Applied Biosystems Data Explorer 4 Series User Manual page 107

Problem
High-mass peaks not
detected
Noise detected as peaks
Peaks of interest are not
detected
Low Mass Gate spike is
identified as the Base
Peak
Peaks detected before
deisotoping are not
detected after
deisotoping
• Deisotope (reflector data only)—Peak
deisotoping reduces the spectrum to a
monoisotopic centroided plot of the monoisotopic
masses. This is useful in identifying overlapping
isotope clusters. Make sure peak detection
thresholds are set low enough to detect the
monoisotopic peak before deisotoping. For more
information, see Section 3.4, Deisotoping a
Spectrum. Deisotoping provides no benefit on linear
data (non-isotopically resolved) or on PSD data
(pure isotope data).
3. If peak detection is not acceptable, keep the Use
Resolution Dependent Settings option enabled, and
adjust the parameter associated with the observed
problem:
Suggested Actions
Decrease Mass Resolution setting. The default Mass
Resolution settings are optimized for masses below
20,000 Da.
Increase the %Max Peak Area.
Decrease the Resolution.
Decrease the %Max Peak Area.
NOTE: %Max Peak Area is calculated above the local
baseline and can compensate for problems related to a
rising global baseline.
Truncate the data to eliminate the Low Mass Gate spike,
then reapply peak detection settings. See Section 5.9,
Truncating a Spectrum.
Set %Max Peak Area and %BP Intensity to 0 before
deisotoping, deisotope, then reset thresholds to
appropriate settings after deisotoping.
Data Explorer
Peak Detection
™
Software User's Guide
3
3-9