The PSI Extended FASTA Format 50 (PEFF) was developed as a format that is broadly compatible with the ubiquitous FASTA format, but defines mechanisms for file-level metadata, multiple sequence collections within a file, collection-level metadata, and how a wide variety of additional information can be encoded on a per-sequence basis. Whereas the description lines in FASTA files are free form and vary widely based on the data provider, the format of description lines for PEFF files are defined in the specification and can be extended with controlled vocabulary terms. This allows PEFF files to encode proteins and their modifications, such as post-translational modifications (PTMs), protein processing such as signal peptides, and sequence variants. Implementations of PEFF support in Comet enables transparent searching for known PTMs and sequence variants. Although it was not originally designed with this use case in mind, PEFF can also be used to represent proteoforms.