Table I. The real FDRs and the numbers of spectral identifications obtained with three FDR estimation approaches (global, separate and transfer FDRs) at 1% FDR control level on the pFind search results of the simulated spectra. “Sub-Correct” means the identified peptide is part of or covers the real peptide sequence.
| Total Spectra | Real FDR |
Identification number |
|||||
|---|---|---|---|---|---|---|---|
| Global | Separate | Transfer | Global | Separate | Transfer | ||
| Unmodified | 800,000 | 0.00% | 0.29% | 0.29% | 127,148 | 601,375 | 601,375 |
| Oxidation | 30,000 | 0.02% | 0.84% | 0.86% | 6,343 | 23,265 | 23,369 |
| Deamidation | 15,000 | 0.00% | 0.86% | 0.56% | 2,240 | 9,506 | 8,940 |
| Tri-Methyl & Acetyl | 10,000 | 0.00% | 1.06% | 1.08% | 1,513 | 5,072 | 5,166 |
| Methyl | 1,000 | 0.00% | 2.30% | 0.45% | 133 | 305 | 222 |
| Di-Methyl | 500 | 0.00% | 1.44% | 1.63% | 70 | 139 | 123 |
| Phospho | 50 | 0.00% | 4.55% | 0.00% | 13 | 22 | 17 |
| Sub-Correct | – | 0.00% | 0.00% | 0.00% | 956 | 1,152 | 681 |
| Other Modifications | – | 100% | 100% | 100% | 1,358 | 951 | 372 |
| Sum | 856,550 | – | – | – | 139,744 | 641,787 | 640,265 |