Assessing Protein Sequence Database Suitability Using De Novo Sequencing
peer-reviewed · Molecular & Cellular Proteomics · 2020
| Date | 2020-01-01 |
| Type | peer-reviewed |
| Venue | Molecular & Cellular Proteomics |
| Publisher | Elsevier BV |
| Contribution | downstream-application |
| DOI | 10.1074/mcp.tir119.001752 |
| Citations (OpenAlex) | 43 |
| Venue 2-year citedness | 4.69 |
Abstract
The analysis of samples from unsequenced and/or understudied species as well as samples where the proteome is derived from multiple organisms poses two key questions. The first is whether the proteomic data obtained from an unusual sample type even contains peptide tandem mass spectra. The second question is whether an appropriate protein sequence database is available for proteomic searches. We describe the use of automated de novo sequencing for evaluating both the quality of a collection of tandem mass spectra and the suitability of a given protein sequence database for searching that data. Applications of this method include the proteome analysis of closely related species, metaproteomics, and proteomics of extinct organisms.
Methods and tools
- De novo database suitability assessment: Uses automated de novo sequencing to test whether a set of spectra holds peptide spectra at all and whether a protein database suits it, for unsequenced species, metaproteomes and extinct organisms.