Given an elemental formula, the relative atomic masses of the isotopes, and the charge state, determine the monoisotopic mass or monoisotopic m/z value.
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.
a list specifing the relative atomic masses of the isotopes.
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
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:
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.
The monoisotopic mass of the unchaged molecule or the monoisotopic m/z value of the charged molecule.
Nathan G. Dodder and Katharine M. Mullen
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.
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## 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))
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