title: Detection and Quantification of Protein Spots by Pinnacle.
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.
authors.affiliation: Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Unit 1411, 301402, Houston, TX, 77230-1402, USA. jefmorris@mdanderson.org.
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Morris
authors.affiliation: Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Unit 1411, 301402, Houston, TX, 77230-1402, USA.
authors.forename: Howard B
authors.initials: HB
authors.lastname: Gutstein
mesh_terms: D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D007091:Image Processing, Computer-Assisted; D011506:Proteins / Q000302:isolation & purification*; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins
keywords: Automated methods; Image processing; Spot detection; Wavelet denoising