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Updated: May 9, 2026

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
De novo sequencing with limited number of post-translational modifications per peptide
1David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1, Canada. l22he@uwaterloo.ca
Abstract:
De novo sequencing derives the peptide sequence from a tandem mass spectrum without the assistance of protein databases. This analysis has been indispensable for the identification of novel or modified peptides in a biological sample. Currently, the speed of de novo sequencing algorithms is not heavily affected by the number of post-translational modification (PTM) types in consideration. However, the accuracy of the algorithms can be degraded due to the increased search space. Most peptides in a proteomics research contain only a small number of PTMs per peptide, yet the types of PTMs can come from a large number of choices. Therefore, it is desirable to include a large number of PTM types in a de novo sequencing algorithm, yet to limit the number of PTM occurrences in each peptide to increase the accuracy. In this paper, we present an efficient de novo sequencing algorithm, DeNovoPTM, for such a purpose. The implemented software is downloadable from http://www.cs.uwaterloo.ca/~l22he/denovo_ptm .
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