GA-Novo: De Novo Peptide Sequencing via Tandem Mass Spectrometry Using Genetic Algorithm
peer-reviewed · Lecture Notes in Computer Science · 2019
| Date | 2019-03-30 |
| Type | peer-reviewed |
| Venue | Lecture Notes in Computer Science |
| Publisher | Springer International Publishing |
| Contribution | algorithm |
| DOI | 10.1007/978-3-030-16692-2_6 |
| Citations (OpenAlex) | 8 |
| Venue 2-year citedness | 1.54 |
Preprint version: GA-Novo: De Novo Peptide Sequencing via Tandem Mass Spectrometry using Genetic Algorithm (2019-02-03, arXiv)
Abstract
Proteomics is the large-scale analysis of the proteins. The common method for identifying proteins and characterising their amino acid sequences is to digest the proteins into peptides, analyse the peptides using mass spectrometry and assign the resulting tandem mass spectra (MS/MS) to peptides using database search tools. However, database search algorithms are highly dependent on a reference protein database and they cannot identify peptides and proteins not included in the database. Therefore, de novo sequencing algorithms are developed to overcome the problem by directly reconstructing the peptide sequence of an MS/MS spectrum without using any protein database. Current de novo sequencing algorithms often fail to construct the completely matched sequences, and produce partial matches. In this study, we propose a genetic algorithm based method, GA-Novo, to solve the complex optimisation task of de novo peptide sequencing, aiming at constructing full length sequences. Given an MS/MS spectrum, GA-Novo optimises the amino acid sequences to best fit the input spectrum. On the testing dataset, GA-Novo outperforms PEAKS, the most commonly used software for this task, by constructing 8% higher number of fully matched peptide sequences, and 4% higher recall at partially matched sequences.
Methods and tools
- GA-Novo: Genetic-algorithm approach for de novo peptide sequencing from tandem mass spectra.
Cites (8)
- De novo Peptide Sequencing (2016) crossref
- Novor: Real-Time Peptide de Novo Sequencing Software (2015) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) both
- Complexity and scoring function of MS/MS peptide de novo sequencing (2006) semanticscholar
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) semanticscholar
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- De novo peptide sequencing via tandem mass spectrometry (1999) semanticscholar
- PAAS 3: A computer program to determine probable sequence of peptides from mass spectrometric data (1984) both
Cited by (5)
- De Novo Sequencing of Peptides from Tandem Mass Spectra and Applications in Proteogenomics (2024) crossref
- Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing (2024) both
- Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing (2023) crossref
- DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data (2020) semanticscholar
- Learning to Rank Peptide-Spectrum Matches Using Genetic Programming (2019) crossref