Constrained search
7 methods · 1999–2020
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 7 methods is Accurate-mass constrained de novo interpretation (1999); 6 more have followed.
| Methods | 7 |
| Papers describing them | 10 |
| Authors | 35 |
| Active | 1999-07-01 to 2020-07-01 |
| Kinds | algorithm (6), adjacent |
| Acquisition | DDA (7) |
Methods (7)
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 (2011): Constrained de novo sequencing algorithm for peptide families such as conotoxins.
- SEQUEST over theoretically complete sequence databases (2015): Enumerates every peptide sequence compatible with the accurate precursor mass and searches them with SEQUEST, turning database search into de novo-like sequencing.
- Constrained neo-epitope de novo sequencing (2018): Constrained de novo sequencing of MHC-I neoepitope peptides, which differ from a reference peptide by a mutation, from immunopeptidomic MS/MS.
- PRESnovo (2020): Prescreens neuropeptide precursors for a conserved family motif before de novo sequencing, so only the variable part of the sequence has to be read.
Papers describing them (10)
- 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)
- Direct Protein Identification from Nonspecific Peptide Pools by High‐Accuracy MS Data Filtering (2006, Angewandte Chemie International Edition, peer-reviewed)
- Accurate Mass as a Bioinformatic Parameter in Data-to-Knowledge Conversion: Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Peptide De Novo Sequencing (2007, European Journal of 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 Peptides with Application to Conotoxins (2011, Lecture Notes in Computer Science, peer-reviewed)
- Constrained De Novo Sequencing of Conotoxins (2012, Journal of Proteome Research, peer-reviewed)
- Using SEQUEST with Theoretically Complete Sequence Databases (2015, Journal of the American Society for Mass Spectrometry, peer-reviewed)
- Constrained De Novo Sequencing of neo-Epitope Peptides Using Tandem Mass Spectrometry (2018, Lecture Notes in Computer Science, peer-reviewed)
- PRESnovo: Prescreening Prior to de novo Sequencing to Improve Accuracy and Sensitivity of Neuropeptide Identification (2020, Journal of the American Society for Mass Spectrometry, peer-reviewed)