UniNovo is a universal de novo peptide sequencing tool that works well for various types of spectra and spectral pairs (e.g., CID, ETD, HCD, CID/ETD, etc). The accuracy of de novo reconstructions generated by UniNovo is better than or comparable to PepNovo+ or PEAKS. Moreover, UniNovo also estimates the error rate of the reported reconstruction.
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Bioinformatics. 2013 Aug 15;29(16):1953-62. doi: 10.1093/bioinformatics/btt338. Epub 2013 Jun 12.
UniNovo: a universal tool for de novo peptide sequencing.
Jeong K1, Kim S, Pevzner PA.