A New Parameterized Algorithm for Rapid Peptide Sequencing
peer-reviewed · PLoS ONE · 2014
| Date | 2014-02-14 |
| Type | peer-reviewed |
| Venue | PLoS ONE |
| Publisher | Public Library of Science (PLoS) |
| Contribution | algorithm |
| DOI | 10.1371/journal.pone.0087476 |
| Citations (OpenAlex) | 14 |
Abstract
De novo sequencing is an important computational approach to determining the amino acid sequence of a peptide with tandem mass spectrometry (MS/MS). Most of the existing approaches use a graph model to describe a spectrum and the sequencing is performed by computing the longest antisymmetric path in the graph. The task is often computationally intensive since a given MS/MS spectrum often contains noisy data, missing mass peaks, or post translational modifications/mutations. This paper develops a new parameterized algorithm that can efficiently compute the longest antisymmetric partial path in an extended spectrum graph that is of bounded path width. Our testing results show that this algorithm can efficiently process experimental spectra and provide sequencing results of high accuracy.
Methods and tools
- Parameterized path-width de novo sequencing: Exploits bounded path width of an extended spectrum graph to compute antisymmetric partial paths for fast de novo sequencing.