Chapter 3 Peak Detection and Labeling

If the expected higher theoretical peak masses and areas are present in the peak list:

• The peak in question is considered to be a monoisotopic

 

peak.

 

• The intensities of the higher mass peaks that correspond

 

to the expected isotope ratios are combined with the

 

intensity of the peak in question (additional intensity that

 

may be related to a contaminant or an overlapping

 

isotope envelope is not combined, and will be evaluated

 

in the next iteration).

 

• The peak in question is represented in the trace as a

 

centroid bar with increased amplitude. The total intensity

 

of the centroid bar represents the total area of each fitted

 

cluster.

 

 

If the expected higher theoretical peak masses and areas are

 

not present in the peak list, the peak in question is

3

represented in the trace as a centroid bar with its original

amplitude.

 

Figure 3-17illustrates how peaks that are and peaks that are

 

not part of an isotope cluster are represented in a deisotoped

 

trace.

 

When to use For most applications, particularly peptide analysis, the

 

 

deisotoping function yields more useful results than

 

monoisotopic peak filtering (described in Section 3.3.4,

 

Sorting, Filtering, and Printing the Peak List) because the

 

deisotoping function:

 

• Can successfully identify the monoisotopic peaks in

 

overlapping clusters.

 

• Does not consider noise peaks that exhibit the mass, but

 

not the area of an expected isotope peak.

 

• Amplifies the intensity of monoisotopic masses at high

 

m/z (due to contribution from other peaks in the cluster),

 

which allows the peak detection thresholds to eliminate

 

chemical noise without eliminating the high m/z peaks of

 

interest, enables improved peak matching in calibration,

 

and provides better results in database searching (which

 

relies on monoisotopic masses).

3-46 Applied Biosystems