Database independent proteomics analysis of the ostrich and human proteome
peer-reviewed · Proceedings of the National Academy of Sciences · 2012
| Date | 2012-01-10 |
| Type | peer-reviewed |
| Venue | Proceedings of the National Academy of Sciences |
| Publisher | National Academy of Sciences |
| Contribution | adjacent |
| DOI | 10.1073/pnas.1108399108 |
| Citations (OpenAlex) | 11 |
| Venue 2-year citedness | 8.56 |
Abstract
Mass spectrometry (MS)-based proteome analysis relies heavily on the presence of complete protein databases. Such a strategy is extremely powerful, albeit not adequate in the analysis of unpredicted postgenome events, such as posttranslational modifications, which exponentially increase the search space. Therefore, it is of interest to explore “database-free” approaches. Here, we sampled the ostrich and human proteomes with a method facilitating de novo sequencing, utilizing the protease Lys-N in combination with electron transfer dissociation. By implementing several validation steps, including the combined use of collision-induced dissociation/electron transfer dissociation data and a cross-validation with conventional database search strategies, we identified approximately 2,500 unique de novo peptide sequences from the ostrich sample with over 900 peptides generating full backbone sequence coverage. This dataset allowed the appropriate positioning of ostrich in the evolutionary tree. The described database-free sequencing approach is generically applicable and has great potential in important proteomics applications such as in the analysis of variable parts of endogenous antibodies or proteins modified by a plethora of complex posttranslational modifications.
Methods and tools
- Lys-N ETD database-independent proteomics: Combines Lys-N digestion, ETD and CID/ETD cross-validation to de novo sequence thousands of peptides from the unsequenced ostrich proteome.
Cites (10)
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) crossref
- LysNDeNovo: An algorithm enabling de novo sequencing of Lys‐N generated peptides fragmented by electron transfer dissociation (2010) crossref
- De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation (2009) crossref
- Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing (2009) crossref
- Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification (2009) crossref
- De novo sequencing of peptides secreted by the skin glands of the Caucasian Green Frog Rana ridibunda (2008) crossref
- MSNovo: A Dynamic Programming Algorithm for de Novo Peptide Sequencing via Tandem Mass Spectrometry (2007) crossref
- Proteomics-Grade de Novo Sequencing Approach (2005) crossref
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) crossref
- De novo sequencing, peptide composition analysis, and composition-based sequencing: A new strategy employing accurate mass determination by Fourier transform ion cyclotron resonance mass spectrometry (2004) crossref
Cited by (4)
- Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra (2013) both
- De Novo Sequencing of Peptides Using Selective 351 nm Ultraviolet Photodissociation Mass Spectrometry (2013) crossref
- High-Confidence de Novo Peptide Sequencing Using Positive Charge Derivatization and Tandem MS Spectra Merging (2013) crossref
- Tutorial on de novo peptide sequencing using MS/MS mass spectrometry (2012) crossref