Better score function for peptide identification with ETD MS/MS spectra
peer-reviewed · BMC Bioinformatics · 2010
| Date | 2010-01-01 |
| Type | peer-reviewed |
| Venue | BMC Bioinformatics |
| Publisher | Springer Science and Business Media LLC |
| Contribution | algorithm |
| DOI | 10.1186/1471-2105-11-s1-s4 |
| Citations (OpenAlex) | 48 |
| Venue 2-year citedness | 4.71 |
Abstract
Background Tandem mass spectrometry (MS/MS) has become the primary way for protein identification in proteomics. A good score function for measuring the match quality between a peptide and an MS/MS spectrum is instrumental for the protein identification. Traditionally the to-be-measured peptides are fragmented with the collision induced dissociation (CID) method. More recently, the electron transfer dissociation (ETD) method was introduced and has proven to produce better fragment ion ladders for larger and more basic peptides. However, the existing software programs that analyze ETD MS/MS data are not as advanced as they are for CID. Results To take full advantage of ETD data, in this paper we develop a new score function to evaluate the match between a peptide and an ETD MS/MS spectrum. Experiments on real data demonstrated that this newly developed score function significantly improved the de novo sequencing accuracy of the PEAKS software on ETD data. Conclusion A new and better score function for ETD MS/MS peptide identification was developed. The method used to develop our ETD score function can be easily reused to train new score functions for other types of MS/MS data.
Methods and tools
- PEAKS: Commercial DP-based de novo
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Cited by (10)
- Discovery of Novel Antimicrobial Peptides from Varanus komodoensis (Komodo Dragon) by Large-Scale Analyses and De-Novo-Assisted Sequencing Using Electron-Transfer Dissociation Mass Spectrometry (2017) crossref
- De novo Peptide Sequencing (2016) crossref
- Large Scale Discovery and De Novo-Assisted Sequencing of Cationic Antimicrobial Peptides (CAMPs) by Microparticle Capture and Electron-Transfer Dissociation (ETD) Mass Spectrometry (2015) crossref
- UniNovo: a universal tool for de novo peptide sequencing (2013) both
- DE NOVO SEQUENCING WITH LIMITED NUMBER OF POST-TRANSLATIONAL MODIFICATIONS PER PEPTIDE (2013) crossref
- Sequencing-Grade De novo Analysis of MS/MS Triplets (CID/HCD/ETD) From Overlapping Peptides (2013) both
- Tutorial on de novo peptide sequencing using MS/MS mass spectrometry (2012) crossref
- PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification (2012) both
- De Novo Sequencing and Homology Searching (2012) both
- ADEPTS: Advanced peptide de novo sequencing with a pair of tandem mass spectra (2010) crossref