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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.
Graphical User Interface (GUI) of the ProteomicsBrowser showing some of the peptide ions identified in the ACTG protein from the Disease-1 sample. The left sidebar allows the user to customize and control the analysis procedure, including using the Selection Options to choose a particular sample, a particular protein in that sample, and changing the scale of visualization with the Zoom control. The center panel presents the overall visualization of the alignment of the identified and quantified peptides. As shown, with the Zoom control near the mid position, it is possible to visualize residues 150-313 as designated by the red font “Start 150” on the left and the “End 313” on the right.