Not all peptide fragment equally well, and we often find ourselves in the situation that the
fragment ions have such a low intensity, that they are difficult to distinguish from the random
The Combine Precursor Scans feature combines all scans from the same precursor into
one new scan. If you have a mediocre dataset with many low-intensity observations, you can
use this feature to increase the signal to noise ratio.
All peaks that are persistent throughout the dataset are copied, and their intensities are
accumulated. The default setting is 35%, which means that any peak must be present in at
least 35% of the scans in order to be copied into the new scan.
When we work with the same precursor, we expect the fragment pattern to share the same
fragment ions, even when the intensity may be low. Random noise peaks however, are not
persitent and will be filtered away.
Increasing the signal to noise ratio this way can often make it possible to validate problem
peptides. It further compresses your dataset so that each precursor is represented by one
The combined scans are saved into a new MGF file, NO changes are made to your original
In the example below, we have combined scans from a noisy dataset, using the defalt settings.
The scan shown has been combined from 10 scans - the number in each case is always written in the headline.
The combines intensities are now acceptable. Notice that most of the exported ion peaks have clear isotope series, while
we have no singletons or random noise peaks left in the final scan.