Table II. For each peptide class, the type (C-Common, U-Unexpected) and peptide description are given, along with numbers of ions in the starting and final libraries, those rejected by five filters, contributions to ion count and total median relative abundance, MRAB.
| Type | Class | Peptide description | Initial | Filter 1 | Filter 2 | Filter 3 | Filter 4 | Filter 5 | Final | Ion% | MRAB% |
|---|---|---|---|---|---|---|---|---|---|---|---|
| C | 1 | Simple Tryptic | 168 | 3 | 5 | 3 | 4 | 0 | 158 | 5.4 | 46.7 |
| C | 2 | Tryptic with Expected Missed-Cleavage | 173 | 10 | 4 | 2 | 11 | 0 | 154 | 5.3 | 23.7 |
| C | 3 | Common Modifications | 92 | 11 | 5 | 4 | 6 | 0 | 74 | 2.5 | 3.8 |
| C | 4 | In-Source Semitryptic | 332 | 43 | 22 | 6 | 6 | 0 | 263 | 9.0 | 3.6 |
| U | 5 | In-Solution Semitryptic | 788 | 136 | 83 | 2 | 7 | 0 | 577 | 19.8 | 4.7 |
| U | 6 | Artifacts and PTMs | 1068 | 109 | 218 | 120 | 36 | 0 | 673 | 23.1 | 8.1 |
| U | 7 | Unexpected Missed-Cleavage | 404 | 67 | 38 | 4 | 20 | 8 | 293 | 10.0 | 5.3 |
| U | 8 | Under/Over Alkylation | 420 | 96 | 68 | 17 | 20 | 10 | 256 | 8.8 | 1.9 |
| U | 9 | Unidentified Modifications | 2546 | 1739 | 349 | 694 | 114 | 133 | 470 | 16.1 | 2.2 |
| Total | 5991* | 2214 | 792 | 852 | 224 | 151 | 2918 | 100 | 100 |
* This process started with 7359 spectra. After discarding peptides falling into multiple “unusual” classes, 5991 spectra remained and then subjected to quality filtering.