Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra
peer-reviewed · Molecular & Cellular Proteomics · 2009
peer-reviewed · Molecular & Cellular Proteomics · 2009. Sangtae Kim et al. Database search tools identify peptides by matching tandem mass spectra against a protein database. We study…
| Date | 2009-01-01 |
| Type | peer-reviewed |
| Venue | Molecular & Cellular Proteomics |
| Publisher | Elsevier BV |
| Contribution | adjacent |
| DOI | 10.1074/mcp.M800103-MCP200 |
| Citations (OpenAlex) | 92 |
| Venue 2-year citedness | 4.69 |
Abstract
Database search tools identify peptides by matching tandem mass spectra against a protein database. We study an alternative approach when all plausible de novo interpretations of a spectrum (spectral dictionary) are generated and then quickly matched against the database. We present a new MS-Dictionary algorithm for efficiently generating spectral dictionaries and demonstrate that MS-Dictionary can identify spectra that are missed in the database search. We argue that MS-Dictionary enables proteogenomics searches in six-frame translation of genomic sequences that may be prohibitively time-consuming for existing database search approaches. We show that such searches allow one to correct sequencing errors and find programmed frameshifts.
Methods and tools
- MS-Dictionary: Hybrid method that integrates de novo spectral dictionaries with database search of tandem mass spectra.
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- SeqNovo: De Novo Peptide Sequencing Prediction in IoMT via Seq2Seq (2023) crossref
- The impact of noise and missing fragmentation cleavages on de novo peptide identification algorithms (2022) both
- De novo sequencing of proteins by mass spectrometry (2020) both
- PRESnovo: Prescreening Prior to de novo Sequencing to Improve Accuracy and Sensitivity of Neuropeptide Identification (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
- Peptide de novo sequencing of mixture tandem mass spectra (2016) crossref
- Using SEQUEST with Theoretically Complete Sequence Databases (2015) semanticscholar
- Lessons in de novo peptide sequencing by tandem mass spectrometry (2015) both
- De novo identification and quantification of single amino-acid variants in human brain (2014) crossref
- UniNovo: a universal tool for de novo peptide sequencing (2013) both
- MS/MS Spectra Interpretation as a Statistical–Mechanics Problem (2013) crossref
- Partial De Novo Sequencing and Unusual CID Fragmentation of a 7 kDa, Disulfide-Bridged Toxin (2012) both
- Multiplex De Novo Sequencing of Peptide Antibiotics (2011) crossref
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra (2011) both
- Multiplex De Novo Sequencing of Peptide Antibiotics (2011) crossref
- Algorithm Development of de novo Peptide Sequencing Via Tandem Mass Spectrometry (2010) crossref
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) crossref
- Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra (2010) crossref
- LysNDeNovo: An algorithm enabling de novo sequencing of Lys‐N generated peptides fragmented by electron transfer dissociation (2010) crossref
- De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation (2009) crossref
- Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification (2009) both
- A Ranking-Based Scoring Function for Peptide-Spectrum Matches (2009) both