Overview

Highlights

  • Automated de novo peptide sequencing of data-dependent acquiestion (DDA) and data-independent acqusion (DIA) datasets
  • Accuracy at amino acid and peptide level
  • AI-based DeepNovo Integration
  • Combines complementary fragmentations to increase de novo sequencing accuracy
  • Supports CID, HCD, ETD/ECD, EThcD, fragmentation methods

PEAKS de novo peptide sequencing

Accuracy

PEAKS and PEAKS AB use a comprehensive scoring system to provide accurate de novo sequencing results. An important feature in these platforms is the ability to assess the Local Confidence Score – the likelihood of each amino acid assignment in a resultant peptide. The local confidence score extends the accuracy to the peptide level with the average local confidence (ALC) and total local confidence (TLC) scores. Below, the string of amino acids, TLCDDEFKADEK is a confident sequence tag since the LC of each amino acids is greater than the LC threshold. The amino acids, NP, at the peptide N-terminus however, have a lower LC score and do not pass the score threshold.

Utilization of Spectrum-Pairs: de novo sequencing using spectrum-pairs that are generated in different fragmentation modes (eg.ETD/HCD). Confident de novo sequence tags from each complementary spectrum are used to reconstruct a peptide sequence, which is optimized to both spectra.
Unique to PEAKS is the ability to combine de novo peptide sequencing results with those of a database search. De novo peptide sequences are aligned with protein database entries to provide additional information about PTMs, mutations, homologous peptides, and novel peptides.
Using peptide sequences derived from de novo sequencing, it is possible to construct a full protein sequence without a reference database. In the past, this required a lot of manual work, however this process can now be automated using PEAKS AB. Using confident de novo peptide sequence tags from orthogonal enzyme digests, PEAKS AB will assemble the tags together to construct a full protein sequence.
PEAKS Studio is a “peptide de novo” sequencing tool whereas PEAKS AB is a “protein de novo” sequencing tool. PEAKS Studio is only capable of de novo sequencing each scan from the raw LC-MS/MS data file. PEAKS AB however, is able to assemble the de novo sequenced peptides to construct the full protein sequence.