Table 2.
Relative amounts of select metabolites in wild-type and cdc48-3 cells.
| A | ID | m/z | MT/RT | Relative Area |
Comparative Analysis |
|||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Compound name | KEGG ID | wild type |
cdc48-3 |
wild type |
cdc48-3 |
cdc48-3 vs wild type |
||||||||||||
| A1 | A2 | A3 | B1 | B2 | B3 | Mean | S.D. | Mean | S.D. | Ratio¶ | p-value|| | |||||||
| A_0057 | Glucose 6-phosphate | C00668, C01172, C00092 | 259.023 | 9.90 | 6.4E-03 | 7.0E-03 | 6.4E-03 | 3.5E-02 | 3.7E-02 | 3.6E-02 | 6.6E-03 | 3.6E-04 | 3.6E-02 | 1.2E-03 | 5.4334 | 0.000244 | *** | |
| A_0058 | Fructose 6-phosphate | C05345, C00085 | 259.023 | 10.00 | 4.1E-03 | 3.9E-03 | 4.0E-03 | N.D. | N.D. | N.D. | 4.0E-03 | 1.2E-04 | N.A. | N.A. | <1 | N.A. | ||
| A_0071 | Fructose 1,6-diphosphate | C00354 | 338.990 | 14.62 | 1.7E-02 | 1.8E-02 | 1.8E-02 | 1.0E-01 | 1.1E-01 | 1.1E-01 | 1.8E-02 | 7.4E-04 | 1.1E-01 | 2.5E-03 | 6.0188 | 0.000081 | *** | |
| A_0031 | Glyceraldehyde 3-phosphate | C00118, C00661 | 168.991 | 11.66 | N.D. | N.D. | N.D. | 1.4E-03 | 1.2E-03 | 1.1E-03 | N.A. | N.A. | 1.2E-03 | 1.7E-04 | 1< | N.A. | ||
| A_0039 | 3-Phosphoglyceric acid | C00197 | 184.986 | 19.64 | 4.3E-02 | 4.1E-02 | 4.6E-02 | 2.8E-02 | 2.3E-02 | 2.4E-02 | 4.4E-02 | 2.6E-03 | 2.5E-02 | 2.6E-03 | 0.5811 | 0.000966 | *** | |
| A_0040 | 2-Phosphoglyceric acid | C00631 | 184.986 | 19.17 | 8.1E-03 | 7.3E-03 | 7.4E-03 | 4.7E-03 | 4.2E-03 | 4.1E-03 | 7.6E-03 | 4.3E-04 | 4.3E-03 | 3.3E-04 | 0.5699 | 0.000651 | *** | |
| A_0030 | Phosphoenolpyruvic acid | C00074 | 166.976 | 21.00 | 2.1E-02 | 2.3E-02 | 2.3E-02 | 1.3E-02 | 1.1E-02 | 1.2E-02 | 2.2E-02 | 1.1E-03 | 1.2E-02 | 1.0E-03 | 0.5243 | 0.000263 | *** | |
| A_0004 | Pyruvic acid | C00022 | 87.009 | 12.91 | 1.6E-02 | 1.7E-02 | 2.1E-02 | 1.5E-02 | 1.5E-02 | 1.6E-02 | 1.8E-02 | 2.6E-03 | 1.5E-02 | 5.7E-04 | 0.8487 | 0.209150 | ||
| B | ID | m/z | MT/RT | Relative Area |
Comparative Analysis |
|||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Compound name | KEGG ID | wild type |
cdc48-3 |
wild type |
cdc48-3 |
cdc48-3 vs wild type |
||||||||||||
| A1 | A2 | A3 | B1 | B2 | B3 | Mean | S.D. | Mean | S.D. | Ratio¶ | p-value|| | |||||||
| A_0043 | Isocitric acid | C00311 | 191.019 | 28.49 | 3.0E-03 | N.D. | 3.6E-03 | 3.4E-03 | 4.4E-03 | 4.0E-03 | 3.3E-03 | 4.4E-04 | 3.9E-03 | 4.9E-04 | 1.1858 | 0.254070 | ||
| A_0019 | Malic acid | C00149, C00497, C00711 | 133.015 | 21.20 | 1.5E-01 | 1.5E-01 | 1.5E-01 | 3.3E-01 | 3.2E-01 | 3.3E-01 | 1.5E-01 | 1.7E-03 | 3.3E-01 | 5.2E-03 | 2.1558 | 0.000079 | *** | |
| A_0016 | Succinic acid | C00042 | 117.020 | 20.78 | 1.4E-01 | 1.4E-01 | 1.5E-01 | 2.4E-01 | 2.2E-01 | 2.5E-01 | 1.4E-01 | 6.4E-03 | 2.4E-01 | 1.1E-02 | 1.6325 | 0.000693 | *** | |
| A_0092 | ADP | C00008 | 426.023 | 10.93 | 1.3E-01 | 1.3E-01 | 1.4E-01 | 1.1E-01 | 9.9E-02 | 1.0E-01 | 1.3E-01 | 6.3E-03 | 1.0E-01 | 4.4E-03 | 0.7704 | 0.003398 | ** | |
| A_0105 | ATP | C00002 | 505.990 | 11.85 | 2.3E-01 | 2.3E-01 | 2.4E-01 | 3.4E-01 | 3.4E-01 | 3.6E-01 | 2.3E-01 | 7.2E-03 | 3.5E-01 | 7.0E-03 | 1.4983 | 0.000037 | *** | |
| A_0112 | NAD+ | C00003 | 662.104 | 6.65 | 2.5E-01 | 2.5E-01 | 2.5E-01 | 2.5E-01 | 2.3E-01 | 2.4E-01 | 2.5E-01 | 8.8E-04 | 2.4E-01 | 9.3E-03 | 0.9702 | 0.301370 | ||
| A_0113 | NADH | C00004 | 664.120 | 8.25 | 9.5E-03 | 9.5E-03 | 1.0E-02 | 1.3E-02 | 1.4E-02 | 1.4E-02 | 9.8E-03 | 4.8E-04 | 1.4E-02 | 4.7E-04 | 1.3813 | 0.000641 | *** | |
| C | ID | m/z | MT/RT | Relative Area |
Comparative Analysis |
|||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Compound name | KEGG ID | wild type |
cdc48-3 |
wild type |
cdc48-3 |
cdc48-3 vs wild type |
||||||||||||
| A1 | A2 | A3 | B1 | B2 | B3 | Mean | S.D. | Mean | S.D. | Ratio¶ | p-value|| | |||||||
| C_0004 | Ala | C00041, C00133, C01401 | 90.055 | 8.83 | 3.1E+00 | 3.1E+00 | 3.2E+00 | 1.9E+00 | 2.1E+00 | 2.0E+00 | 3.1E+00 | 4.4E-02 | 2.0E+00 | 7.5E-02 | 0.6353 | 0.000110 | *** | |
| C_0040 | Arg | C00062, C00792 | 175.119 | 6.91 | 1.5E+00 | 1.6E+00 | 1.7E+00 | 1.5E+00 | 1.6E+00 | 1.6E+00 | 1.6E+00 | 1.1E-01 | 1.6E+00 | 4.6E-02 | 1.0109 | 0.814850 | ||
| C_0025 | Asn | C00152, C01905, C16438 | 133.061 | 10.31 | 4.3E-01 | 4.5E-01 | 4.6E-01 | 3.1E-01 | 3.4E-01 | 3.1E-01 | 4.5E-01 | 1.2E-02 | 3.2E-01 | 1.8E-02 | 0.7119 | 0.000830 | *** | |
| C_0027 | Asp | C00049, C00402, C16433 | 134.045 | 11.41 | 2.5E+00 | 2.5E+00 | 2.5E+00 | 9.0E-01 | 9.4E-01 | 9.0E-01 | 2.5E+00 | 3.3E-02 | 9.1E-01 | 2.7E-02 | 0.3689 | 0.000001 | *** | |
| C_0019 | Cys | C00097, C00736, C00793 | 122.027 | 11.17 | 1.9E-03 | 1.5E-03 | 2.3E-03 | 1.1E-03 | 9.1E-04 | 9.9E-04 | 1.9E-03 | 4.0E-04 | 9.9E-04 | 8.2E-05 | 0.5184 | 0.051546 | ||
| C_0033 | Gln | C00064, C00303, C00819 | 147.076 | 10.57 | 2.3E+00 | 2.4E+00 | 2.5E+00 | 3.5E+00 | 3.9E+00 | 3.6E+00 | 2.4E+00 | 9.0E-02 | 3.7E+00 | 1.8E-01 | 1.5538 | 0.001801 | ** | |
| C_0035 | Glu | C00025, C00217, C00302 | 149.064 | 10.69 | 7.4E-01 | 7.5E-01 | 7.5E-01 | 6.5E-01 | 7.1E-01 | 6.5E-01 | 7.5E-01 | 8.7E-03 | 6.7E-01 | 3.6E-02 | 0.8943 | 0.055789 | ||
| C_0001 | Gly | C00037 | 76.039 | 8.13 | 7.7E-01 | 7.7E-01 | 8.4E-01 | 7.1E-01 | 7.4E-01 | 7.2E-01 | 7.9E-01 | 3.9E-02 | 7.2E-01 | 1.1E-02 | 0.9132 | 0.082860 | ||
| C_0038 | His | C00135, C00768, C06419 | 156.077 | 7.10 | 1.7E+00 | 1.8E+00 | 1.9E+00 | 1.1E+00 | 1.2E+00 | 1.1E+00 | 1.8E+00 | 1.2E-01 | 1.1E+00 | 3.7E-02 | 0.6397 | 0.006336 | ** | |
| C_0023 | Ile | C00407, C06418, C16434 | 132.102 | 10.07 | 7.2E-01 | 7.6E-01 | 7.8E-01 | 5.1E-01 | 5.1E-01 | 5.1E-01 | 7.5E-01 | 2.9E-02 | 5.1E-01 | 3.1E-03 | 0.6764 | 0.004439 | ** | |
| C_0024 | Leu | C00123, C01570, C16439 | 132.102 | 10.17 | 1.7E+00 | 1.6E+00 | 1.7E+00 | 8.2E-01 | 8.5E-01 | 8.3E-01 | 1.7E+00 | 4.9E-02 | 8.4E-01 | 1.7E-02 | 0.5052 | 0.000366 | *** | |
| C_0034 | Lys | C00047, C00739, C16440 | 148.116 | 6.62 | 6.2E-01 | 6.4E-01 | 6.7E-01 | 3.2E-01 | 3.3E-01 | 3.2E-01 | 6.4E-01 | 2.5E-02 | 3.3E-01 | 4.4E-03 | 0.5054 | 0.001625 | ** | |
| C_0036 | Met | C00073, C00855, C01733 | 150.059 | 10.54 | 2.8E-01 | 2.8E-01 | 2.9E-01 | 1.4E-01 | 1.5E-01 | 1.4E-01 | 2.8E-01 | 4.0E-03 | 1.4E-01 | 2.5E-03 | 0.5086 | 0.000005 | *** | |
| C_0039 | Phe | C00079, C02057, C02265 | 166.086 | 10.94 | 7.3E-01 | 7.4E-01 | 7.6E-01 | 3.2E-01 | 3.5E-01 | 3.4E-01 | 7.4E-01 | 1.5E-02 | 3.4E-01 | 1.4E-02 | 0.4569 | 0.000005 | *** | |
| C_0013 | Pro | C00148, C00763, C16435 | 116.071 | 10.65 | 8.2E-01 | 8.5E-01 | 8.0E-01 | 7.7E-01 | 8.2E-01 | 7.7E-01 | 8.2E-01 | 2.8E-02 | 7.9E-01 | 2.8E-02 | 0.9566 | 0.192940 | ||
| C_0009 | Ser | C00065, C00716, C00740 | 106.050 | 9.81 | 7.0E-01 | 7.2E-01 | 7.4E-01 | 7.2E-01 | 7.7E-01 | 7.1E-01 | 7.2E-01 | 1.9E-02 | 7.3E-01 | 3.3E-02 | 1.0177 | 0.601030 | ||
| C_0017 | Thr | C00188, C00820 | 120.066 | 10.35 | 1.3E+00 | 1.3E+00 | 1.3E+00 | 9.9E-01 | 1.0E+00 | 9.8E-01 | 1.3E+00 | 4.9E-02 | 1.0E+00 | 3.1E-02 | 0.7765 | 0.002050 | ** | |
| C_0044 | Trp | C00078, C00525, C00806 | 205.097 | 10.80 | 1.1E-02 | 1.0E-02 | 1.2E-02 | 8.4E-03 | 9.2E-03 | 8.8E-03 | 1.1E-02 | 7.2E-04 | 8.8E-03 | 3.6E-04 | 0.7815 | 0.014066 | * | |
| C_0042 | Tyr | C00082, C01536, C06420 | 182.082 | 11.22 | 8.6E-02 | 8.7E-02 | 9.4E-02 | 8.2E-02 | 8.8E-02 | 8.1E-02 | 8.9E-02 | 4.5E-03 | 8.4E-02 | 3.7E-03 | 0.9400 | 0.192220 | ||
| C_0014 | Val | C00183, C06417, C16436 | 118.086 | 9.87 | 1.4E+00 | 1.5E+00 | 1.5E+00 | 1.0E+00 | 1.1E+00 | 1.0E+00 | 1.5E+00 | 4.2E-02 | 1.0E+00 | 2.6E-02 | 0.6949 | 0.000301 | *** | |
| D | ID | m/z | MT/RT | Relative Area |
Comparative Analysis |
|||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Compound name | KEGG ID | wild type |
cdc48-3 |
wild type |
cdc48-3 |
cdc48-3 vs wild type |
||||||||||||
| A1 | A2 | A3 | B1 | B2 | B3 | Mean | S.D. | Mean | S.D. | Ratio¶ | p-value|| | |||||||
| A_0107 | GTP | C00044 | 521.985 | 11.53 | 4.6E-02 | 4.6E-02 | 5.0E-02 | 7.4E-02 | 7.5E-02 | 7.8E-02 | 4.7E-02 | 2.4E-03 | 7.6E-02 | 2.0E-03 | 1.5999 | 0.000111 | *** | |
| A_0101 | CTP | C00063 | 481.980 | 12.42 | 1.7E-02 | 1.8E-02 | 1.7E-02 | 3.4E-02 | 3.3E-02 | 3.6E-02 | 1.7E-02 | 6.6E-04 | 3.4E-02 | 1.3E-03 | 1.9569 | 0.000303 | *** | |
| A_0104 | dATP | C00131 | 489.996 | 11.80 | 4.8E-03 | 4.7E-03 | 4.7E-03 | 9.9E-03 | 9.6E-03 | 1.0E-02 | 4.8E-03 | 6.3E-05 | 9.9E-03 | 3.9E-04 | 2.0859 | 0.001461 | ** | |
| A_0100 | dTTP | C00459 | 480.984 | 12.17 | 6.0E-03 | 5.1E-03 | 5.6E-03 | 1.4E-02 | 1.4E-02 | 1.3E-02 | 5.5E-03 | 4.5E-04 | 1.4E-02 | 7.3E-04 | 2.4781 | 0.000264 | *** | |
| A_0106 | dGTP | C00286 | 505.991 | 11.54 | 1.6E-03 | 1.5E-03 | 1.7E-03 | 2.8E-03 | 2.8E-03 | 3.1E-03 | 1.6E-03 | 1.0E-04 | 2.9E-03 | 1.6E-04 | 1.8463 | 0.000698 | *** | |
| A_0099 | dCTP | C00458 | 465.984 | 12.50 | 2.6E-03 | 2.8E-03 | 2.7E-03 | 7.0E-03 | 7.2E-03 | 7.6E-03 | 2.7E-03 | 1.2E-04 | 7.3E-03 | 3.4E-04 | 2.6934 | 0.000653 | *** | |
ID consists of analysis mode and number. ‘C’ and ‘A’ showed cation and anion modes, respectively.
N.D. (Not Detected): The target peak or metabolite was below detection limits.
N.A. (Not Available): The calculation was impossible because of insufficience of the data.
¶ The ratio is of computed by using averaged detection values. The latter was used as denominator.
|| The p-value is computed by Welch’s t-test. (*<0.05, **<0.01, ***<0.001).
Glu, Lys: Peak intensity is saturated. Relative area was computed by using 13C isotope ion peak.