Table 4.
Summary of peptide and protein identification after application of depletion methods and peptides prefractionation.
| Number of spectra identified | Number of unique peptides identified1 | Number of proteins identified2 | |
|---|---|---|---|
| IgY14_1 | 893 | 571 | 136 |
| IgY14_2 | 823 | 473 | 124 |
| IgY14_3 | 881 | 463 | 120 |
| Total unique | 775 | 156 | |
| IgYHSA_1 | 837 | 518 | 105 |
| IgYHSA_2 | 804 | 493 | 112 |
| IgYHSA_3 | 652 | 366 | 84 |
| Total unique | 665 | 131 | |
| Undepl_1 | 724 | 277 | 67 |
| Undepl_2 | 795 | 355 | 78 |
| Undepl_3 | 773 | 384 | 75 |
| Total unique | 466 | 90 | |
| IgYHSA-RP30_1 | 15,992 | 2,470 | 433 |
| IgYHSA-RP30_2 | 12,549 | 2,282 | 396 |
| IgYHSA-RP30_3 | 12,381 | 2,164 | 390 |
| Total unique | 3,026 | 535 | |
CSF samples were analyzed as triplicates following depletion of 14 proteins (IgY14), albumin only (IgYHSA) or no depletion (Undepl). Additionally CSF samples were analyzed after albumin depletion and further fractionation by reversed-phase liquid chromatography (IgYHSA-RP30).
1. only hits with Peptide Prophet ≥ 0.95
2. protein identification with Peptide Prophet ≥ 0.9.