For mzPAF, the working group identified the following design principles for the encoding of peak annotations. First, mzPAF should be designed as a compact human-readable and unambiguous software-parsable format. Second, the format is also mapped to an object model that may be serialized as JSON for certain applications. Third, to set a manageable scope for the project, mzPAF is designed for linear peptides with simple modifications, i.e. those routinely identified by typical proteomics pipelines, and for fragmentation methods commonly used in proteomics such as collision-induced dissociation (CID), higher-energy collisional dissociation (HCD), and electron-transfer dissociation (ETD).