DeNovoX is a fully-automated de novo sequencing software program that is capable of determining complete or partial amino acid sequences of unknown peptides by interpreting full scan MS/MS spectra.This probability-based program has been optimized for data collected with Thermo's Finnigan LCQ ion trap instruments, and is ideally suited for high-throughput analyses of peptide mixtures.
The DeNovoX probability algorithm combines two parallel modules, an Expert System and a Search Engine, which interact simultaneously at several levels. The Expert System, taking into account over 25 different factors known to be relevant to de novo peptide sequencing, assimilates the information available from each MS2 spectrum. The probability values are calculated rigorously, and reflect the real probability that a given sequence is in the peptide spectrum analyzed.
The advantage of DeNovoX is its ability to identify any kind of unknown modification of a protein with a high degree of confidence, whether the result of a single amino acid deletion in the peptide chain, a mutation, or a post-translational modification such as phosphorylation, resulting from some type of cellular processing.
With DeNovoX software, peptides of up to 14 amino acids have been sequenced, including those with post-translational modifications. It also automates and accelerates sequencing, returning results equal to or better than those formerly achieved through expert manual sequencing of peptides within proteins. Data from triply-charged fragmentations, which normally are beyond human interpretation, are also successfully interpreted by the program.