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.
Cites (10)
- FAST DE NOVO PEPTIDE SEQUENCING AND SPECTRAL ALIGNMENT VIA TREE DECOMPOSITION (2005) both
- NovoHMM: A Hidden Markov Model for de Novo Peptide Sequencing (2005) both
- Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry (2005) both
- A graph-theoretic approach for the separation of b and y ions in tandem mass spectra (2005) both
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) both
- A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (2001) both
- De novo peptide sequencing via tandem mass spectrometry (1999) both
- Sequence database searches via de novo peptide sequencing by tandem mass spectrometry (1997) both
- Fast algorithm for peptide sequencing by mass spectroscopy (1990) semanticscholar
- PAAS 3: A computer program to determine probable sequence of peptides from mass spectrometric data (1984) both