The Power and the Limitations of Cross-Species Protein Identification by Mass Spectrometry-driven Sequence Similarity Searches
peer-reviewed · Molecular & Cellular Proteomics · 2004
| Date | 2004-03-01 |
| Type | peer-reviewed |
| Venue | Molecular & Cellular Proteomics |
| Publisher | Elsevier BV |
| Contribution | adjacent |
| DOI | 10.1074/mcp.m300073-mcp200 |
| Citations (OpenAlex) | 150 |
| Venue 2-year citedness | 4.69 |
Abstract
Mass spectrometry-driven BLAST (MS BLAST) is a database search protocol for identifying unknown proteins by sequence similarity to homologous proteins available in a database. MS BLAST utilizes redundant, degenerate, and partially inaccurate peptide sequence data obtained by de novo interpretation of tandem mass spectra and has become a powerful tool in functional proteomic research. Using computational modeling, we evaluated the potential of MS BLAST for proteome-wide identification of unknown proteins. We determined how the success rate of protein identification depends on the full-length sequence identity between the queried protein and its closest homologue in a database. We also estimated phylogenetic distances between organisms under study and related reference organisms with completely sequenced genomes that allow substantial coverage of unknown proteomes.
Methods and tools
- MS BLAST: Homology search of error-tolerant de novo sequences against a protein database, introduced for charting the proteomes of organisms with unsequenced genomes and later used to validate borderline identifications.