DE NOVO SEQUENCING WITH LIMITED NUMBER OF POST-TRANSLATIONAL MODIFICATIONS PER PEPTIDE

peer-reviewed · Journal of Bioinformatics and Computational Biology · 2013

peer-reviewed · Journal of Bioinformatics and Computational Biology · 2013. Lin He et al. De novo sequencing derives the peptide sequence from a tandem mass spectrum without the assistance of protein…
Date 2013-08-01
Type peer-reviewed
Venue Journal of Bioinformatics and Computational Biology
Publisher World Scientific Pub Co Pte Lt
Contribution algorithm
DOI 10.1142/s0219720013500078
Citations (OpenAlex) 11
Venue 2-year citedness 0.89

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 .

Authors

  1. Lin He · Bioinformatics Solutions Inc., University of Waterloo
  2. XI HAN · University of Waterloo
  3. Bin Ma · Rapid Novor Inc., University of Waterloo, University of Western Ontario, Western University

Methods and tools

  • DeNovoPTM: A de novo sequencing algorithm that allows many PTM types while bounding the number of modifications per peptide to keep accuracy.

Cites (9)

Cited by (4)

Seen in the charts

Back to the full map

Back to top