Table 2.
TCA cycle-related proteins identified by dMS and SC after search of the iCitrus database by X!Tandem using LC-MS/MS spectra
| Annotation | iCitrus ID | Blast hit to TAIR | Stage II versus early stage II |
Stage III versus stage II |
||||||||
| dMS | Ratio | Direction | SC | Fold change | dMS | Ratio | Direction | SC | Fold change | |||
| No. peptides | Bayes factor | No.peptides | Bayes factor | |||||||||
| Pyruvate dehydrogenase complex E1 | 22606 | At1g24180 | 4 | 9.90 | 0 | 1.87 | 2.14 | – | – | 0 | 0.69 | 1.08 |
| 1564 | At1g24180 | 2 | 0.01 | – | – | – | – | – | – | – | – | |
| 23699 | At5g50850 | 6 | 0.20 | –1 | 21.69 | 8.81 | 3 | 24.16 | 0 | 3.64 | 2.84 | |
| 17446 | At5g50850 | 2 | 0.22 | – | – | – | – | – | – | – | – | |
| Dihydrolipoamide S-acetyltransferase E2 | 42695 | At3g17240 | 2 | 0.11 | – | – | – | – | – | – | – | – |
| Dihydrolipoamide dehydrogenase E3 | 4911 | At1g48030 | 4 | 0.26 | – | – | – | – | – | – | – | – |
| 44669 | At1g48030 | 7 | 0.33 | –1 | 142.43 | 10.83 | 3 | 4.74 | 0 | 0.71 | 1.13 | |
| Aconitase | 43680 | At2g05710 | 2 | 25.29 | 0 | 1.00 | 1.00 | 2 | 13.64 | 1 | 143.42 | 12.24 |
| 45840 | At2g05710 | 4 | 49.72 | 0 | 0.40 | 1.08 | 4 | 4.77 | 0 | 0.58 | 1.29 | |
| 39802 | At2g05710 | 3 | 24.94 | 0 | 0.66 | 1.88 | 4 | 33.48 | 1 | 30.46 | 5.52 | |
| Isocitrate dehydrogenase (NADP+) | 30767 | At1g54340 | 2 | 2.15 | 0 | 4.329 | 7.19 | 7 | 8.92 | 0 | 0.744 | 1.03 |
| 2385 | At1g65930 | – | – | – | – | – | 2 | 8.40 | – | – | – | |
| 3923 | At1g65930 | – | – | – | – | – | 3 | 4.43 | – | – | – | |
| 24612 | At3g09810 | 2 | 1.31 | 0 | 1.16 | 2.03 | 2 | 0.80 | 0 | 1.57 | 1.95 | |
| 149 | At4g35260 | 3 | 0.53 | 0 | 4.43 | 2.77 | – | – | 0 | 0.80 | 1.28 | |
| 2-oxoglutarate dehydrogenase E1 | 53498 | At3g55410 | – | – | 0 | 1.76 | 3.59 | 2 | 335.26 | 1 | 22.20 | 4.96 |
| 1249 | At3g55410 | – | – | 0 | 1.52 | 2.86 | 2 | 39.54 | 0 | 0.70 | 1.22 | |
| 38819 | At3g55410 | – | – | 0 | 0.98 | 1.03 | 2 | 136.04 | 1 | 22.11 | 4.73 | |
| succinyl-CoA ligase | 26895 | At2g20420 | 3 | 5.29 | 1 | 104.00 | 17.39 | 4 | 298.60 | 0 | 0.65 | 1.05 |
| 5556 | At2g20420 | – | – | – | – | – | 3 | 327 | – | – | – | |
| 22272 | At5g08300 | 2 | 0.95 | 0 | 0.62 | 1.23 | 2 | 3.41 | 0 | 1.19 | 1.53 | |
| Succinate dehydrogenase | 61503 | At2g18450 | 4 | 0.20 | 0 | 0.54 | 1.27 | x | x | 0 | 0.78 | 1.20 |
| 55144 | At5g40650 | – | – | –1 | 14.30 | 6.42 | – | – | 0 | 9.83 | 3.68 | |
| 1184 | At5g66760 | 2 | 0.24 | – | – | – | – | – | – | – | – | |
| Fumarase | 23918 | At2g47510 | – | – | 0 | 1.57 | 3.97 | 4 | 23.59 | 1 | 26.92 | 5.03 |
| 920 | At2g47510 | – | – | – | – | – | 2 | 6.64 | – | – | – | |
| Malate dehydrogenase | 2641 | At1g04410 | 2 | 11.92 | – | – | – | 6 | 4.65 | – | – | – |
| 2305 | At3g15020 | 3 | 0.49 | 0 | 1.63 | 2.90 | 2 | 2.55 | 0 | 0.87 | 1.64 | |
| 33986 | At5g43330 | 3 | 6.84 | 1 | 12.60 | 3.68 | 9 | 9.00 | 1 | 41.23 | 4.25 | |
| NADP-malic enzyme | 37162 | At1g79750 | 7 | 0.48 | 0 | 0.70 | 1.08 | 11 | 2.57 | 0 | 0.23 | 1.35 |
| 1735 | At1g79750 | 4 | 0.45 | – | – | – | 6 | 2.57 | – | – | – | |
| 35283 | At5g25880 | 2 | 0.42 | – | – | – | 2 | 4.86 | – | – | – | |
| 4879 | At5g25880 | 2 | 0.42 | – | – | – | – | – | – | – | – | |
| 36024 | At2g13560 | 2 | 0.10 | 0 | 2.47 | 5.78 | – | – | 0 | 1.00 | 1.00 | |
| 30233 | At2g13560 | 2 | 0.26 | –1 | 24.60 | 11.91 | – | – | 0 | 1.65 | 2.07 | |
Proteins identified by dMS were considered to be up-regulated when expression fold change >2, not changed when fold change >0.5 but <2, and down-regulated when fold change was <0.5. For SC, a Bayes factor of >10 was considered significant difference. The column ‘Direction’ under SC represents up-regulated=1, no change=0, own-regulated= –1.