Name
Abstract | ||
|---|---|---|
One of the major problems in shotgun proteomics is the low peptide coverage when analyzing complex protein samples. Identifying more peptides, e.g. non-tryptic peptides, may increase the peptide coverage and improve protein identification and/or quantification that are based on the peptide identification results. Searching for all potential non-tryptic peptides is, however, time consuming for shotgun proteomics data from complex samples, and poses a challenge for a routine data analysis.We hypothesize that non-tryptic peptides are mainly created from the truncation of regular tryptic peptides before separation. We introduce the notion of truncatability of a tryptic peptide, i.e. the probability of the peptide to be identified in its truncated form, and build a predictor to estimate a peptide's truncatability from its sequence. We show that our predictions achieve useful accuracy, with the area under the ROC curve from 76% to 87%, and can be used to filter the sequence database for identifying truncated peptides. After filtering, only a limited number of tryptic peptides with the highest truncatability are retained for non-tryptic peptide searching. By applying this method to identification of semi-tryptic peptides, we show that a significant number of such peptides can be identified within a searching time comparable to that of tryptic peptide identification. |
Year | DOI | Venue |
|---|---|---|
2008 | 10.1093/bioinformatics/btm545 | Bioinformatics |
Keywords | Field | DocType |
potential non-tryptic peptides,peptide identification result,shotgun proteomics,truncated peptides,accurate identification,peptide coverage,non-tryptic peptide,non-tryptic peptides,low peptide coverage,tryptic peptides,regular tryptic peptides,semi-tryptic peptides,roc curve,data analysis | Sequence database,Proteomics,Computer science,Peptide,Complex protein,Bottom-up proteomics,Peptide spectral library,Bioinformatics,Shotgun proteomics,Peptide mass fingerprinting | Journal |
Volume | Issue | ISSN |
24 | 1 | 1367-4811 |
Citations | PageRank | References |
1 | 0.38 | 2 |
Authors | ||
10 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Pedro Alves | 1 | 44 | 9.37 |
| Randy J Arnold | 2 | 66 | 12.84 |
| David E Clemmer | 3 | 36 | 8.27 |
| Yixue Li | 4 | 789 | 60.24 |
| James Reilly | 5 | 457 | 43.42 |
| Quanhu Sheng | 6 | 22 | 5.61 |
| Haixu Tang | 7 | 683 | 96.67 |
| Zhiyin Xun | 8 | 31 | 7.53 |
| Rong Zeng | 9 | 1 | 0.38 |
| Predrag Radivojac | 10 | 646 | 58.89 |