The mzPAF proposed standard is a specification for a fragment ion peak annotation format for mass spectra, focused on peptides. This provides for a standardized format for describing the origin of fragment ions to be used in spectral libraries, other formats that aim to describe fragment ions, and software tools that annotate fragment ions.
Status
Updated: 2026-03-23
Version 1.0 of the mzPAF specification was formally ratified via the PSI Document Process and released in final form on 2025-08-10.
Subsequently, during further implementations in software tools, a few minor errors and ambiguities were reported. These minor shortcomings are being addressed in a patch update to the mzPAF specifications, currently under review as mzPAF 1.0.1 draft 4.
If you have questions or comments on this specification, please submit an issue at the repo to provide your feedback.
Available Materials
- The DRAFT Patch specification: 1.0.1 Draft4 (.PDF) or (.docx)
- The FINAL 1.0 specification (2025-08-10): (.PDF) or (.docx)
- The GitHub repo associated with mzPAF, including examples: https://github.com/HUPO-PSI/mzPAF
- Related mzSpecLib standard (GitHub repo: https://github.com/HUPO-PSI/mzSpecLib)
- Release paper: https://doi.org/10.1021/acs.analchem.4c04091
Implementations
- C++: OpenMS
- Rust: mzannotate
- Python: mzpaf reference implementation, paftacular, spxtacular, quetzal