Table 3.
Summary of LC-ESI-MS/MS data when considering urea denaturation as a special factor in ProteinPilot. Detected peptides were limited to 1% global FDR. Detected proteins were limited to 2 peptides and 1% global FDR. Percent total carbamyl lysine was calculated as the number of total carbamyl groups out of the total number of peptides. Percent missed cleavages were calculated as the total number of missed cleavages out of the total number of peptides.
| Extraction | Control | Qkit | (A) | (B) | (C) | (D) | (E) | (F) |
|---|---|---|---|---|---|---|---|---|
| Detected spectra | 63337 | 67411 | 46279 | 64889 | 59074 | 49213 | 68932 | 48689 |
| Detected proteins | 1252 | 1141 | 905 | 1236 | 1208 | 852 | 1181 | 1060 |
| Median percent sequence coverage | 11.4 | 15.2 | 15.5 | 11.9 | 10.6 | 16.0 | 10.9 | 10.7 |
| Percent sequence coverage interquartile range | 15.9 | 21.1 | 21.0 | 17.5 | 14.8 | 23.7 | 16.3 | 15.7 |
| Detected peptides | 9025 | 9628 | 7596 | 10055 | 8431 | 7731 | 9125 | 7862 |
| Mean peptide length | 15 ± 6 | 13 ± 5 | 14 ± 5 | 15 ± 6 | 15 ± 6 | 14 ± 5 | 15 ± 6 | 16 ± 6 |
| K-terminal peptides | 244 | 4394 | 2911 | 966 | 209 | 2739 | 513 | 369 |
| R-terminal peptides | 8624 | 4986 | 4530 | 8936 | 8074 | 4875 | 8474 | 7343 |
| Peptide K : R | 0.028 | 0.881 | 0.643 | 0.108 | 0.026 | 0.562 | 0.061 | 0.050 |
| Carbamyl N-terminus | 283 | 12 | 76 | 200 | 200 | 136 | 180 | 194 |
| Carbamyl lysine | 3722 | 2 | 89 | 3866 | 3466 | 1127 | 3427 | 3009 |
| Total carbamyl groups | 5438 | 30 | 170 | 5268 | 4821 | 1368 | 4727 | 4196 |
| Percent total carbamylation | 60.3 | 0.02 | 2.2 | 52.4 | 57.2 | 17.7 | 51.8 | 53.4 |
| Total missed cleavages | 6795 | 1004 | 2747 | 6835 | 5950 | 2994 | 6485 | 6367 |
| Missed lysine cleavages | 5705 | 781 | 2000 | 5908 | 5106 | 2438 | 5265 | 4717 |
| Missed arginine cleavages | 1090 | 223 | 747 | 927 | 844 | 556 | 1220 | 1650 |
| Percent missed cleavages out of total peptides | 75.3 | 8.1 | 36.1 | 68.0 | 70.6 | 38.7 | 71.1 | 81.0 |