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 | 2.96 |
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 (7)
- Performance Evaluation of Existing De Novo Sequencing Algorithms (2006) crossref
- InsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra (2005) crossref
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) crossref
- High-Throughput Identification of Proteins and Unanticipated Sequence Modifications Using a Mass-Based Alignment Algorithm for MS/MS de Novo Sequencing Results (2004) 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 (10)
- Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) crossref
- Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra (2013) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- Algorithm Development of de novo Peptide Sequencing Via Tandem Mass Spectrometry (2010) 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
- OVNIp: An open source application facilitating the interpretation, the validation and the edition of proteomics data generated by MS analyses and de novo sequencing (2010) crossref
- De novo sequencing of peptides by MS/MS (2010) crossref
- De Novo Sequencing Methods in Proteomics (2009) crossref
- A comparative study of the accuracy of several de novo sequencing software packages for datasets derived by matrix‐assisted laser desorption/ionisation and electrospray (2008) crossref