De novo sequencing of peptides by MS/MS
peer-reviewed · Proteomics · 2010
peer-reviewed · Proteomics · 2010. Joerg Seidler et al. The current status of de novo sequencing of peptides by MS/MS is reviewed with focus on collision cell MS/MS…
| Date | 2010-02-18 |
| Type | peer-reviewed |
| Venue | Proteomics |
| Publisher | Wiley |
| Contribution | review |
| DOI | 10.1002/pmic.200900459 |
| Citations (OpenAlex) | 221 |
| Venue 2-year citedness | 2.96 |
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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- Compositional profiling of protein hydrolysates by high resolution liquid chromatography–mass spectrometry and chemometric analysis (2025) both
- 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
- Accurate discrimination of leucine and isoleucine residues by combining continuous digestion with multiple MS3 spectra integration in protein sequence (2022) crossref
- The Current State-of-the-Art Identification of Unknown Proteins Using Mass Spectrometry Exemplified on De Novo Sequencing of a Venom Protease from Bothrops moojeni (2022) both
- Metaproteomic Characterization of Forensic Samples (2022) crossref
- Affinity Selection from Synthetic Peptide Libraries Enabled by De Novo MS/MS Sequencing (2022) both
- Highly Robust de Novo Full-Length Protein Sequencing (2021) both
- The lysosomal endopeptidases Cathepsin D and L are selective and effective proteases for the middle‐down characterization of antibodies (2021) both
- Full-length Protein Sequencing Based on Continuous Digestion Using Non-specific Proteases (2021) crossref
- Tri‐ and dipeptides identification in whey protein and porcine liver protein hydrolysates by fast LC–MS/MS neutral loss screening and de novo sequencing (2021) crossref
- ProAlanase is an Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping (2020) both
- Lys-Sequencer: An algorithm for de novo sequencing of peptides by paired single residue transposed Lys-C and Lys-N digestion coupled with high-resolution mass spectrometry (2020) crossref
- Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics (2019) both
- A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref
- De Novo Sequencing of Proteins and Peptides: Algorithms, Applications, Perspectives (2018) crossref
- Antibody de novo Sequencing (2017) crossref
- A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom (2017) both
- Database-independent Protein Sequencing (DiPS) Enables Full-length de Novo Protein and Antibody Sequence Determination (2017) both
- 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
- De Novo Peptide Sequencing: Deep Mining of High-Resolution Mass Spectrometry Data (2016) crossref
- Sequence Protein Identification by Randomized Sequence Database and Transcriptome Mass Spectrometry (SPIDER-TMS): From Manual to Automatic Application of a ‘ de Novo Sequencing’ Approach (2016) crossref
- Benefits of selective peptide derivatization with sulfonating reagent at acidic pH for facile matrix‐assisted laser desorption/ionization de novo sequencing (2016) 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
- Using PepExplorer to Filter and Organize De Novo Peptide Sequencing Results (2015) crossref
- Bromine isotopic signature facilitates de novo sequencing of peptides in free‐radical‐initiated peptide sequencing (FRIPS) mass spectrometry (2015) crossref
- Lessons in de novo peptide sequencing by tandem mass spectrometry (2015) both
- Mass spectrometric de novo sequencing of natural non‐tryptic peptides: comparing peculiarities of collision‐induced dissociation (CID) and high energy collision dissociation (HCD) (2014) crossref
- A Simplified Method for Peptide De Novo Sequencing Using 18 O Labeling (2014) crossref
- A method combining SPITC and 18O labeling for simultaneous protein identification and relative quantification (2014) crossref
- Application of de novo sequencing tools to study abiogenic peptide formations by tandem mass spectrometry. The case of homo‐peptides from glutamic acid complicated by substitutions of hydrogen by sodium or potassium atoms (2014) crossref
- Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra (2013) both
- Differential 14N/15N-Labeling of Peptides Using N-Terminal Charge Derivatization with a High-Proton Affinity for Straightforward de novo Peptide Sequencing (2013) crossref
- De Novo Sequencing of Peptides Using Selective 351 nm Ultraviolet Photodissociation Mass Spectrometry (2013) crossref
- Primary sequence determination of a monoclonal antibody against α-synuclein using a novel mass spectrometry-based approach (2012) crossref
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- Improving peptide fragmentation by N‐terminal derivatization with high proton affinity (2011) crossref