MS peak purity calculation

The MS peak purity calculation is based on the percentage of the component ions from spectra that group together and constitute the target relative to other components present.

The application performs the following steps to calculate the MS peak purity:

1. Run a deconvolution on the entire chromatographic range.

   1. For the top (n) detected m/z values, create an Extracted Ion Chromatogram (EIC). You can set the number in the processing method under Compounds > Spectra , MS Peak Purity tab.
   2. In each EIC, find the peak retention time.
   3. Define components based on EIC peaks that elute at the same retention time.

2. Determine the target component that matches the target compound.

   1. Get basic parameters for further calculations:

   • m/z delta range, from internal default settings (m/z -0.3 to +0.7)

   • Target quantifier m/z, by extracting the MS spectrum at the TIC peak apex and finding the m/z of highest abundance

   • Retention time window for the target compound (current compound), from the processing method under Compounds > Identification

   2. For each component found by deconvolution, find all m/z values that fall within the m/z delta range of the target quantifier m/z.
   3. For every such m/z value, check if the EIC has an apex within the retention time window of the target quantifier EIC peak.
   4. Get the component with the largest such peak, and use it as the target component.

3. If the system fails to find a target component, it re-tries by running the full-sample deconvolution in high-resolution mode, using an RT window size factor that is reduced by a factor of 2. The high-resolution results are cached and are searched for any target component that cannot be found in the normal-resolution component list. The automatic generation of the high-resolution results allows many target components to be identified that were previously missed.

4. The system attempts to detect double components that share the same RT and base peak m/z. The presence of such component doublets can strongly bias the purity estimate to the downside. Component doublets can occur if the RT window size factor is too small. Therefore, the system attempts to recover automatically by re-running the full-sample deconvolution in low-resolution mode, using a window size factor that is increased by a factor of 2. The low-resolution results are cached and are searched for any target that is matched to a component doublet.

5. Get all contributing components, that is, any component that has spectral peaks within m/z delta range of the target quantifier m/z and overlaps the target peak in retention time.

6. Calculate the purity using the following formula: