annotate_isotope | R Documentation |
This function identifies isotopic peaks for a given molecular formula and adduct, matching them with observed peaks based on mass-to-charge ratio (m/z) and retention time (RT).
annotate_isotope(
formula = "C9H14N2O12P2",
adduct = "M-H",
charge = 1,
mz = 402.9998,
rt = 823.1462,
peak.mz,
peak.rt,
rt.tol = 5,
mz.tol = 15,
max.isotope = 4
)
formula |
Character. The molecular formula of the compound (e.g., '"C9H14N2O12P2"'). |
adduct |
Character. The adduct ion type (e.g., '"M-H"'). |
charge |
Numeric. The charge state of the ion. Default is '1'. |
mz |
Numeric. The accurate mass-to-charge ratio (m/z) of the monoisotopic peak. |
rt |
Numeric. The retention time (RT) of the compound in seconds. |
peak.mz |
Numeric vector. Observed m/z values of peaks in the dataset. |
peak.rt |
Numeric vector. Observed retention times (RT) of peaks in the dataset. |
rt.tol |
Numeric. The retention time tolerance (in seconds) for matching peaks. Default is '5'. |
mz.tol |
Numeric. The m/z tolerance (in ppm) for matching peaks. Default is '15'. |
max.isotope |
Numeric. The maximum number of isotopes to consider. Default is '4'. |
The function calculates the theoretical isotope distribution using 'Rdisop::getMolecule()' and then matches observed peaks based on m/z and RT tolerances. The function ensures that at least the '[M+1]' isotope is present for a valid match.
A data frame containing:
peakIndex |
Index of the matched peak in the dataset. |
mzError.ppm |
Mass error (in ppm) between the observed and theoretical isotope peak. |
isotopes |
Label of the identified isotope (e.g., '[M+1]', '[M+2]'). |
rtError.s |
Retention time error (in seconds). |
If no isotopic peaks are matched within the given tolerances, the function returns 'NULL'.
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