Applied Biosystems Data Explorer 4 Series User Manual page 147

Troubleshooting
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
mass of the monoisotopic peak. The height of the
vertical bar is proportional to the peak areas of all
peaks in the isotope cluster.
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
Deisotoping a Spectrum
CAUTION
™
Software User's Guide
3
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