ConvertPeptide {OrgMassSpecR}

Convert peptide sequence.

Description

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

Usage

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).

Value

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"))