Assessing peptide de novo sequencing algorithms performance on large and diverse data sets
peer-reviewed · Proteomics · 2007
peer-reviewed · Proteomics · 2007. Erik Pitzer et al. De novo peptide sequencing algorithms are often tested on relatively small data sets made of excellent…
| Date | 2007-09-01 |
| Type | peer-reviewed |
| Venue | Proteomics |
| Publisher | Wiley |
| Contribution | benchmark |
| DOI | 10.1002/pmic.200700224 |
| Citations (OpenAlex) | 39 |
| Venue 2-year citedness | 2.58 |
Abstract
De novo peptide sequencing algorithms are often tested on relatively small data sets made of excellent spectra. Since there are always more and more tandem mass spectra available, we have assembled six large, reliable, and diverse (three mass spectrometer types) data sets intended for such tests and we make them accessible via a web server. To exemplify their use we investigate the performance of Lutefisk, PepNovo, and PepNovoTag, three well-established peptide de novo sequencing programs.
Methods and tools
- Peptide de novo sequencing benchmark data sets: Large and diverse benchmark data sets for evaluating peptide de novo sequencing algorithms.
Cites (5)
- Performance Evaluation of Existing De Novo Sequencing Algorithms (2006) crossref
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) crossref
- Searching Sequence Databases via De Novo Peptide Sequencing by Tandem Mass Spectrometry (2002) crossref
- Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry (2001) crossref
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994) crossref
Cited by (5)
- Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) crossref
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- Identification of a novel Plasmopara halstedii elicitor protein combining de novo peptide sequencing algorithms and RACE-PCR (2010) semanticscholar
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) crossref
- De novo sequencing of peptides by MS/MS (2010) crossref