Peak Detection

•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:

Problem

Suggested Actions

 

3

 

 

 

 

 

 

High-mass peaks not

Decrease Mass Resolution setting. The default Mass

 

 

detected

Resolution settings are optimized for masses below

 

 

 

20,000 Da.

 

 

 

 

 

 

Noise detected as peaks

Increase the %Max Peak Area.

 

 

 

Decrease the Resolution.

 

 

 

 

 

 

Peaks of interest are not

Decrease the %Max Peak Area.

 

 

detected

NOTE: %Max Peak Area is calculated above the local

 

 

 

baseline and can compensate for problems related to a

 

 

 

rising global baseline.

 

 

 

 

 

 

Low Mass Gate spike is

Truncate the data to eliminate the Low Mass Gate spike,

 

 

identified as the Base

then reapply peak detection settings. See Section 5.9,

 

 

Peak

Truncating a Spectrum.

 

 

 

 

 

 

Peaks detected before

Set %Max Peak Area and %BP Intensity to 0 before

 

 

deisotoping are not

deisotoping, deisotope, then reset thresholds to

 

 

detected after

appropriate settings after deisotoping.

 

 

deisotoping

 

 

 

 

 

 

 

Data Explorer™ Software User’s Guide

3-9