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: 
In the Mass Spec settings you can:
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Add/subtract fragments to/from your initial structure
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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: 
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): 
Isotopic patterns, qualifier and quantifier ions
It’s possible to fine-tune which of the ions that Peaksel calculated
should be used: 
Some use cases:
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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.
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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: 