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Standard Adduct Type
IDSL.UFA, IDSL.SUFA, IDSL.UFAx, and IDSL.FSA can process adduct types defined as [CoeffM+gainFormula-lossFormula]+/-charge, where gainFormula and lossFormula should be complete molecular formulas compatible with IUPAC molecular formula notation system. IDSL.UFA can also generate IPDBs with multiple charged adduct types through the parameter FS0006 in the formula_source tab of the parameter spreadsheet.
The complexities of formal charge calculations require structural analysis of the adduct to assign charge for ions. However, IDSL.UFA is able to correct ionization formal charge for adduct types when known functional groups contribute to the total charge. After the formal charge is calculated properly, IDSL.SUFA and IDSL.UFA can adjust isotopic profiles with respect to the ionization charge. IDSL.UFA only includes the following functional groups to measure the ionization charge:
| +1 | -1 |
|---|---|
| +H | -H |
| +Na | -Na |
| +NH4 | -NH4 |
| -Br | +Br |
| -Cl | +Cl |
| -I | +I |
IDSL.UFA uses the coefficients of these ions to calculate charges similar to the adduct types presented by the Fiehn lab. For example, ionization charges for [2M+2Na] [M-2H], and [M-Cl] are +2, -2 and +1, respectively. Br/Cl/I can only contribute to the ionization charge in case other ions are not available in the adduct formula.