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 |
| 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). |