Adducts, Multiply charged species, isotope patterns

Fragments, Adducts, charge

When creating/editing a substance that's used for Mass Spec you can set which ions are used by Peaksel:

Mass Spec settings button

In the Mass Spec settings you can:

  • Add/subtract fragments to/from your initial structure
  • Set max charge count to define how many times you expect your compound to be ionized

When extracting a chromatogram, now Peaksel will add up all the intensities of all the adducts:

Mass Spec settings - pointing out fragments

It's possible to set multiple fragments to be added to or removed from the compound. They can be charged (like H+, Na+, Cl- ions) or neutral (like deprotected compound):

Mass Spec settings - configuring fragments

Isotopic patterns, qualifier and quantifier ions

It's possible to fine-tune which of the ions that Peaksel calculated should be used:

Mass Spec settings - pointing out qualifier and quantifier ions

Some use cases:

  • You may want to use one set of ions as quantifiers (they'll be part of the peak area), while others are used as qualifiers to determine if the peak is actually our compound and not some isobar with very similar mass.
  • Or maybe you work with isopure compounds, and you want to uncheck all but one isotope from quantification

By default, Peaksel will use only the most abundant isotopes (of the same adduct!) as qualifiers, but only if their predicted intensities are higher than the tolerance level:

Mass Spec settings - selecting qualifier and quantifier ions