Table 4. Number of PSMs, Peptides, and Proteins Observed Using the Identifications of Proteotypic Peptides from the neXtProt Database (PSM FDR < 1%) in the Samples Selected from PRIDE for the Analysis of the Missing Proteins.
| PXD001468 | PXD002367 | PXD001242 | PXD000754 | PXD000605 | PXD000004 | PRD000269 | PXD002145 | Total | |
|---|---|---|---|---|---|---|---|---|---|
| Spectra | 836145 | 114970 | 452880 | 519326 | 1299378 | 357899 | 370218 | 1198042 | 5148858 |
| Total PSMs | 332417 | 49100 | 115861 | 82856 | 19182 | 138704 | 23199 | 6676 | 767995 |
| Total Peptides | 71277 | 10311 | 16329 | 11739 | 1271 | 17570 | 2521 | 199 | 98319 |
| Total Peptides (proteotypic) | 25734 | 4187 | 6259 | 4848 | 804 | 6092 | 988 | 56 | 35922 |
| Total Peptides (nonproteotypic) | 45543 | 6124 | 10070 | 6891 | 467 | 11478 | 1533 | 143 | 62397 |
| Total Proteins (≥1 peptide) | 5341 | 1293 | 2420 | 2208 | 245 | 1929 | 569 | 41 | 6333 |
| Total Proteins (≥2 peptides) | 3326 | 750 | 1260 | 1000 | 120 | 924 | 169 | 22 | 3950 |
| Total Assigned Spectra | 193971 | 25083 | 71118 | 53398 | 18187 | 135285 | 15969 | 2495 | 515506 |
| Missing PSMs | 96 | 246 | 33 | 22 | 0 | 14 | 4 | 0 | 415 |
| Missing Peptides | 48 | 163 | 14 | 10 | 0 | 8 | 4 | 0 | 242 |
| Missing Proteins (≥1 peptide) | 30 | 67 | 14 | 10 | 0 | 8 | 4 | 0 | 122 |
| Missing Proteins (≥2 peptides) | 8 | 30 | 3 | 2 | 0 | 2 | 2 | 0 | 39 |
| Missing Assigned Spectra | 62 | 195 | 29 | 16 | 0 | 14 | 4 | 0 | 320 |