De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry
peer-reviewed · Journal of Proteome Research · 2007
| Date | 2007-01-05 |
| Type | peer-reviewed |
| Venue | Journal of Proteome Research |
| Publisher | ACS |
| Contribution | algorithm |
| DOI | 10.1021/pr060271u |
| Citations (OpenAlex) | 196 |
| Venue 2-year citedness | 3.48 |
Abstract
The recent proliferation of novel mass spectrometers such as Fourier transform, QTOF, and OrbiTrap marks a transition into the era of precision mass spectrometry, providing a 2 orders of magnitude boost to the mass resolution, as compared to low-precision ion-trap detectors. We investigate peptide de novo sequencing by precision mass spectrometry and explore some of the differences when compared to analysis of low-precision data. We demonstrate how the dramatically improved performance of de novo sequencing with precision mass spectrometry paves the way for novel approaches to peptide identification that are based on direct sequence lookups, rather than comparisons of spectra to a database. With the direct sequence lookup, it is not only possible to search a database very efficiently, but also to use the database in novel ways, such as searching for products of alternative splicing or products of fusion proteins in cancer. Our de novo sequencing software is available for download at http://peptide.ucsd.edu/.
Methods and tools
- PepNovo: Probabilistic network + DP
Cites (7)
- De novo peptide sequencing using exhaustive enumeration of peptide composition (2006) crossref
- Proteomics-Grade de Novo Sequencing Approach (2005) crossref
- NovoHMM: A Hidden Markov Model for de Novo Peptide Sequencing (2005) crossref
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) crossref
- De novo peptide sequencing via tandem mass spectrometry (1999) crossref
- Sequence database searches via de novo peptide sequencing by tandem mass spectrometry (1997) crossref
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994) crossref
Cited by (24)
- Framework for de novo sequencing of peptide mixtures via network analysis and two-dimensional tandem mass spectrometry (2025) crossref
- Limitations of de novo sequencing in resolving sequence ambiguity (2025) crossref
- InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments (2025) both
- Transforming de novo peptide sequencing by explainable AI (2024) crossref
- De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments (2023) both
- Metaproteomic Characterization of Forensic Samples (2022) crossref
- Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification (2020) crossref
- pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization (2017) crossref
- Combining De Novo Peptide Sequencing Algorithms, A Synergistic Approach to Boost Both Identifications and Confidence in Bottom-up Proteomics (2017) crossref
- Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation (2017) crossref
- Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications (2017) crossref
- Peptide de novo sequencing of mixture tandem mass spectra (2016) both
- Revealing the functional structure of a new PLA2 K49 from Bothriopsis taeniata snake venom employing automatic “de novo” sequencing using CID/HCD/ETD MS/MS analyses (2015) crossref
- Sequencing-Grade De novo Analysis of MS/MS Triplets (CID/HCD/ETD) From Overlapping Peptides (2013) both
- pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra (2013) crossref
- Shotgun Protein Sequencing with Meta-contig Assembly (2012) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- Dimethyl isotope labeling assisted de novo peptide sequencing (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
- A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry (2010) both
- De novo sequencing of peptides by MS/MS (2010) crossref
- Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009) both
- MSNovo: A Dynamic Programming Algorithm for de Novo Peptide Sequencing via Tandem Mass Spectrometry (2007) crossref