Friday, August 9, 2013

de novo only peptides in PEAKS

One of the unique features in PEAKS is that it provides a list of de novo only peptides. What does it mean?

de novo only peptides are the de novo sequences derived from the spectra that do not a have confident database match.

In PEAKS, de novo only peptides are listed in the de novo only tab in every PEAKS DB, PEAKS PTM, SPIDER and inChorus results. The actual de novo only peptides displayed in the list will be affected by the filters in the summary tab. Let's use PEAKS DB result as an example.

The de novo only peptides are defined in the second row of the filters. The first part, TLC and ALC filters are the same as it is in the de novo result. It tells PEAKS what should be considered as a good de novo sequence. The second part, peptide -10lgP filter tells PEAKS what should not be considered as a confident database match. After the filters are applied, PEAKS will go through all the de novo sequences that passed the TLC and ALC filters. For each of such de novo sequence, PEAKS will look at the corresponding spectrum. If the spectrum does not produce any database matches that have a score higher than the de novo only peptide -10lgP filter, the de novo sequence of the spectrum will be considered as a de novo only peptide.

PEAKS does not stop at just providing a list of de novo only peptides, it also tries to associate them with the proteins. In the protein coverage view below, the gray bars represents the de novo only peptides that share at least 10 consecutive AAs with the protein sequence. This is particularly useful when looking for unexpected PTMs or glycosylation site.

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