Local confidence score and de novo tags

PEAKS de novo sequencing not only produces accurate de novo sequences from the spectrum, it also provides confidence score at amino acid level.

In the de novo table, when you hover the mouse cursor on a de novo sequence, the following window will show up to display the local confidence score for each amino acid.

The sequence is color coded. Red represents a very high confidence (greater than 90%), purple represents a high confidence (80 to 90%), blue represents a medium confidence (60 to 80%), and black represents low confidence (less than 60%).

PEAKS also provide a slider to change the low confident amino acid to mass tag. We call the remaining consecutive high confident amino acids de novo tag.

Those de novo tags may then be used in BLAST.