Constrained De Novo Sequencing of Conotoxins
peer-reviewed · Journal of Proteome Research · 2012
| Date | 2012-08-03 |
| Type | peer-reviewed |
| Venue | Journal of Proteome Research |
| Publisher | American Chemical Society (ACS) |
| Contribution | algorithm |
| DOI | 10.1021/pr300312h |
| Citations (OpenAlex) | 34 |
| Venue 2-year citedness | 3.48 |
Abstract
De novo peptide sequencing by mass spectrometry (MS) can determine the amino acid sequence of an unknown peptide without reference to a protein database. MS-based de novo sequencing assumes special importance in focused studies of families of biologically active peptides and proteins, such as hormones, toxins, and antibodies, for which amino acid sequences may be difficult to obtain through genomic methods. These protein families often exhibit sequence homology or characteristic amino acid content; yet, current de novo sequencing approaches do not take advantage of this prior knowledge and, hence, search an unnecessarily large space of possible sequences. Here, we describe an algorithm for de novo sequencing that incorporates sequence constraints into the core graph algorithm and thereby reduces the search space by many orders of magnitude. We demonstrate our algorithm in a study of cysteine-rich toxins from two cone snail species (Conus textile and Conus stercusmuscarum) and report 13 de novo and about 60 total toxins.
Methods and tools
- Conovo: Constrained de novo sequencing algorithm for peptide families such as conotoxins.
Cites (10)
- Automated de novo protein sequencing of monoclonal antibodies (2008) both
- Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry (2007) both
- De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning (2006) both
- SPIDER: software for protein identification from sequence tags with de novo sequencing error (2005) crossref
- GutenTag: High-Throughput Sequence Tagging via an Empirically Derived Fragmentation Model (2003) both
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (2001) both
- Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry (2001) both
- De novo peptide sequencing via tandem mass spectrometry (1999) both
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994) both
Cited by (3)
- 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
- High-Confidence de Novo Peptide Sequencing Using Positive Charge Derivatization and Tandem MS Spectra Merging (2013) crossref