Table 4.
Impact of considering additional amino acid modifications on global and individual protein iTRAQ ratios.
| Protein changes relative to the 144KNt condition | 144KNt | 144KNt_144Y | 144KNt_144C | 144KNt_14K | 144KNt_42K | 144KNt_43K | 144KNt_48C | 144KNt_16M |
|---|---|---|---|---|---|---|---|---|
| 1. Protein overlap #(%) | 183(100%) | 174 (95%) | 173 (95%) | 161 (88%) | 163 (89%) | 164 (90%) | 172 (94%) | 173 (95%) |
| 2. Global iTRAQ | 1.6 | 1.5 | 1.6 | 1.6 | 1.6 | 1.5 | 1.6 | 1.5 |
| 3. False positive IDs % | 0 | 1.1 | 1.2 | 3.5 | 1.2 | 3.6 | 3.6 | 2.4 |
| 4. Proteins w. iTRAQ/2 #(%) | 7 (4%) | 8 (5%) | 21 (13%) | 19 (12%) | 17 (10%) | 10 (6%) | 9 (5%) | |
| 5. Protein losses # | 7 | 8 | 20 | 18 | 17 | 9 | 8 | |
| 6. Protein gains #(%) | 23 (13%) | 6 (3%) | 21 (13%) | 34 (21%) | 27 (16%) | 10 (6%) | 10 (6%) | |
| 7. Protein gains w. iTRAQ/2 # | 4 | 1 | 1 | 4 | 6 | 1 | 1 |
Note: The row of “Proteins w. iTRAQ/2” refers to the #(%) of proteins with larger than 2-fold changes in iTRAQ ratios after enabling additional amino acid modifications, as denoted by entries in Appendix 1 with the ratio of iTRAQ ratios≥2 or ≤0.5. The row of “Protein losses #” is denoted by entries in Appendix 1 with the ratio of iTRAQ ratios = 0. The row of “Protein gains #(%)” refers to the #/(%) of proteins that were newly identified after enabling additional amino acid modifications, and are entries with iTRAQ≠0 listed at the bottom of Appendix 1. The row of “Proteins gains w. iTRAQ/2 #“ refers to proteins that were newly identified after enabling additional amino acid modifications, and are entries with iTRAQ≥2 or iTRAQ≤0.5 listed at the bottom of Appendix 1.