Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics
peer-reviewed · Bioinformatics · 2005
| Date | 2005-10-01 |
| Type | peer-reviewed |
| Venue | Bioinformatics |
| Publisher | Oxford University Press (OUP) |
| Contribution | adjacent |
| DOI | 10.1093/bioinformatics/bti620 |
| Citations (OpenAlex) | 27 |
| Venue 2-year citedness | 6.16 |
Abstract
Motivation The key to MS -based proteomics is peptide sequencing. The major challenge in peptide sequencing, whether library search or de novo, is to better infer statistical significance and better attain noise reduction. Since the noise in a spectrum depends on experimental conditions, the instrument used and many other factors, it cannot be predicted even if the peptide sequence is known. The characteristics of the noise can only be uncovered once a spectrum is given. We wish to overcome such issues. Results We designed RAId to identify peptides from their associated tandem mass spectrometry data. RAId performs a novel de novo sequencing followed by a search in a peptide library that we created. Through de novo sequencing, we establish the spectrum-specific background score statistics for the library search. When the database search fails to return significant hits, the top-ranking de novo sequences become potential candidates for new peptides that are not yet in the database. The use of spectrum-specific background statistics seems to enable RAId to perform well even when the spectral quality is marginal. Other important features of RAId include its potential in de novo sequencing alone and the ease of incorporating post-translational modifications.
Methods and tools
- RAId: Robust Accurate Identification of peptides: runs de novo sequencing first to estimate spectrum-specific background statistics for a structured peptide library search, falling back on top de novo sequences for novel peptides.
Cites (3)
- Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry (2001) crossref
- Charting the Proteomes of Organisms with Unsequenced Genomes by MALDI-Quadrupole Time-of-Flight Mass Spectrometry and BLAST Homology Searching (2001) crossref
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994) crossref
Cited by (11)
- Limitations of de novo sequencing in resolving sequence ambiguity (2025) both
- Metaproteomic Characterization of Forensic Samples (2022) crossref
- De novo sequencing of proteins by mass spectrometry (2020) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- ProbPS: A new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity (2011) both
- Algorithm Development of de novo Peptide Sequencing Via Tandem Mass Spectrometry (2010) crossref
- TVNovo: De novo peptide sequencing for high resolution LTQ-FT mass spectrometry using virtual database searching (2010) crossref
- De Novo Sequencing Methods in Proteomics (2009) crossref
- Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification (2009) both
- Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009) both
- Multi-spectra peptide sequencing and its applications to multistage mass spectrometry (2008) both