Mass spectrometry-based protein identification by integrating de novo sequencing with database searching
peer-reviewed · BMC Bioinformatics · 2013
| Date | 2013-01-21 |
| Type | peer-reviewed |
| Venue | BMC Bioinformatics |
| Publisher | Springer Science and Business Media LLC |
| Contribution | adjacent |
| DOI | 10.1186/1471-2105-14-S2-S24 |
| Citations (OpenAlex) | 32 |
| Venue 2-year citedness | 4.50 |
Abstract
BACKGROUND: Mass spectrometry-based protein identification is a very challenging task. The main identification approaches include de novo sequencing and database searching. Both approaches have shortcomings, so an integrative approach has been developed. The integrative approach firstly infers partial peptide sequences, known as tags, directly from tandem spectra through de novo sequencing, and then puts these sequences into a database search to see if a close peptide match can be found. However the current implementation of this integrative approach has several limitations. Firstly, simplistic de novo sequencing is applied and only very short sequence tags are used. Secondly, most integrative methods apply an algorithm similar to BLAST to search for exact sequence matches and do not accommodate sequence errors well. Thirdly, by applying these methods the integrated de novo sequencing makes a limited contribution to the scoring model which is still largely based on database searching. RESULTS: We have developed a new integrative protein identification method which can integrate de novo sequencing more efficiently into database searching. Evaluated on large real datasets, our method outperforms popular identification methods.
Methods and tools
- NovoDB: Protein identification method integrating de novo sequencing with database searching.
Cites (9)
- De Novo Sequencing and Homology Searching (2012) both
- De Novo Peptide Identification via Tandem Mass Spectrometry and Integer Linear Optimization (2007) both
- Identification of Protein Modifications Using MS/MS de Novo Sequencing and the OpenSea Alignment Algorithm (2005) both
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) both
- GutenTag: High-Throughput Sequence Tagging via an Empirically Derived Fragmentation Model (2003) both
- A Suboptimal Algorithm for De Novo Peptide Sequencing via Tandem Mass Spectrometry (2003) both
- Searching Sequence Databases via De Novo Peptide Sequencing by Tandem Mass Spectrometry (2002) both
- De novo peptide sequencing via tandem mass spectrometry (1999) both
- Sequence database searches via de novo peptide sequencing by tandem mass spectrometry (1997) semanticscholar