This app generates a list of mass-over-charges (m/z) for PCAs and structural analogues to investigate potential overlapping m/z during mass spectrometric analysis. It utilizes the isopattern function of the R package Envipat (Loos et al, Analytical Chemistry, 2015, 87, 5738-5744) to generate isotopic patterns from chemical formula and adducts. The app will also generate a list of m/z for selected adducts which can be used as a transition list in the Skyline software for quantification purposes. Several adducts have been included and more can be added upon request.
Choose the parameters in the Normal settings or Advanced settings tab. Press submit and wait for calculation to finish. A table will then be generated with all ions that conform with the initial setting parameters. The table can be exported to excel by clicking on the "Excel" button at the top.
The Interfering ions tab can be used to check for ions that interfer with each other at the set resolution of the mass spectrometer. Default is set to R=60,000. The plots and tables are interactive and the user can filter the "Interference at MS res?" by clicking on FALSE on the plot legend (and thereby keeping all TRUE ions, which will remove all ions that can be resolved by the set MS resolution).
The generated ion tables can be exported using the Skyline tab for data processing of MS data.
C atoms min and C atoms max: the range of carbon atoms.
Cl atoms min and Cl atoms max: the range of chlorine atoms.
Br atoms min and Br atoms max: the range of bromine atoms. This is only used if BCA (bromo-chloro alkanes) is choosen as adducts (otherwise this parameter can be ignored).
Add adducts/fragments: refers to the formula of adducts and/or fragments to generate from a set list of available options. Multiple selections are possible.
[PCA] and [PCO]: refers to the main groups of polychlorinated alkanes [PCA] or polychlorinated alkenes (mono olefins) [PCO].
[BCA]: bromo-chloro alkanes.
[xxx-yy] or [xxx-yy-zz]: where xxx refers to the main groups, -yy refers to the adduct/fragment ions or -yy-zz which are the consecutive loss fragments. Currently, a limited selection is available but more can be added upon request.
[ ]- and [ ]+ refers to the charge of the ion (limited to single charged species, +1 or -1).
Note that [M+Cl-HCl]- can also be written as [M-H]-
Isotope rel ab threshold (%): is the threshold for relative abundance for isotopologues for each chemical formula of the adduct/fragment ion. Ions below this threshold will not be included into the generated ion table.
Mostly same initial parameters as Normal settings. In advanced settings, there is more flexibility to combine and mix the Compound Class, Adduct, Charge, and Transformation product.
Parent_Formula: the chemical formula of the molecular ion.
Halo_perc: for PCA, PCO chlorinated groups, the chlorination degree (mass percentage of Cl). If BCA, then it is the combined Cl+Br percentage.
Charge: The charge of the ion.
Fragment: The fragment and isotopic type of the ion species.
Adduct_Formula: the chemical formula of the adduct/fragment ion.
Isotopologue: the isotopologue in relation to the monoisotopic ion.
Isotope_Formula: the exact isotopic formula of the adduct/fragment ion.
m/z: the mass-over-charge of the adduct/fragment ion.
Rel_ab: the relative abundance of the different isotopologues of each adduct/fragment ion.
12C, 13C, 1H, 2H, 35Cl, 37Cl, 79Br, 81Br: the number of atoms for each element
difflag, difflead: internal calculations for the difference in m/z values between the two nearest ions. If "interference at MS res?" filter has been used, then the previous/next ions might not be shown.
reslag, reslead: internal calculations for the MS resolution needed to separate the two nearest ions. If "interference at MS res?" filter has been used, then the previous/next ions might not be shown.
interference: indicate whether or not the m/z two nearest ions can interfere with each other at the set MS resolution value. "false" means no interference and "true" means there is interference (and therefore the MS resolution cannot resolve these peaks).
Note: Some bars can exceed 100% in relative abundance in the y-axis, and this indicates that some isotopologues have the exact same ion formula. You can hover over the different segments of these bars to check the overlapping mass ions.
Hover text:
difflag & difflead (prev and next): the difference between the m/z with previous and next ions (axis ordered from lowest to highest m/z).
reslag & reslead (prev and next): the MS resolution needed to resolve previous and next ion (axis ordered from lowest to highest m/z).
This will output a transition list for import in Skyline for integration and quantification. User need to indicate either the Normal setting or Advanced setting as input.