The Top N Peaks Filter node improves the number of peptides identified with high confidence by reducing the number of peaks in the searched peak lists. It avoids matching peptide candidates to spurious or noise peaks, so it produces fewer false peptide matches.
A commonly used method when searching proteomics data is to remove all but the n most abundant peaks within a given mass window from the generated peak lists. Normal settings keep only the top six to ten peaks within every 100 Da mass window.
You can place the Top N Peaks Filter node anywhere between the Spectrum Selector node and a search engine node, such as Mascot or Sequest HT. You can use multiple Top N Peaks Filter nodes within the same workflow, if necessary.
The following table describes the parameters for the Top N Peaks Filter node.
Parameter | Description |
|---|---|
Top N | Specifies the number of the most abundant peaks to keep within the specified mass window. Range: 1–no maximum; default: 6. |
Mass Window | Specifies the size of the mass window, in daltons. The application divides the spectrum into mass windows of the specified size, and in each of these mass windows, it filters out all peaks except the number of the most abundant peaks specified by the Top N parameter. Range: 1.0 Da–no maximum; default: 100 Da |
The Top N Filter node divides each input spectrum or peak list into consecutive mass windows of the specified size. The first mass window is placed at m/z = 0 Da. After that, this filter removes all peaks except the specified number of the most abundant peaks from every mass window.
You might prefer to filter the top n most abundant peaks within the entire spectrum, for example, the top 50 peaks of every spectrum. Set the Mass Window parameter to a large width that always spans the whole mass range of the entire spectrum, for example, 10 000 Da. Set the Top N parameter to the number of the most abundant peaks to keep for every spectrum, for example, 50.