In the past several years there have been very important extremely useful advances in proteomics methods based on bottom-up display and bottom-up identification using peptides [222] . These methods offer more sensitivity, greater rapidity and greater proteome coverage are often made with the explicit or implicit assertion that these methods are bound to replace more traditional methods based on topdown analysis, especially using 2D gels [223, 224] . The combination of bottom-up display and bottom-up identification has achieved very important successes in detecting the presence of large numbers of different proteins in cells or subcellular organelles [225, 226] . The use of specific fractionation schemes and prudent adoption of methods to increase the number of proteins able to be identified and quantified is enabling significant biological advances to be made. Further technological developments that enable a larger proportion of the proteome to be visualized will further enhance our ability to characterize biological systems. As such, these advances in proteomics will impact not only academic pursuits but also pharmaceutical, biotechnology and diagnostic research and development [227] .