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The GUI module of the PRIDE Inspector organizes itself in the form of several views, where each view focuses on a particular aspect of the data. There are currently six views:

1. ‘Overview’ view – shows experimental metadata.

2. Protein view – shows protein identifications

3. Peptide view – shows peptides used to generate the protein identifications

4. Spectrum view – shows spectra and chromatograms

5. Quantification view – show quantitative data for both proteins and peptides

6. ‘Summary charts’ view – provides data chars for assessing data quality

To enable maximum reusability, each view is implemented as an independent component using Java Swing [http://download.oracle.com/javase/tutorial/uiswing/]. This way, more views can be added easily in the future. Inspector-mzgraph-browser [https://github.com/PRIDE-Toolsuite/inspector-mzgraph-browser], the component responsible for visualizing spectra and chromatograms, is released and available as self-contained Java library and distributed as part of the PRIDE Inspector. Both this component and the statistical charts in the ‘Summary Charts’ view, are implemented using the JFreeChart [http://www.jfree.org/jfreechart/] API.

Next to the previous six layers, a generic application management framework maintains the context and information shared by the whole environment. It consists of features frequently required by medium or large Java Swing based applications, such as: lifecycle services for background tasks, in-memory caching, event bus, user property management and error handling. The framework is independent from the PRIDE Inspector and therefore can be reused for other rich client applications.