OrgMassSpecR (version 0.5-3)

MonoisotopicMass: Calculate the monoisotopic mass or monoisotopic m/z value of an organic molecule.

Description

Given an elemental formula, the relative atomic masses of the isotopes, and the charge state, determine the monoisotopic mass or monoisotopic m/z value.

Usage

MonoisotopicMass(formula = list(), isotopes = list(), charge = 0)

Arguments

formula

a list describing the uncharged elemental formula. The allowed elements are C, H, N, O, S, P, Br, Cl, F, Si, and a user defined "x". See Examples.

isotopes

a list specifing the relative atomic masses of the isotopes.

charge

an integer specifying the number of positive or negative charges. If a charge is specified, the m/z of the molecule is calculated by adding or subtracting the specified number of protons. If charge = 0, the monoisotopic mass is returned. See details.

Value

The monoisotopic mass of the unchaged molecule or the monoisotopic m/z value of the charged molecule.

Details

The elemental formula describes the uncharged molecule; the charge argument will add or remove hydrogens as needed. This assumes an electrospray or MALDI type ionization. In electron impact ionization a positive charge is generated by loss of an electron, not additon of H+, therefore to calculate the correct m/z, the charge should be set to zero as a workaround.

The relative atomic masses of the most abundant isotopes (carbon-12, hydrogen-1, nitrogen-14, and oxygen-16) are set as the default values. For reference, the relative atomic masses of some common isotopic labels are:

carbon-13	13.0033548378
hydrogen-2	2.0141017780
nitrogen-15	15.0001088984

The user defined element x can be used to define an additional element, such as a metal, or to specify a certain number of isotopically labeled atoms in a molecule. See Examples.

This function will accept values that do not correspond to known physical reality, such as a fractional number of elements, a fractional charge, or the wrong relative atomic mass value for an isotope.

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

Digest, FragmentPeptide, MolecularWeight

Examples

# NOT RUN {
## monoisotopic m/z of creatinine (C4H7N3O), +1 charge
## unlabeled
MonoisotopicMass(formula = list(C=4, H=7, N=3, O=1), charge = 1)
## with all carbon-13 atoms
MonoisotopicMass(formula = list(C=4, H=7, N=3, O=1), 
                 isotopes = list(C = 13.0033548378),
                 charge = 1) 
## with 2 carbon-12 atoms and 2 carbon-13 atoms
MonoisotopicMass(formula = list(C=2, H=7, N=3, O=1, x=2), 
                 isotopes = list(x = 13.0033548378),
                 charge = 1)

## monoisotopic mass of cyanocobalamin (C63H88CoN14O14P)
MonoisotopicMass(formula = list(C=63, H=88, N=14, O=14, P=1, x=1),
                 isotopes = list(x = 58.9332002))
# }