Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy
peer-reviewed · Bioinformatics · 2009
| Date | 2009-09-01 |
| Type | peer-reviewed |
| Venue | Bioinformatics |
| Publisher | Oxford University Press (OUP) |
| Contribution | adjacent |
| DOI | 10.1093/bioinformatics/btp366 |
| Citations (OpenAlex) | 40 |
| Venue 2-year citedness | 5.93 |
Abstract
Motivation The bottom-up tandem mass spectrometry (MS/MS) is regularly used in proteomics nowadays for identifying proteins from a sequence database. De novo sequencing software is also available for sequencing novel peptides with relatively short sequence lengths. However, automated sequencing of novel proteins from MS/MS remains a challenging problem. Results Very often, although the target protein is novel, it has a homologous protein included in a known database. When this happens, we propose a novel algorithm and automated software tool, named Champs, for sequencing the complete protein from MS/MS data of a few enzymatic digestions of the purified protein. Validation with two standard proteins showed that our automated method yields >99% sequence coverage and 100% sequence accuracy on these two proteins. Our method is useful to sequence novel proteins or ‘re-sequence’ a protein that has mutations comparing with the database protein sequence.
Methods and tools
- Champs: Sequences a complete novel protein by de novo sequencing its peptides and then assembling them against a HOMOLOGOUS database rather than an exact one, reaching near-full coverage and accuracy where neither approach alone would.