De novo sequencing of peptides by MS/MS
peer-reviewed · Proteomics · 2010
| Date | 2010-02-18 |
| Type | peer-reviewed |
| Venue | Proteomics |
| Publisher | Wiley |
| Contribution | review |
| DOI | 10.1002/pmic.200900459 |
| Citations (OpenAlex) | 217 |
| Venue 2-year citedness | 2.58 |
Abstract
The current status of de novo sequencing of peptides by MS/MS is reviewed with focus on collision cell MS/MS spectra. The relation between peptide structure and observed fragment ion series is discussed and the exhaustive extraction of sequence information from CID spectra of protonated peptide ions is described. The partial redundancy of the extracted sequence information and a high mass accuracy are recognized as key parameters for dependable de novo sequencing by MS. In addition, the benefits of special techniques enhancing the generation of long uninterrupted fragment ion series for de novo peptide sequencing are highlighted. Among these are terminal (18)O labeling, MS(n) of sodiated peptide ions, N-terminal derivatization, the use of special proteases, and time-delayed fragmentation. The emerging electron transfer dissociation technique and the recent progress of MALDI techniques for intact protein sequencing are covered. Finally, the integration of bioinformatic tools into peptide de novo sequencing is demonstrated.
Methods and tools
- De novo sequencing of peptides by MS/MS (Proteomics review): Tutorial review (Proteomics 2010) surveying de novo peptide sequencing by MS/MS: fragmentation chemistry, manual interpretation, and the algorithmic landscape pre-deep-learning.
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Cited by (15)
- Unveiling the Diversity and Modifications of Short Peptides in Scorpion Venom through Liquid Chromatography-High Resolution Mass Spectrometry (2024) both
- Introducing π-HelixNovo for practical large-scale de novo peptide sequencing (2024) crossref
- Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review (2023) crossref
- Introducing PandaNovo for practical large-scale de novo peptide sequencing (2023) semanticscholar
- Quantification of snake venom proteomes by mass spectrometry - considerations and perspectives (2023) both
- Metaproteomic Characterization of Forensic Samples (2022) crossref
- Highly Robust de Novo Full-Length Protein Sequencing (2021) both
- A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref
- Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation (2017) both
- Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) crossref
- UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry (2016) both
- Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets (2016) crossref
- Lessons in de novo peptide sequencing by tandem mass spectrometry (2015) both
- A method combining SPITC and 18O labeling for simultaneous protein identification and relative quantification (2014) crossref
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref