Table 2.
Comparison of quantification efficiencies between LTQ and LTQ-Orbitrap for 11 different 6-step MudPIT experiments.
| Sample | # Spectra Identified | LTQ # Spectra Quantified * | LTQ Quantification Efficiency | Orbitrap # Spectra Quantified* | Orbitrap Quantification Efficiency |
|---|---|---|---|---|---|
| 1:1 | 528 | 266 | 0.50 | 361 | 0.68 |
| 1:1 | 1267 | 595 | 0.47 | 741 | 0.58 |
| 1:1 | 1637 | 832 | 0.51 | 1336 | 0.82 |
| 5:1 | 3099 | 328 | 0.11 | 1662 | 0.54 |
| 5:1 | 1121 | 127 | 0.11 | 591 | 0.53 |
| 5:1 | 2885 | 464 | 0.16 | 1475 | 0.51 |
| 10:1 | 4019 | 378 | 0.09 | 1856 | 0.46 |
| 10:1 | 3900 | 350 | 0.09 | 1683 | 0.43 |
| 10:1 | 2674 | 180 | 0.07 | 839 | 0.31 |
| 50:1 | 2283 | 1 | 0.00 | 210 | 0.09 |
| 100:1 | 2767 | 4 | 0.00 | 224 | 0.08 |
*
criteria used for quantification include an r2 value > 0.5 and accuracy within 2 fold of the expected ratio. In addition, statistical outliers were removed using grubbs test with an outlier threshold p-value of 0.1.