Spectral assembly
4 methods · 2004–2017
Spectral assembly: Assemble the overlapping spectra into contigs BEFORE any sequence is called, so a protein is read from the assembled evidence rather than from peptides interpreted one at a time. Sequence assembly is the other way round.
Assemble the overlapping spectra into contigs BEFORE any sequence is called, so a protein is read from the assembled evidence rather than from peptides interpreted one at a time. Sequence assembly is the other way round.
The earliest of its 4 methods is Shotgun Protein Sequencing (2004); 3 more have followed.
| Methods | 4 |
| Papers describing them | 6 |
| Authors | 17 |
| Active | 2004-12-01 to 2017-01-06 |
| Kinds | algorithm (2), downstream-application (2) |
| Acquisition | DDA (4) |
Methods (4)
Oldest first, by the paper that describes each one.
- Shotgun Protein Sequencing (2004): Assembles overlapping MS/MS spectra of related peptides into contigs before any sequence is called, so a protein is sequenced from the assembly rather than from individual spectra. Tolerates mixtures and unanticipated modifications.
- Automated mAb de novo (Bandeira SPS) (2008): Landmark Nat Biotech 2008 paper by Bandeira, Pham, Pevzner, Arnott & Lill: applies Shotgun Protein Sequencing (SPS), that is MS/MS spectral assembly, end-to-end to a monoclonal antibody, recovering both chains without any prior sequence.
- Meta-SPS (2012): Shotgun protein sequencing with meta-contig assembly for longer de novo protein contigs.
- Native antibody de novo MS/MS (2017): De novo MS/MS sequencing workflow for native human antibodies.
Applied in
Papers describing them (6)
- Shotgun Protein Sequencing by Tandem Mass Spectra Assembly (2004, Analytical Chemistry, peer-reviewed)
- Protein identification by spectral networks analysis (2007, Proceedings of the National Academy of Sciences, peer-reviewed)
- Shotgun Protein Sequencing: Assembly of Peptide Tandem Mass Spectra from Mixtures of Modified Proteins (2007, Molecular & Cellular Proteomics, peer-reviewed)
- Automated de novo protein sequencing of monoclonal antibodies (2008, Nature Biotechnology, peer-reviewed)
- Shotgun Protein Sequencing with Meta-contig Assembly (2012, Molecular & Cellular Proteomics, peer-reviewed)
- De Novo MS/MS Sequencing of Native Human Antibodies (2017, Journal of Proteome Research, peer-reviewed)