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Protein complexes are formed when two or more proteins non-covalently interact to form a larger three dimensional structure with specific biological function. Understanding the composition of such complexes is vital to understanding cell biology at the molecular level. MassVis is a visual analysis tool designed to assist the interpretation of data from a new workflow for detecting the composition of such protein complexes in biological samples. The data generated by the laboratory workflow naturally lends itself to a scatter plot visualization. However, characteristics of this data give rise to some unique aspects not typical of a standard scatter plot. We are able to take the output from tandem mass spectrometry and render the data in such a way that it mimics more traditional two-dimensional gel techniques and at the same time reveals the correlated behavior indicative of protein complexes. By computationally measuring these correlated patterns in the data, membership in putative complexes can be inferred. User interactions are provided to support both an interactive discovery mode as well as an unsupervised clustering of likely complexes. The specific analysis tasks led us to design a unique arrangement of item selection and coordinated detail views in order to simultaneously view different aspects of the selected item.