Investigation of VUV photodissociation propensities using peptide libraries
peer-reviewed · International Journal of Mass Spectrometry · 2011
peer-reviewed · International Journal of Mass Spectrometry · 2011. Xiaohui Liu et al. PSD does not usually generate a complete series of y-type ions, particularly at high mass, and this is a…
| Date | 2011-12-01 |
| Type | peer-reviewed |
| Venue | International Journal of Mass Spectrometry |
| Publisher | Elsevier BV |
| Contribution | algorithm |
| DOI | 10.1016/j.ijms.2011.04.008 |
| Citations (OpenAlex) | 6 |
Abstract
PSD does not usually generate a complete series of y-type ions, particularly at high mass, and this is a limitation for de novo sequencing algorithms. It is demonstrated that b(2) and b(3) ions can be used to help assign high mass x(N-2) and x(N-3) fragments that are found in vacuum ultraviolet (VUV) photofragmentation experiments. In addition, v(N)-type ion fragments with side chain loss from the N-terminal residue often enable confirmation of N-terminal amino acids. Libraries containing several thousand peptides were examined using photodissociation in a MALDI-TOF/TOF instrument. 1345 photodissociation spectra with a high S/N ratio were interpreted.
Methods and tools
- 157 nm photodissociation de novo sequencing: De novo sequencing algorithm written for 157 nm photodissociation spectra, which yield clean x-ion series rather than the mixed b/y ions of CID. Reports per-residue accuracy and distinguishes leucine from isoleucine, which equal-mass residues normally make impossible.
Cites (10)
- De NovoSequencing of Tryptic Peptides Derived fromDeinococcus radioduransRibosomal Proteins Using 157 nm Photodissociation MALDI TOF/TOF Mass Spectrometry (2010) both
- Peptide de Novo Sequencing Using 157 nm Photodissociation in a Tandem Time-of-Flight Mass Spectrometer (2010) both
- MSNovo: A Dynamic Programming Algorithm for de Novo Peptide Sequencing via Tandem Mass Spectrometry (2007) both
- De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning (2006) both
- Proteomics-Grade de Novo Sequencing Approach (2005) both
- NovoHMM: A Hidden Markov Model for de Novo Peptide Sequencing (2005) both
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) both
- De Novo Peptide Sequencing Based on a Divide-and-Conquer Algorithm and Peptide Tandem Spectrum Simulation (2004) both
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry (2001) both