Various segmentation methods have been proposed over the last years. Olsen et al. (2004) suggested a circular binary segmentation (CBS) algorithm, based on recursively applying a statistical test to detect significant breakpoints in the data. Picard et al. (2005) developed a dynamic programming procedure to segment the data when the number of segments is known in advance, which is referred to as CGHseg. The actual number of segments in real data is determined by maximizing a penalized likelihood function. While other segmentation methods exist, such as Lipson et al. (2005, 2006), a comparison study (Lai et al., 2005) which tested 11 segmentation methods, concluded that CBS and CGHseg tend to have the best performance under various conditions. Another comparison study (Willenbrock and Fridlyand, 2005) compared three methods and proclaimed CBS as the method with the best results.
MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported. MaxQuant is freely available and can be downloaded from this site. The download includes the search engine Andromeda which is integrated into MaxQuant as well as the Viewer application for inspection of raw data and identification and quantification results.