We outline the application of a framework for managing information quality (IQ) in proteomics. The approach allows scientists to define the quality characteristics that are of importance in their particular domain, by extending a generic ontology of IQ concepts. Two quality indicators are defined for proteomic experiments: hit ratio and mass coverage. We describe how our framework allows experiments marked-up in a standard format (e.g. PEDRo) to be annotated with these computed indicators, and how the annotations can be viewed using a convenient plugin to the commonly-used Pedro data entry tool.