Table I Organization of the PRIDE Inspector Toolsuite modules
Library or GUI componentDescriptionGitHub repository
PRIDE-UtilitiesPRIDE UtilitiesIt contains functionalities shared by different PRIDE Toolsuite libraries such as controlled vocabulary data structures and prediction algorithms of peptide/protein propertieshttps://github.com/PRIDE-Utilities/pride-utilities
PRIDE Data Object Model (ms-data-core-api)Data model representation of MS proteomics data with special emphasis in metadata informationhttps://github.com/PRIDE-Utilities/ms-data-core-api
PRIDE Protein InferenceIt implements a set of protein inference algorithms, coupled with the ms-data-core-api data modelhttps://github.com/PRIDE-Utilities/pride-protein-inference
PRIDE ModificationIt retrieves the information from the main protein modification controlled vocabularies and/or ontologies (Unimod and PSI-MOD)https://github.com/PRIDE-Utilities/pride-mod
PRIDE-ToolsuitePRIDE Inspector Quality ChartChart library developed using Java Swing and JFreeChart, which provides a way to assess the quality of MS experimentshttps://github.com/PRIDE-Toolsuite/inspector-quality-chart
PRIDE Spectrum BrowserJava Swing library to visualize and annotate MS/MS spectra, chromatograms and fragment annotationshttps://github.com/PRIDE-Toolsuite/inspector-mzgraph-browser
PRIDE Inspector ToolDesktop application toolhttps://github.com/PRIDE-Toolsuite/pride-inspector
PRIDE Inspector Toolsuite examplesSet of example files from different sources (mzIdentML, PRIDE XML, mzTab, and mass spectra files) that can be used for testing purposeshttps://github.com/PRIDE-Toolsuite/inspector-example-files