VIP: Visualization of integrated proteomics data

The post-genomic era is characterized by the rapid data accumulation leading to unwieldy and large volumes of biological data. The proteomics results (large sets of identified proteins or peptides) that originate from several workflow steps, play an important role in the analysis of a proteomics experiment. As a result, the area of high-through-put proteomics created new visualization challenges in interpreting large-scale datasets. We present VIP, an interactive visualization tool for proteomics data, which integrates protein or peptide features emanating at every step of the proteomics analysis and combines them visually in synthetic maps. Our novel tool offers the flexibility to choose any desired features according to the analysis objectives, examine simultaneously more than one maps and interact with the visualization by querying and filtering the results. The synthetic maps visualization aims not only at summarizing proteomics experiments in a unified manner for both 2DE-MS and LC-MS based analyses, but also at providing a quick and combined overview of protein/peptide features, thus facilitating the data analysis and interpretation.