Spectra pair
8 methods · 2005–2020
Spectra pair: Two spectra of the same peptide, from complementary fragmentation or from a paired digest, interpreted together so that one ion series fills the gaps in the other.
Two spectra of the same peptide, from complementary fragmentation or from a paired digest, interpreted together so that one ion series fills the gaps in the other.
The earliest of its 8 methods is ICATcher (2005); 7 more have followed.
| Methods | 8 |
| Papers describing them | 8 |
| Authors | 47 |
| Active | 2005-03-25 to 2020-02-15 |
| Kinds | algorithm (6), adjacent (2) |
| Acquisition | DDA (8) |
Methods (8)
Oldest first, by the paper that describes each one.
- ICATcher (2005): Open-source algorithm that finds pairs of light and heavy isotope-tagged MS/MS spectra without a sequence database, as a basis for de novo sequencing and PTM discovery.
- CompNovo (2009): De novo sequencing algorithm combining complementary CID and ETD tandem MS spectra.
- ADEPTS (2010): Advanced peptide de novo sequencing framework using a pair of tandem mass spectra.
- NovoPair (2014): Extends the authors’ spectrum graph model to pairs of CID or HCD and ECD or ETD spectra of the same peptide, using the ion types of both to improve full-length de novo sequencing accuracy over pNovo+.
- Paired Lys-N/Lys-C transposed de novo sequencing (2015): Pairs spectra from Lys-N and Lys-C digests whose sequences are single-residue transposed and solves them together as one de novo problem, with residue-level confidence.
- Lys-C/Lys-N FT-ICR de novo sequencing (2017): Pairs Lys-C and Lys-N digests, whose peptides share mass and retention time but fragment differently, with ultrahigh-resolution FT-ICR MS/MS for de novo amino acid sequencing.
- pNovoM (2019): De novo sequencing from mirror spectrum pairs: digesting the same sample with Ac-LysargiNase and with trypsin yields two spectra whose b and y ion series complement each other, which pins down the sequence far more confidently than either alone.
- Lys-Sequencer (2020): Database-independent de novo sequencing from paired Lys-C and Lys-N digests, whose single-residue-transposed peptides yield complementary high-resolution spectra, with residue-level confidence reported per call.
Papers describing them (8)
- Database independent detection of isotopically labeled MS/MS spectrum peptide pairs (2005, Journal of Chromatography B, peer-reviewed)
- De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation (2009, Electrophoresis, peer-reviewed)
- ADEPTS: Advanced peptide de novo sequencing with a pair of tandem mass spectra (2010, Journal of Bioinformatics and Computational Biology, peer-reviewed)
- NovoPair: De novo peptide sequencing for tandem mass spectra pair (2014, 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), peer-reviewed)
- Paired single residue‐transposed Lys‐N and Lys‐C digestions for label‐free identification of N‐terminal and C‐terminal MS/MS peptide product ions: ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry and tandem mass spectrometry for peptide de novo sequencing (2015, Rapid Communications in Mass Spectrometry, peer-reviewed)
- Ultrahigh‐resolution Fourier transform ion cyclotron resonance mass spectrometry and tandem mass spectrometry for peptide de novo amino acid sequencing for a seven‐protein mixture by paired single‐residue transposed Lys‐N and Lys‐C digestion (2017, Rapid Communications in Mass Spectrometry, peer-reviewed)
- Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics (2019, Molecular & Cellular Proteomics, peer-reviewed)
- 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, Rapid Communications in Mass Spectrometry, peer-reviewed)