Deisotoping a Spectrum

CAUTION

If you enter an invalid value in the Adduct field, for example, numbers, the spectrum is still converted to a deisotoped spectrum, and the peak height is proportional to the original peak area.

7.In the Formula text box, type the generic formula (using any elements in the Periodic table) that approximates the isotopic pattern for the compound class you are examining. Generic formulas include:

•Peptides— C6H5NO

•DNA— C38H49N15O24P4

•RNA— C38H47N15O28P4

•Carbohydrate— C6H12O6

8.Click OK.

The deisotoped spectrum is displayed with a DI trace

label. The mass of the vertical bar corresponds to the 3 mass of the monoisotopic peak. The height of the

vertical bar is proportional to the peak areas of all peaks in the isotope cluster.

Troubleshooting If you see several small peaks around a very large peak after deisotoping, the software has successfully identified a monoisotopic peak, but the isotope cluster does not exactly match the theoretical elemental composition that you specified. This may be caused by the following:

•The signal-to-noise ratio of the spectrum is poor and the calculated peak areas are not accurate.

•The specified elemental composition is not correct for the compound. For example, if the peptide contains sulfur, and sulfur was not in the specified formula, a small peak may occur 2 Da higher than the expected monoisotopic mass.

•There are two overlapping isotope clusters but the intensity of one cluster is stronger than the intensity of the other.

Increase the peak detection threshold after deisotoping to remove the residual peaks from the peak list.

Data Explorer™ Software User’s Guide

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