De Novo Sequencing

  • Local Confidence is the confidence that a particular amino acid is present in the de novo peptide at a particular position. It is presented as a percentage.
  • Total Local Confidence (TLC) is the sum of the local confidence scores (0 to 1) from each amino acid in the peptide sequence.
  • Average Local Confidence (ALC) is the average of the TLC. It is TLC divided by the number of amino acids in the peptide sequence.

Usually you will find good peptides at 55% and above. This does not mean that the whole sequence is the correct sequence. This is because the beginning and end of the spectrum are much more difficult to interpret when it comes to de novo sequencing due to the high mass/low mass of the ions produced by these fragments. This is why we added the colour coding to the results so you can see where in the sequence there is higher confidence.

You can definitely chop off the low scoring amino acids from the ends of the de novo sequence tags. To do this, click on the score threshold slider button (green, yellow, red symbol at the top of the de novo results). Use the slider to set a score threshold and any amino acid below that threshold will be reduced to its mass in Daltons. Once you export the tags, the last column in the excel export will follow this confidence threshold.


Bottom line: result quality. PEAKS consistently gives more accurate peptide sequences and with better confidence than other programs. This is a result of PEAKS’ global optimization algorithms and sophisticated scoring schema.

SPIDER (Sequence Tag Homology/Mutated Peptides)


“-1” means that a ratio was found but it was not derived from any high scoring peptides. If you want the ratio to be displayed, you can raise the peptide score threshold set in the run parameters.

The most likely reason is users must have at least two samples and the same number of fractions in each sample.