Constrained search
4 methods · 1999–2012
Constrained search: Replace the database with the set of sequences the measurement itself allows. An accurate precursor mass, a determined composition or a known peptide family bounds the candidate set tightly enough to enumerate it outright.
Replace the database with the set of sequences the measurement itself allows. An accurate precursor mass, a determined composition or a known peptide family bounds the candidate set tightly enough to enumerate it outright.
The earliest of its 4 methods is Accurate-mass constrained de novo interpretation (1999); 3 more have followed.
| Methods | 4 |
| Papers describing them | 4 |
| Authors | 20 |
| Active | 1999-07-01 to 2012-08-03 |
| Kinds | algorithm (3), adjacent |
| Acquisition | DDA (4) |
Methods (4)
Oldest first, by the paper that describes each one.
- Accurate-mass constrained de novo interpretation (1999): Uses 10 ppm parent-mass accuracy plus immonium-ion composition to replace the database with the set of sequence permutations the mass allows, then feeds the resulting de novo sequences into a similarity search. An early statement of the hybrid de novo plus homology strategy.
- Composition-based sequencing (2004): Two-step database-free strategy enabled by FT-ICR mass accuracy: determine the peptide’s amino acid COMPOSITION first, then score only the permutations that composition allows, which is a far smaller search space than conventional de novo sequencing explores.
- TVNovo (2010): Turns de novo sequencing into a search problem by generating a VIRTUAL database per spectrum, enumerating the candidate sequences the precursor mass allows, then scoring them as a database search would. Built for high-resolution LTQ-FT data.
- Conovo (2012): Constrained de novo sequencing algorithm for peptide families such as conotoxins.
Papers describing them (4)
- Role of Accurate Mass Measurement (±10 ppm) in Protein Identification Strategies Employing MS or MS/MS and Database Searching (1999, Analytical Chemistry, peer-reviewed)
- De novo sequencing, peptide composition analysis, and composition-based sequencing: A new strategy employing accurate mass determination by Fourier transform ion cyclotron resonance mass spectrometry (2004, Journal of the American Society for Mass Spectrometry, peer-reviewed)
- TVNovo: De novo peptide sequencing for high resolution LTQ-FT mass spectrometry using virtual database searching (2010, 2010 3rd International Conference on Biomedical Engineering and Informatics, peer-reviewed)
- Constrained De Novo Sequencing of Conotoxins (2012, Journal of Proteome Research, peer-reviewed)