Name
Title | ||
|---|---|---|
A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data. |
Abstract | ||
|---|---|---|
Tandem mass spectrometry (MS/MS) is a powerful tool for protein identification. Although great efforts have been made in scoring the correlation between tandem mass spectra and an amino acid sequence database, improvements could be made in three aspects, including characterization ofpeaks in spectra, adoption of effective scoring functions and access to thereliability of matching between peptides and spectra.A novel scoring function is presented, along with criteria to estimate the performance confidence of the function. Through learning the typesof product ions and the probability of generating them, a hypothetic spectrum was generated for each candidate peptide. Then relative entropy was introduced to measure the similarity between the hypothetic and the observed spectra. Based on the extreme value distribution (EVD) theory, a threshold was chosen to distinguish a true peptide assignment from a random one. Tests on a public MS/MS dataset demonstrated that this method performs better than the well-known SEQUEST.A reliable identification of proteins from the spectra promises a more efficient application of tandem mass spectrometry to proteomes with high complexity. |
Year | DOI | Venue |
|---|---|---|
2006 | 10.1186/1471-2105-7-222 | BMC Bioinformatics |
Keywords | Field | DocType |
tandem mass spectrometry,spectrum,algorithms,score function,sequence alignment,mass spectra,mass spectrometry,microarrays,amino acid sequence,bioinformatics,protein sequence,extreme value distribution,relative entropy | Sequence alignment,Tandem,Biology,Protein sequencing,Mass spectrum,Tandem mass spectrometry,Mass spectrometry,Bioinformatics,Database,DNA microarray,Peptide sequence | Journal |
Volume | Issue | ISSN |
7 | 1 | 1471-2105 |
Citations | PageRank | References |
24 | 0.55 | 4 |
Authors | ||
8 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Zhuo Zhang | 1 | 24 | 0.55 |
| Shiwei Sun | 2 | 72 | 4.38 |
| Xiaopeng Zhu | 3 | 79 | 5.85 |
| Suhua Chang | 4 | 105 | 7.18 |
| Xiaofei Liu | 5 | 24 | 0.55 |
| Chungong Yu | 6 | 31 | 1.99 |
| Dongbo Bu | 7 | 157 | 21.54 |
| Runsheng Chen | 8 | 404 | 31.48 |