Table 1.
Effect of Match-between-Runs (MBR) on Protein Identifications Per Run
| sample | n | species | no MBR | with MBR | |||
|---|---|---|---|---|---|---|---|
| protein IDs | % totala | protein IDs | % totala | fold ↑b | |||
| all runs | 40 | totalc | 3738 ± 190 | 81 ± 4 | 4290 ± 195 | 93 ± 4.2 | 1.15 ± 0.01 |
| human | 3521 ± 47 | 85 ± 1 | 4023 ± 18_ | 98 ± 0.4 | 1.14 ± 0.01 | ||
| yeast | 217 ± 212 | 44 ± 43. | 267 ± 209 | 54 ± 42. | 4.49 ± 3.61 | ||
| H (human only) | 20 | totalc | 3554 ± 40 | 77 ± 1 | 4097 ± 10 | 89 ± 0.2 | 1.15 ± 0.01 |
| human | 3546 ± 40 | 86 ± 1 | 4037 ± 9 | 98 ± 0.2 | 1.14 ± 0.01 | ||
| yeast | 8±2 | 1.6 ± 0.4 | 60 ± 5 | 12 ± 0.9 | 7.87 ± 1.64 | ||
| HY (human with yeast) | 20 | totalc | 3922 ± 43 | 85 ± 1 | 4482 ± 14 | 97 ± 0.3 | 1.14 ± 0.01 |
| human | 3496 ± 40 | 85 ± 1 | 4009 ± 14 | 97 ± 0.3 | 1.15 ± 0.01 | ||
| yeast | 426 ± 6 | 87 ± 1 | 473 ± 3 | 93 ± 0.7 | 1.11 ± 0.01 | ||
a
Percent total is calculated with respect to protein identification counts in Figure 1.
b
Fold increase is calculated per run as the ratio of protein identifications with MBR to that without MBR.
c
Total protein is the sum of human and yeast proteins (4122 + 492).