OrgMassSpecR (version 0.5-3)

IsotopicDistributionN: Isotopic Distribution of a Nitrogen-15 Labeled Peptide.

Description

Simulates the isotopic distribution of a nitrogen-15 labeled peptide. Intended for peptides from proteins grown in media with, for example, nitrogen-15 labeled ammonium chloride as the only nitrogen source.

Usage

IsotopicDistributionN(sequence, incorp, IAA = TRUE, 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 nitrogen-15.

IAA

logical. TRUE specifies iodoacetylated cysteine and FALSE specifies unmodified cystine.

charge

numeric value specifying the number of positive charges. Must be 1, 2, or 3. One proton per charge is added to the amino acid sequence (\([M + nH]^{n+}\)).

custom

a list specifying a user defined residue as custom = list(code, elements), where code is a one letter character vector representing the custom residue and elements is a vector of the number of elements in the character vector, with the indicies equal to C,H,N,O,S,or P.

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 will NOT be used in place of the predefined residue; doing so will cause errors.

The natural nitrogen-15 incorporation is 0.00368.

The argument IAA specifies treatment of the protein with iodoacetamide. This treatment produces iodoacetylated cysteine residues (elemental formula C5H8N2O2S). The nitrogen(s) added is not labeled.

The algorithm used in this function is based on sample, and will give a slightly different result each time it is run. It is similar to the algorithm used in reference 1. IsotopicDistributionN has not been tested for sequences over approximately 3000 amu and charges greater that 3+.

References

1. "Method for Estimating the Isotopic Distributions of Metabolically Labeled Proteins by MALDI-TOFMS: Application to NMR Samples." Choudhary K, Spicer VL, Donald LJ, Duckworth HW, Ens W, Loewen PC, Standing KG, Analytical Chemistry, 2006, 78, 5419-5423.

2. "Perturbation and Interpretation of Nitrogen Isotope Distribution Patterns in Proteomics" Snijders APL, de Koning B, Wright PC, Journal of Proteome Research, 2005, 4, 2185-2191.

3. "Measurement of the Isotope Enrichment of Stable Isotope-Labeled Proteins Using High-Resolution Mass Spectra of Peptides" MacCoss MJ, Wu CC, Matthews DE, and Yates III JR, Analytical Chemistry, 2005, 77, 7646-7653.

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.

Note that in reference 3 "a biologically relevant 13C/12C isotope ratio of 1.096% was used instead of the more carbonate specific ratio of 1.112%." The 13C/12C ratio used by IsotopicDistributionN is 1.081%.

See Also

IsotopicDistribution, IsotopicDistributionHDX, sample

Examples

# NOT RUN {
## simulate a peptide with 0.368 to 100 percent incorporation and plot
dn <- IsotopicDistributionN("NECFLQHK", incorp = 0.00368)
dn$t <- "incorp = 0.368%"
d50 <- IsotopicDistributionN("NECFLQHK", incorp = 0.5)
d50$t <- "incorp = 50%"
d99 <- IsotopicDistributionN("NECFLQHK", incorp = 0.99)
d99$t <- "incorp = 99%"
x <- rbind(dn, d50, d99)
library(lattice)
xyplot(percent ~ mz | t, data = x,
    type = "h", 
    xlab = "m/z", 
    ylab = "intensity (%)",
    main = "Isotopic distribution of peptide NECFLQHK with 
            varying nitrogen-15 incorporation")
# }
# NOT RUN {
## simulate peptide DVFLGMFLYPYAR with oxidized methionine
IsotopicDistributionN("DVFLGmFLYPYAR", incorp = 0.5, 
                      custom = list(code = "m", 
                                    elements = c(C=5, H=9, N=1, O=2, S=1)))
# }
# NOT RUN {
# }
# NOT RUN {
<!-- % To simulate a peptide with more than one modified amino acid, try  -->
# }
# NOT RUN {
<!-- % using something like IsotopicDistributionN("DVFLGFLYPYARx", incorp = 0.5,  -->
# }
# NOT RUN {
<!-- % custom = list(code = "x", elements = c(C=10, H=18, N=2, O=4, S=2))) -->
# }
# NOT RUN {
<!-- % where x represents all modified residues and elements is the sum of all  -->
# }
# NOT RUN {
<!-- % modified residues. -->
# }
# NOT RUN {
# }