Blog
Articles tagged: selenocysteine
Ambiguity residues B, X, Z and custom residues J, O, U
Mascot uses the IUPAC one-letter code for protein and peptide sequences. The 20 standard amino acids are encoded using the uppercase Latin letters ACDEFGHIKLMNPQRSTVWY. The remaining letters – B, J, O, U, X, Z – are also supported by Mascot and have a special meaning. Ambiguity residues B, X, Z The IUPAC one-letter symbols B, X and Z encode ambiguity: [...]
Selenocysteine
David Fenyö and Ron Beavis have a short paper in J. Proteome Research that draws attention to a potential problem with peptides containing selenocysteine (1-letter code U, 3-letter code Sec). Samples are frequently alkylated, yet modified U is unlikely to be considered in the search. This need not be an issue for Mascot searches, but you may have no modifications [...]