Peak Separation

Peak separation field needs to contain the minimum allowed m/z separation between peaks in the theoretical spectrum. It is provided in atomic mass units (amu) and must contain a floating point value greater than or equal to zero. If peak separation is set to zero, an experimental spectrum will be generated and used as is. Otherwise, peaks that are closer to each other than the threshold will be merged into a peak with an average m/z and intensity. Peak separation needs to approximately correspond to the resolution of the instrument.

If it is too low, the theoretical spectrum may contain multiple peaks very close to each other. In the best-case scenario, only one peak from each cluster will be matched to an experimental peak in a low-resolution spectrum. Due to a large number of unmatched peaks, candidate scores will be low and a correct match can be missed.

If it is too high, the theoretical spectrum maybe too coarse and may have a shape dissimilar to the experimental spectrum. Due to poor shape similarity, candidate scores will be low and a correct match can be missed.