PEFF

PEFF encodes extended metadata for protein sequences, developed by the Proteomics Standards Initiative (PSI), to represent known sequence variants, post-translational modifications (PTMs), and proteoforms within a FASTA-compatible format for mass-spectrometry-based proteomics.

Key Features:

• Enhanced Metadata Encoding: Supports annotation of known sequence variants, post-translational modifications (PTMs), and proteoforms alongside primary peptide or protein sequences.
• Backward Compatibility: Maintains compatibility with existing FASTA parsers so PEFF files remain readable by tools that accept standard FASTA input.
• Standardization and Specification: Provides a formal specification and controlled-vocabulary terms with example files to standardize structure and annotations across implementations.
• Supporting Software and Resources: Is supported by sequence search engine Comet and knowledge bases such as neXtProt and UniProtKB to enable integration into proteomics workflows.

Scientific Applications:

• Variant- and PTM-aware database searching: Enables inclusion of known sequence variants and PTMs in mass-spectrometry search spaces to improve detection of modified and variant peptides.
• Proteogenomics: Facilitates integration of genomic variation information with proteomic data by encoding sequence variants for combined analyses.
• Top-down proteomics: Supports representation of intact proteoforms and their PTMs for analyses that characterize whole proteins rather than peptides.
• Mass-spectrometry-based protein identification and quantification: Standardizes encoding of sequence diversity to enhance the accuracy and depth of protein identification and quantification workflows.

Methodology:

PEFF encodes sequence collections and individual entries using a FASTA-compatible text format with controlled-vocabulary annotations and example files defined in a formal specification to represent known sequence variants, PTMs, and proteoforms for inclusion in mass-spectrometry data-analysis workflows.