OrgMassSpecR (version 0.5-3)

FragmentPeptide: Predict Peptide Fragment Ions

Description

Determine the b- and y-ions or c- and z-ions produced by the fragmentation of a peptide by tandem mass spectrometry.

Usage

FragmentPeptide(sequence, fragments = "by", IAA = TRUE, 
                N15 = FALSE, custom = list())

Arguments

sequence

a vector of character strings representing the amino acid sequences to be fragmented by the mass spectrometer.

fragments

character string specifying the fragmentation rules. Options are "by" (default) for the b- and y-ions, or "cz" for the c- and z-ions.

IAA

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

N15

logical indicating if the nitrogen-15 isotope should be used in place of the default nitrogen-14 isotope.

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. See Details and Examples.

Value

A data frame with the following column names. The data frame is arranged this way to facilitate selection of product-precursor ion pairs.

ms1seq

precursor ion sequence.

ms1z1

monoisotopic m/z value for the $[M+H{]}^{1+}$ precursor ions (where M is the precursor mass).

ms1z2

monoisotopic m/z value for the $[M+2H{]}^{2+}$ precursor ions.

ms1z3

monoisotopic m/z value for the $[M+3H{]}^{3+}$ precursor ions.

ms2seq

product ion sequence.

ms2type

the type and charge state of the product ions.

ms2mz

monoisotopic m/z values for the product ions.

Details

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

The fragmentation rules can be set for collision induced dissociation (b- and y-ions) or electron transfer dissociation (c- and z-ions).

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

If TRUE, the argument N15 specifies 100% nitrogen-15 incorporation. It is intended for proteins grown with a nitrogen-15 labeled food source. (Although the experiment itself may grow a protein with less than 100% nitrogen-15 incorporation). Setting N15 = TRUE does not modify the mass of a custom residue, or the mass of the nitrogen(s) added if IAA = TRUE.

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.

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/cgi-bin/cuu/Value?mmp.

See Also

MonoisotopicMass, Digest, PeptideSpectrum

Examples

# NOT RUN {
## fragment unlabeled peptide
FragmentPeptide("NECFLQHK")

## fragment peptide with carbon-13 labeled lysine
k.mass <- MonoisotopicMass(formula = list(C = 6, H = 12, N = 2, O = 1),
                       isotopes = list(C = 13.0033548378)) 
FragmentPeptide("NECFLQHk", custom = list(code = "k", mass = k.mass))

## fragment peptide with two modifications
m.mass <- MonoisotopicMass(formula = list(C=5, H=9, N=1, O=2, S=1))
FragmentPeptide("NDmELWk", custom = list(code = c("m", "k"), mass = c(m.mass, k.mass)))

## fragment a vector of peptides produced by Digest
x <- Digest(example.sequence)
y <- subset(x, nchar(x$peptide) > 5 & nchar(x$peptide) < 12)
FragmentPeptide(y$peptide)
# }