Table II. The identification numbers of chemically synthesized peptides from the modified-peptide spiked-in proteome data with three FDR approaches (global, separate and transfer FDRs) at 1% FDR. “PSMs” was the number when no filtering was used. Here “ph,” “me,” “ac,” and “pr” represent phosphorylation, methylation, acetylation, and propionyl, respectively.
| Separate FDR (1%) | P62805 | P0A870 | P0A7K2 | P62807 | A4FNV9 | A4FBI4 |
|---|---|---|---|---|---|---|
| Species | Homo | E. coli | E. coli | Homo | S. erythraea | S. erythraea |
| Sequence | DNIQGITKPAIR | EYAPAEDPGVVSVSEIYQYYK | GATGLGLKEAK | KESKYSVYVYK | TYKLYVGGK | HGGGAFSGKDPSK |
| Mod | 7,T (ph) | 7,D (me) | 9,E (me) | 4,K (ac) | 3,K (pr) | 9,K (pr) |
| HeLa | ||||||
| PSMs | 21 | 86 | 19 | 68 | 41 | 32 |
| Global FDR (1%) | 5 | 48 | 0 | 33 | 4 | 14 |
| Separate FDR (1%) | 0 | 67 | 8 | 33 | 0 | 9 |
| Transfer FDR (1%) | 21 | 61 | 1 | 19 | 41 | 32 |
| E. coli | ||||||
| PSMs | 24 | 77 | 22 | 69 | 37 | 31 |
| Global FDR (1%) | 9 | 52 | 0 | 33 | 17 | 15 |
| Separate FDR (1%) | 9 | 63 | 10 | 17 | 26 | 17 |
| Transfer FDR (1%) | 0 | 56 | 1 | 69 | 22 | 15 |