Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis using the PSI Extended FASTA Format (PEFF).

Document Type


Publication Date


Publication Title



Protein identification by tandem mass spectrometry sequence database searching is a standard practice in many proteomics laboratories. The de facto standard for the representation of sequence databases used as input to sequence database search tools is the FASTA format. The Human Proteome Organization's Proteomics Standards Initiative has developed an extension to the FASTA format termed the PSI extended FASTA format or PEFF where additional information such as structural annotations are encoded in the protein description lines. Comet has been extended to automatically analyze the post translational modifications and amino acid substitutions encoded in PEFF databases. Comet's PEFF implementation and example analysis results searching a HEK293 dataset against the neXtProt PEFF database are presented. This article is protected by copyright. All rights reserved.


Institute for Systems Biology