Peak Spacing and Intensity Cutoff
The peak spacing and intensity cutoff parameters are used to trim theoretical isotopic profile models to appropriately compare them against experimental spectra.
The peak spacing (Da) parameter is defined to integrate continuum theoretical isotopic profile models into centroid models. This parameter attempts to regulate merging a cluster of adjacent isotopologues within the peak spacing window (Da) into one isotopologue. Peak spacing is suggested to be adjusted according to the instrument resolution.
The intensity cutoff (%) parameter is defined to remove isotopologues below a cutoff which can not be detected naturally. Intensity cutoff is suggested to be adjusted according to the instrument sensitivity.
Tip: To preserve continuum isotopic profiles, 0 should be used for the peak spacing and intensity cutoff parameters.
IDSL.UFA allows users to customize intensity cutoff for each individual molecular formula to get the most realistic isotopic profiles for a batch of molecular formulas with various elemental compositions. For example, to preserve 13C, 34S, and 30Si isotopologues in sulfonated/siliconated compounds, you may use the following piece of script:
if (s>0 & si>0) {
min(c(c, 5, si*3, s*4))
} else if (s>0 & si==0) {
min(c(c, 5, s*4))
} else if (s==0 & si>0) {
min(c(c, 5, si*3))
} else if (s==0 & si==0) {
min(c(c, 5))
}
Likewise, to preserve only 13C isotopologues for carbon-containing compounds:
if (c < 10) { # 'c' represents number of carbon atoms
c
} else {
10
}
This unique feature embedded in the IDSL.UFA package is especially beneficial to adjust profiles depending on the instrument sensitivity and type. For instance, it is empirically known that Orbitrap instruments generally can not detect isotopologues below 10%, but QToF instruments can go down up to 5%. Generally, it is advised to estimate the instrument threshold to adjust the intensity cutoff by inspection of detected isotopic profile of existing analytes in the HRMS data.
Fakouri Baygi, S., Crimmins, B.S., Hopke, P.K. Holsen, T.M. Comprehensive emerging chemical discovery: novel polyfluorinated compounds in Lake Michigan trout. Environmental Science and Technology, 2016, 50(17), 9460-9468.
Fakouri Baygi, S., Fernando, S., Hopke, P.K., Holsen, T.M. and Crimmins, B.S. Automated Isotopic Profile Deconvolution for High Resolution Mass Spectrometric Data (APGC-QToF) from Biological Matrices. Analytical chemistry, 2019, 91(24), 15509-15517.