TABLE 4.
An iTRAQ Experiment Testing Four iTRAQ Labeling Conditions
| 114/117 | 115/117 | 116/117 | SwissProt entry name | prot_mass | emPAI | emPAI* protein mass | 20 μg total | 114 protein (μg) | 115 protein (μg) | 116 protein (μg) | 117 protein (μg) | Normalized to 5 μg | Normalized to 5 μg | Normalized to 5 μg | Normalized to 5 μg | sd/average CV % |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q |
| 0.55 | 1.13 | 1.38 | EFTU1_ECO24 | 46886 | 3.30 | 1.55E+05 | 0.23 | 0.03 | 0.06 | 0.08 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.84 |
| 0.56 | 1.07 | 1.31 | TNAA_ECOBW | 57462 | 2.98 | 1.71E+05 | 0.25 | 0.04 | 0.07 | 0.08 | 0.06 | 0.07 | 0.06 | 0.06 | 0.06 | 3.91 |
| 0.58 | 1.27 | 1.70 | ODP1_ECO57 | 107009 | 1.50 | 1.61E+05 | 0.24 | 0.03 | 0.07 | 0.09 | 0.05 | 0.06 | 0.06 | 0.07 | 0.05 | 9.67 |
| 0.55 | 1.07 | 1.33 | ATPB_ECOBW | 53377 | 1.95 | 1.04E+05 | 0.15 | 0.02 | 0.04 | 0.05 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 2.53 |
| 0.57 | 1.28 | 1.72 | RPOC_ECODH | 168599 | 0.61 | 1.03E+05 | 0.15 | 0.02 | 0.04 | 0.06 | 0.03 | 0.03 | 0.04 | 0.04 | 0.03 | 10.60 |
| 0.59 | 1.12 | 1.35 | EFG_ECOBW | 84188 | 1.17 | 9.85E+04 | 0.14 | 0.02 | 0.04 | 0.05 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 4.46 |
| 0.52 | 1.09 | 1.35 | RS1_ECO57 | 67575 | 1.91 | 1.29E+05 | 0.19 | 0.02 | 0.05 | 0.06 | 0.05 | 0.05 | 0.05 | 0.05 | 0.05 | 2.38 |
| 0.54 | 1.05 | 1.27 | TIG_ECOBW | 53351 | 2.61 | 1.39E+05 | 0.20 | 0.03 | 0.06 | 0.07 | 0.05 | 0.05 | 0.05 | 0.05 | 0.05 | 3.80 |
| 0.54 | 1.10 | 1.41 | PFLB_ECOLI | 92937 | 1.76 | 1.64E+05 | 0.24 | 0.03 | 0.07 | 0.08 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 2.78 |
| 0.54 | 1.65 | 1.48 | OMPA_ECOLI | 40174 | 3.17 | 1.27E+05 | 0.19 | 0.02 | 0.07 | 0.06 | 0.04 | 0.04 | 0.06 | 0.04 | 0.04 | 19.18 |
| 0.50 | 1.00 | 1.09 | ENO_ECOBW | 51159 | 1.87 | 9.57E+04 | 0.14 | 0.02 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.03 | 0.04 | 9.06 |
| 0.61 | 1.26 | 1.62 | TALB_ECOLI | 38683 | 3.02 | 1.17E+05 | 0.17 | 0.02 | 0.05 | 0.06 | 0.04 | 0.04 | 0.04 | 0.05 | 0.04 | 7.11 |
| 0.59 | 1.04 | 1.24 | CH60_ECO24 | 63372 | 1.79 | 1.13E+05 | 0.17 | 0.03 | 0.04 | 0.05 | 0.04 | 0.05 | 0.04 | 0.04 | 0.04 | 7.81 |
| 0.55 | 1.08 | 1.36 | RBSB_ECOLI | 34822 | 2.43 | 8.46E+04 | 0.12 | 0.02 | 0.03 | 0.04 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 2.61 |
| 0.58 | 1.22 | 1.61 | DNAK_ECOHS | 76495 | 0.76 | 5.81E+04 | 0.09 | 0.01 | 0.02 | 0.03 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 7.15 |
| 0.56 | 1.05 | 1.13 | RPOB_ECOBW | 162610 | 0.60 | 9.76E+04 | 0.14 | 0.02 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.04 | 8.96 |
| 0.55 | 0.98 | 1.13 | RL7_ECO24 | 14305 | 3.27 | 4.68E+04 | 0.07 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 9.71 |
| 0.59 | 1.19 | 1.25 | HTPG_ECOHS | 78151 | 1.20 | 9.38E+04 | 0.14 | 0.02 | 0.04 | 0.04 | 0.03 | 0.04 | 0.04 | 0.03 | 0.03 | 6.97 |
| 0.59 | 1.32 | 1.58 | CLPB_ECOLI | 102182 | 0.59 | 6.03E+04 | 0.09 | 0.01 | 0.03 | 0.03 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 7.28 |
| 0.56 | 1.20 | 1.54 | GRCA_ECOBW | 15485 | 10.72 | 1.66E+05 | 0.24 | 0.03 | 0.07 | 0.09 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 5.54 |
| 0.59 | 1.11 | 1.33 | ODP2_ECOLI | 73893 | 1.19 | 8.79E+04 | 0.13 | 0.02 | 0.04 | 0.04 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 4.29 |
| 0.58 | 1.05 | 1.10 | PUR9_ECO24 | 61944 | 0.79 | 4.89E+04 | 0.07 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 10.89 |
| 0.56 | 1.20 | 1.20 | 6PGD_ECOLI | 55742 | 1.17 | 6.52E+04 | 0.10 | 0.01 | 0.03 | 0.03 | 0.02 | 0.02 | 0.03 | 0.02 | 0.02 | 7.95 |
| 0.59 | 1.23 | 1.47 | KPYK1_ECO57 | 56083 | 1.46 | 8.19E+04 | 0.12 | 0.02 | 0.03 | 0.04 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 3.83 |
| 0.54 | 1.20 | 1.56 | SYGB_ECOBW | 82988 | 0.84 | 6.97E+04 | 0.10 | 0.01 | 0.03 | 0.04 | 0.02 | 0.02 | 0.03 | 0.03 | 0.02 | 7.00 |
| 0.56 | 1.25 | 1.55 | SYP_ECOBW | 67889 | 0.61 | 4.14E+04 | 0.06 | 0.01 | 0.02 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 6.36 |
| 0.57 | 1.06 | 1.12 | ATPA_ECOBW | 59018 | 0.96 | 5.67E+04 | 0.08 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 9.86 |
| 0.57 | 1.05 | 1.21 | GLYA_ECOBW | 49782 | 1.38 | 6.87E+04 | 0.10 | 0.02 | 0.03 | 0.03 | 0.03 | 0.03 | 0.02 | 0.02 | 0.03 | 7.60 |
| 0.50 | 1.01 | 1.11 | SYD_ECOBW | 70912 | 0.94 | 6.67E+04 | 0.10 | 0.01 | 0.03 | 0.03 | 0.03 | 0.02 | 0.02 | 0.02 | 0.03 | 8.30 |
| 0.59 | 1.09 | 1.25 | RL9_ECO24 | 17489 | 3.04 | 5.32E+04 | 0.08 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 6.82 |
| Sum | 1.37E+07 | 20.0 | ||||||||||||||
| Only bold red and ion score >20 | iTRAQ-emPAI calculated protein amounts* | 2.7 | 5.6 | 6.7 | 5.0 | |||||||||||
| Original planned amounts** | 5 | 5 | 5 | 5 | ||||||||||||
Proteins (653) of the E. coli lysate were compared by iTRAQ labeling (Supplemental Data 2), but only the top 30 are shown in this table.
*The calculated protein amounts reflect the relative efficiencies of the iTRAQ labeling reaction under the different reagent composition designs.
**The original amounts of protein planned for each iTRAQ labeling were 5 μg. Only peptides with bold red and ion score >20 in Mascot output were used in this analysis.