ExchangeableAmides {OrgMassSpecR}

Determine the Number of Backbone Amide Hydrogens

Description

Determine the number of backbone amide hydrogens given a protein/peptide sequence. Used in hydrogen-deuterium exchange experiments.

Usage

ExchangeableAmides(sequence)

Arguments

sequence

character vector containing one or more amino acid sequences.

Details

The number of backbone amide hydrogens in an amino acid sequence is the number of residues, minus the number of prolines, minus 1.

Value

A numeric vector containing the number of exchangeable hydrogens.

Author(s)

Nathan G. Dodder

See Also

IsotopicDistributionHDX

Examples

ExchangeableAmides(c("VDVMCTA", "VSTPTL"))

## find the number of exchangeable amides for 
## each peptide in a digest of human serum albumin
x <- Digest(example.sequence, enzyme = "pepsin", IAA = FALSE, missed = 4)
transform(x, exchange = ExchangeableAmides(x$peptide))