quantification of Protein Spots by Pinnacle

Jeffrey S Morris; Howard B Gutstein

doi:10.1007/978-1-4939-3255-9_11

Detection and Quantification of Protein Spots by Pinnacle

Methods Mol Biol. 2016:1384:185-201. doi: 10.1007/978-1-4939-3255-9_11.

Authors

Jeffrey S Morris¹, Howard B Gutstein²

Affiliations

¹ Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Unit 1411, 301402, Houston, TX, 77230-1402, USA. jefmorris@mdanderson.org.
² Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Unit 1411, 301402, Houston, TX, 77230-1402, USA.

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.

Keywords: Automated methods; Image processing; Spot detection; Wavelet denoising.

MeSH terms

Electrophoresis, Gel, Two-Dimensional / methods*
Image Processing, Computer-Assisted
Proteins / isolation & purification*
Proteomics / methods*
Software*

Substances

Proteins

Abstract

MeSH terms

Substances

Grants and funding