Spectral alignment / assembly
3 methods · 2008–2014
Spectral alignment / assembly: Reads a peptide from the relationships between spectra rather than from one spectrum alone, aligning or assembling overlapping acquisitions so that evidence missing from any single fragmentation is supplied by another.
Reads a peptide from the relationships between spectra rather than from one spectrum alone, aligning or assembling overlapping acquisitions so that evidence missing from any single fragmentation is supplied by another.
The earliest of its 3 methods is NRP dereplication and sequencing (2008); 2 more have followed.
| Methods | 3 |
| Papers describing them | 6 |
| Authors | 28 |
| Active | 2008-04-01 to 2014-07-03 |
| Kinds | algorithm (3) |
| Acquisition | DDA (3) |
Methods (3)
Oldest first, by the paper that describes each one.
- NRP dereplication and sequencing (2008): Sequences cyclic nonribosomal peptides from multistage mass spectrometry by spectral alignment, and dereplicates them comparatively against known NRPs. The first high-throughput route to a compound class with no genome to search and considerable pharmacological interest.
- MS/MS Triplets (2013): Sequencing-grade de novo analysis from overlapping CID/HCD/ETD MS/MS triplets.
- Top-down plus bottom-up de novo protein sequencing (2014): Uses top-down spectra of the intact protein as a scaffold to assemble bottom-up de novo peptide reads into a full protein sequence.
Papers describing them (6)
- De Novo Sequencing of Nonribosomal Peptides (2008, Lecture Notes in Computer Science, peer-reviewed)
- Dereplication and de novo sequencing of nonribosomal peptides (2009, Nature Methods, peer-reviewed)
- Multiplex De Novo Sequencing of Peptide Antibiotics (2011, Lecture Notes in Computer Science, peer-reviewed)
- Multiplex De Novo Sequencing of Peptide Antibiotics (2011, Journal of Computational Biology, peer-reviewed)
- Sequencing-Grade De novo Analysis of MS/MS Triplets (CID/HCD/ETD) From Overlapping Peptides (2013, Journal of Proteome Research, peer-reviewed)
- De Novo Protein Sequencing by Combining Top-Down and Bottom-Up Tandem Mass Spectra (2014, Journal of Proteome Research, peer-reviewed)