PepTiger: Search Engine for Error-Tolerant Protein Identification from de Novo Sequences
peer-reviewed · The Open Spectroscopy Journal · 2007
| Date | 2007-12-05 |
| Type | peer-reviewed |
| Venue | The Open Spectroscopy Journal |
| Publisher | Bentham Science Publishers Ltd. |
| Contribution | adjacent |
| DOI | 10.2174/1874383800701010001 |
| Citations (OpenAlex) | 2 |
Abstract
In recent years a number of de novo sequencing software products became available providing possible partial or complete amino acid sequence tags for MS/MS spectra of peptides. However, for a variety of reasons including spectral chemical noise and imperfect fragmentation these sequence tags almost always contain errors. Additional difficulties arise from actual protein sequence variation and post-translational modifications. We present a search engine named PepTiger which is capable of correctly matching de novo sequence tags with errors to protein sequences in a protein database. The algorithm is based on approximate string matching followed by a novel scoring procedure which takes into account mass differences and the string distance between de novo sequence and matched peptides and similarities between theoretical and experimental MS/MS spectra. Comparison of PepTiger with other protein identification software shows that PepTiger is better able to assign de novo sequence tags with errors to the correct peptide sequences.
Methods and tools
- PepTiger: Matches error-prone de novo sequences to database peptides with approximate string matching and a combined mass and spectrum score.