Table 1.
Results of parametric optimization of IRMPD for large-scale LC-MS/MS analysis. We varied photon flux, irradiation time, and q-value for IRMPD activation. For each experiment, CAD activation conditions were held constant to provide an internal benchmark of success. Shown in bold and red are IRMPD conditions which resulted in more peptide spectral matches (PSMs) than activation with CAD. Each number represents the number of peptide PSMs (1% FDR) resulting from the use of CAD or IRMPD for a single LC-MS/MS experiment.
| IRMPD Peptide Identifications under various conditions | |||||||
|---|---|---|---|---|---|---|---|
| q-value | IR Time (ms) | 36 W laser power
|
48 W laser power
|
60 W laser power
|
|||
| IRMPD IDs | CAD IDs | IRMPD IDs | CAD IDs | IRMPD IDs | CAD IDs | ||
| 0.10 | 3 | 2926 | 6821 | 4977 | 6782 | 5862 | 6364 |
| 5 | 5143 | 6946 | 6717 | 7003 | 6242 | 6224 | |
| 10 | 6788 | 6834 | 7223 | 6969 | 6017 | 6263 | |
| 15 | 6960 | 6742 | 6634 | 6763 | 4721 | 6315 | |
| 25 | 4224 | 5965 | 3627 | 6489 | 915 | 6480 | |
| 0.15 | 3 | 4000 | 7015 | 5968 | 6907 | 6237 | 6416 |
| 5 | 5950 | 6723 | 6667 | 6648 | 6306 | 6222 | |
| 10 | 6937 | 6862 | 6350 | 6868 | 4959 | 6824 | |
| 15 | 6001 | 6721 | 4201 | 6731 | 603 | 6243 | |
| 25 | 866 | 5962 | 163 | 6576 | 30 | 6363 | |
| 0.20 | 3 | 4881 | 7005 | 6172 | 6953 | 6204 | 6486 |
| 5 | 6582 | 6945 | 6676 | 6886 | 5937 | 6479 | |
| 10 | 6533 | 6756 | 5043 | 6670 | 2224 | 6377 | |
| 15 | 4470 | 6868 | 1191 | 6799 | 106 | 6382 | |
| 25 | 106 | 6134 | 5 | 6620 | 1 | 6356 | |
| 0.25 | 3 | 5505 | 6840 | 6481 | 6786 | 6272 | 6649 |
| 5 | 6628 | 6941 | 6320 | 6557 | 5778 | 6444 | |
| 10 | 5318 | 6875 | 3288 | 6756 | 663 | 6364 | |
| 15 | 1517 | 6317 | 147 | 6454 | 16 | 6522 | |
| 25 | 29 | 6288 | 0 | 6543 | 0 | 6207 | |