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 properties
PRIDE Data Object Model (ms-data-core-api)Data model representation of MS proteomics data with special emphasis in metadata information
PRIDE Protein InferenceIt implements a set of protein inference algorithms, coupled with the ms-data-core-api data model
PRIDE ModificationIt retrieves the information from the main protein modification controlled vocabularies and/or ontologies (Unimod and PSI-MOD)
PRIDE-ToolsuitePRIDE Inspector Quality ChartChart library developed using Java Swing and JFreeChart, which provides a way to assess the quality of MS experiments
PRIDE Spectrum BrowserJava Swing library to visualize and annotate MS/MS spectra, chromatograms and fragment annotations
PRIDE Inspector ToolDesktop application tool
PRIDE Inspector Toolsuite examplesSet of example files from different sources (mzIdentML, PRIDE XML, mzTab, and mass spectra files) that can be used for testing purposes