ConvertPeptide function

Convert peptide sequence.

Convert peptide sequence.

Convert single amino acid codes to an elemental formula or three letter codes.

ConvertPeptide(sequence, output = "elements", IAA = TRUE)

Arguments

  • sequence: a character string representing the amino acid sequence.
  • output: a character string specifying the output. Options are "elements" (default) for the elemental formula or "3letter" for the three letter codes.
  • IAA: logical. TRUE specifies iodoacetylated cysteine and FALSE specifies unmodified cystine. Used only in determining the elemental formula, not the three letter codes.

Details

The amino acid residues must be specified by the one letter codes defined in the help for Digest.

The argument IAA specifies treatment of the protein with iodoacetamide to break the disulfide bonds. This treatment produces iodoacetylated cysteine residues (elemental formula C5H8N2O2S).

Returns

If output = "elements", the value is a list specifying the number of each element. This list can be used as input to other functions, see the examples. If output = "3letter", the value is a vector of length 1, containing the amino acid sequence in three letter codes.

Author(s)

Nathan G. Dodder

Examples

ConvertPeptide("SEQENCE", output = "3letter") # as input to MonoisotopicMass MonoisotopicMass(formula = ConvertPeptide("SEQENCE"), charge = 1) # as input to MolecularWeight MolecularWeight(formula = ConvertPeptide("SEQENCE"))