OrgMassSpecR (version 0.5-3)

IsotopicDistributionHDX: Isotopic Distribution of a Peptide Undergoing H-D Exchange

Description

Simulates the isotopic distribution of a peptide undergoing hydrogen-deuterium exchange. Only the peptide backbone amides are labeled with deuterium.

Usage

IsotopicDistributionHDX(sequence, incorp, charge = 1, 
                        custom = list(code = NULL, elements = NULL))

Arguments

sequence

character vector specifying the amino acid sequence.

incorp

numeric value from 0 to 1, specifying the fraction of deuterium incorporation in the backbone amides.

charge

numeric value specifying the number of positive charges (\([M + nH]^{n+}\))

custom

a list specifying user defined residues as custom = list(code, mass), where code is a vector of one letter characters and mass is a vector of the respective monoisotopic masses.

Value

A data frame with the following column names.

mz

the m/z value

intensity

the number of counts at each m/z value. The total is 10000.

percent

the intensity at each m/z value, expressed as a percent of the maximum intensity.

Details

The amino acid residues must be specified by the one letter codes defined in the help for Digest. If a custom residue code is identical to a predefined residue code, the custom residue mass will be used in place of the predefined mass.

The natural incorporation of deuterium is 0.000115.

The algorithm used in this function is based on sample, and will give a slightly different result each time it is run. IsotopicDistributionHDX has not been tested for sequences over approximately 3000 amu and charges greater that 3+.

References

The relative atomic masses of the isotopes are from the NIST Physical Reference Data Website http://physics.nist.gov/PhysRefData/Compositions/. The molar mass of a proton (H+) is from the NIST CODATA Website http://physics.nist.gov/cuu/Constants/index.html.

See Also

IsotopicDistribution, IsotopicDistributionN, sample

Examples

# NOT RUN {
## simulate a peptide with 0.0115 and 100 percent incorporation and plot
x <- IsotopicDistributionHDX("NECFLQHK", incorp = 0.000115)
x$t <- "incorp = 0.0115%"
y <- IsotopicDistributionHDX("NECFLQHK", incorp = 1)
y$t <- "incorp = 100%"
z <- rbind(x, y)
library(lattice)
print(xyplot(percent ~ mz | t, data = z,
       type = "h", main = "H-D exchange simulation",
       xlab = "m/z", ylab = "intensity (%)"))
# }