Table 3.
Amino acid metabolism related proteins identified by dMS and SC after search of the iCitrus database using X!Tandem with LC-MS/MS uninterpreted 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 | |||||||||
| Acetyl-CoA C-acyltransferase | 55738 | at1g04710 | – | – | 0 | 1.25 | 3.23 | – | – | 1 | 11.30 | 7.63 |
| BCAT-2; branched-chain-amino-acid transaminase | 15175 | at1g10070 | – | – | 0 | 0.98 | 1.03 | – | – | 0 | 3.69 | 2.90 |
| Aminomethyltransferase | 40906 | at1g11860 | – | – | 0 | 0.98 | 1.03 | 2 | 13.50 | 0 | 1.51 | 1.81 |
| Glycine dehydrogenase | 56681 | at2g26080 | 3 | 0.20 | –1 | 452.08 | 20.99 | – | – | 0 | 0.99 | 1.24 |
| ALAAT1 (alanine aminotransferase) | 35404 | at1g17290 | – | – | 0 | 1.00 | 1.00 | – | – | 1 | 587.23 | 15.56 |
| PGDH (3-phosphoglycerate dehydrogenase) | 33085 | at1g17745 | 7 | 23.49 | 0 | 0.32 | 1.19 | 4 | 2.04 | 0 | 5.82 | 2.29 |
| PGDH (3-phosphoglycerate dehydrogenase) | 4033 | at4g34200 | 3 | 0.73 | – | – | – | 2 | 2.26 | – | – | – |
| AGT2 (alanine:glyoxylate aminotransferase 2) | 12839 | at4g39660 | – | – | – | – | – | 3 | 18.30 | – | – | – |
| AGT2 (alanine:glyoxylate aminotransferase 2) | 27165 | at4g39660 | – | – | 0 | 0.98 | 1.03 | 4 | 16.42 | 0 | 1.69 | 1.93 |
| ASP4 (aspartate aminotransferase 4) | 40919 | at1g62800 | 2 | 9.08 | – | – | – | 3 | 41.05 | – | – | – |
| ASP4 (aspartate aminotransferase 4) | 25228 | at1g62800 | 2 | 9.08 | 1 | 64.43 | 7.15 | 4 | 38.73 | 1 | 14.81 | 3.34 |
| ASP3 (aspartate aminotransferase 3) | 14798 | at5g11520 | – | – | – | – | – | 2 | 7.30 | – | – | – |
| GAD2 (glutamate decarboxylase 2) | 45590 | at1g65960 | 2 | 1924.40 | 0 | 1.00 | 1.00 | 4 | 2.15 | 0 | 1.75 | 2.1 |
| GAD2 (glutamate decarboxylase 2) | 60356 | at1g65960 | 2 | 239.09 | 1 | 696.64 | 26.44 | 5 | 2.06 | 0 | 0.49 | 1.06 |
| GAD1 (glutamate decarboxylase 1) | 58418 | at3g17760 | – | – | – | – | – | 2 | 1.47 | – | – | – |
| GDH3(glutamate dehydrogenase 3) | 45569 | at3g03910 | – | – | -1 | 41.11 | 11.21 | 2 | 6.64 | 0 | 2.31 | 2.23 |
| GDH2 (glutamate dehydrogenase 2) | 37770 | at5g07440 | – | – | – | – | – | 2 | 6.64 | – | – | – |
| GLN1;3 (glutamine synthetase) | 2123 | at3g17820 | – | – | 0 | 1.00 | 1.00 | – | – | 0 | 7.38 | 6.85 |
| GLN1;1-GSR1(glutamine synthetase) | 25117 | at5g37600 | 5 | 161.07 | 1 | 1197.34 | 4.24 | 6 | 0.67 | –1 | 16.77 | 1.88 |
| GLN1;1-GSR1(glutamine synthetase) | 41697 | at5g37600 | – | – | 0 | 1.00 | 1.00 | – | – | 1 | 92.46 | 12.23 |
| GLN1;1-GSR1(glutamine synthetase) | 678 | at5g37600 | 2 | 180.37 | – | – | – | – | – | – | – | – |
| ?-Aminobutyrate transaminase | 22281 | at3g22200 | – | – | – | – | – | 3 | 13.87 | – | – | – |
| P5CS1 (delta1-pyrroline-5-carboxylate synthase 1) | 37246 | at2g39800 | 3 | 0.32 | –1 | 24.08 | 7.09 | – | – | 0 | 1.07 | 1.48 |
| ALDH12A1, 1-pyrroline-5-carboxylate dehydrogenase | 27988 | at5g62530 | 2 | 0.17 | 0 | 7.46 | 8.52 | – | – | 0 | 1.00 | 1.00 |
| MS2 (methionine synthase 2) | 41927 | at3g03780 | 5 | 0.14 | – | – | – | 4 | 1.16 | – | – | – |
| MS2 (methionine synthase 2) | 43263 | at3g03780 | 11 | 0.16 | –1 | 13256.47 | 31.34 | 11 | 5.38 | 0 | 0.51 | 1.60 |
| MS1 (methionine synthase 1) | 24003 | at5g17920 | – | – | – | – | – | 3 | 16.69 | – | – | – |
| SAHH2 (S-adenosyl-L-homocysteine hydrolase 2) | 11482 | at3g23810 | – | – | – | – | – | 2 | 1.73 | – | – | – |
| SAHH2 (S-adenosyl-L-homocysteine hydrolase 2) | 49170 | at3g23810 | 9 | 0.17 | –1 | 130.58 | 4.57 | 14 | 170.98 | 0 | 0.86 | 1.41 |
| SAHH2 (S-adenosyl-L-homocysteine hydrolase 2) | 51358 | at3g23810 | 7 | 0.17 | 0 | 0.19 | 1.13 | 14 | 170.98 | 0 | 0.86 | 1.41 |
| SAHH1 (S-adenosyl-L-homocysteine hydrolase 1) | 1927 | at4g13940 | 7 | 0.16 | – | – | – | 9 | 182.30 | – | – | – |
| Ketol-acid reductoisomerase | 22397 | at3g58610 | 2 | 0.26 | –1 | 23.24 | 10.72 | – | – | –1 | 88.90 | 12.39 |
| O-acetylserine(thiol)lyase | 11065 | at4g14880 | 2 | 14.31 | 1 | 33.25 | 12.26 | – | – | 0 | 9.65 | 3.28 |
| Acetyl-CoA C-acyltransferase | 33619 | at5g47720 | – | – | 0 | 1.00 | 1.00 | – | – | 0 | 1.05 | 2.23 |
| Succinate semialdehyde dehydrogenase | 56374 | at1g79440 | 2 | 2.3 | 0 | 1.27 | 1.74 | – | – | 0 | 0.75 | 1.07 |
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 a significant difference. The column ‘Direction’ under SC represents up-regulated=1, no change=0, down-regulated= –1.