ProteomicsBrowser

Large-scale, quantitative proteomics data are being generated at ever increasing rates by high-throughput, mass spectrometry technologies. However, due to the complexity of these large datasets as well as the increasing numbers of post-translational modifications (PTMs) that are being identified, often at low stoichiometry; developing effective methods for proteomic visualization has been challenging. ProteomicsBrowser was developed to meet this need for comprehensive data visualization. Using peptide information files exported from mass spectrometry search engines or quantitative tools as input, the peptide sequences are aligned to an internal protein database such as UniProtKB. Each identified peptide ion including those with PTMs are then visualized along the parent protein in the Browser. A unique property of ProteomicsBrowser is the ability to combine overlapping peptides in different ways to focus analysis of sequence coverage, charge state, or post-translational modifications. ProteomicsBrowser also includes other useful functions, such as a novel data filtering tool and basic statistical analyses to qualify quantitative data.