Table 2.
Peptides Detected by Standard and Stripped Libraries
| A. Yeast | |||
|---|---|---|---|
| FDR threshold | standard library (conformance) | stripped library (conformance) overlap | stripped library (conformance) overlap |
| 5%a | 1840 (87.1%) | 1973 (86.2%) | 1578 |
| 1% | 1838 (87.1%) | 1920 (86.3%)b | 1574 |
| B. Yeast | |||
| N-terminal AnnPeptides (FDR) | standard (5%) | stripped (2%) | |
| total distinct | 464 | 509 | |
| uniquec | 16 | 51 | |
| overlapd | 448 | ||
| N-terminal DownPeptides (FDR) | standard (5%) | stripped (2%) | |
| total distinct | 139 | 149 | |
| uniquec | 27 | 37 | |
| overlapd | 112 | ||
| C. Yeast and Drosophila | |||
| species library (FDR) | yeast stripped (2%) | Drosophila stripped (2%) | |
| N-terminal AnnPeptides | 509 | 504 | |
| N-terminal DownPeptides | 149 | 178 | |
a
Because of the default stringency of the OMSSA algorithm, the 5% threshold data had actual decoy FDRs of 0.5 to 1.7% (standard library) and 0.9 to 1.7% (stripped library).
b
Bootstrap analysis of 1000 samplings with replacement of the 1920 peptides showed 95% confidence limits between 85.6 and 87.1%.
c
Unique: distinct peptides in either standard or stripped library.
d
Overlap: distinct peptides detected with both standard and stripped library.