Fluxomers: a new approach for 13C metabolic flux analysis

Srour, Orr; Young, Jamey D; Eldar, Yonina C

doi:10.1186/1752-0509-5-129

BMC Systems Biology

Table 4 Relative mass isotopomer fractions comparison for wild-type and mutant C. glutamicum

From: Fluxomers: a new approach for ¹³C metabolic flux analysis

		Wildtype							Mutant
Fragment		Non-normalized	Exp.	Ad-hoc	OpenFLUX	FIA			Exp.	Ad-hoc	OpenFLUX	FIA
						const.	meas.	ratios				const.	meas.
ALA 260	M0	206.3562	0.5085	0.509	0.509	0.5099	0.5099	0.5097	0.5230	0.525	0.525	0.5247	0.5247
	M1	102.8634	0.3529	0.354	0.354	0.3534	0.3534	0.3537	0.3410	0.342	0.342	0.3425	0.3425
	M2	4.8452	0.1058	0.106	0.106	0.1063	0.1063	0.1062	0.1030	0.104	0.104	0.1037	0.1037
VAL 288	M0	41.4005	0.3455	0.348	0.348	0.3459	0.3458	0.3457	0.3640	0.366	0.366	0.3661	0.3663
	M1	39.6134	0.3983	0.398	0.398	0.3986	0.3986	0.3987	0.3920	0.392	0.392	0.3921	0.3922
	M2	10.7340	0.1845	0.184	0.184	0.1846	0.1846	0.1847	0.1750	0.175	0.175	0.1750	0.1749
THR 404	M0	194.9082	0.3330	0.334	0.334	0.3343	0.3343	0.3340	0.3440	0.344	0.344	0.3439	0.3439
	M1	159.2226	0.3764	0.376	0.376	0.3757	0.3757	0.3759	0.3730	0.371	0.371	0.3715	0.3721
	M2	35.2094	0.1957	0.196	0.196	0.1956	0.1956	0.1957	0.1910	0.192	0.192	0.1920	0.1918
ASP 418	M0	159.9111	0.3343	0.333	0.333	0.3337	0.3337	0.3334	0.3450	0.343	0.343	0.3432	0.3433
	M1	128.3755	0.3732	0.375	0.375	0.3750	0.3750	0.3752	0.3700	0.370	0.371	0.3708	0.3714
	M2	28.7782	0.1955	0.196	0.196	0.1960	0.1959	0.1960	0.1920	0.193	0.192	0.1924	0.1922
GLU 432	M0	3.8009	0.2469	0.25	0.249	0.2474	0.2473	0.2469	0.2570	0.264	0.264	0.2634	0.2624
	M1	4.4232	0.3648	0.366	0.366	0.3661	0.3661	0.3660	0.3650	0.365	0.365	0.3656	0.3658
	M2	1.7429	0.2412	0.239	0.240	0.2406	0.2406	0.2409	0.2360	0.232	0.232	0.2322	0.2327
SER 390	M0	224.9043	0.4497	0.449	0.448	0.4487	0.4488	0.4490	0.4620	0.463	0.463	0.4635	0.4628
	M1	108.4056	0.3576	0.358	0.358	0.3578	0.3578	0.3580	0.3490	0.349	0.349	0.3491	0.3492
	M2	3.5199	0.1428	0.143	0.144	0.1437	0.1437	0.1434	0.1400	0.140	0.140	0.1399	0.1403
PHE 336	M0	250.7079	0.2712	0.274	0.274	0.2764	0.2764	0.2769	0.2870	0.289	0.289	0.2881	0.2874
	M1	303.6304	0.3816	0.381	0.381	0.3817	0.3817	0.3822	0.3800	0.381	0.381	0.3809	0.3806
	M2	129.5861	0.2282	0.228	0.228	0.2263	0.2264	0.2261	0.2200	0.220	0.220	0.2206	0.2210
GLY 246	M0	738.7580	0.7407	0.742	0.742	0.7417	0.7417	0.7421	0.7410	0.743	0.743	0.7426	0.7426
	M1	39.7395	0.1845	0.185	0.185	0.1852	0.1852	0.1849	0.1830	0.184	0.184	0.1844	0.1844
TYR 466	M0	36.7321	0.2344	0.236	0.236	0.2380	0.2380	0.2384	0.2460	0.249	0.249	0.2481	0.2475
	M1	43.7966	0.3530	0.356	0.356	0.3567	0.3567	0.3572	0.3510	0.358	0.357	0.3572	0.3569
	M2	18.6839	0.2423	0.245	0.245	0.2433	0.2433	0.2431	0.2340	0.238	0.238	0.2387	0.2390
TRE 361	M0	34.1048	0.0613	0.062	0.062	0.0612	0.0612	0.0608	0.0880	0.088	0.088	0.0884	0.0884
	M1	327.3441	0.6040	0.607	0.606	0.6051	0.6051	0.6057	0.5730	0.577	0.574	0.5743	0.5742
	M2	27.0318	0.2070	0.207	0.207	0.2084	0.2084	0.2084	0.2130	0.213	0.213	0.2128	0.2126
Sum of weighted residuals				761	684	654	650	718	1735	1461	1451	1308

Experimental and calculated isotopomer MS fractions. The experimental data and ad-hoc simulation results are taken from Becker et al. [18]. The OpenFLUX results are taken from [15]. The simulated "non-normalized" data is generated by multiplying the given values after natural isotope correction by random factors. Several FIA estimations are provided: using the given fluxes as constants (under "const."), as measurements (under "meas."), and when using the simulated non-normalized data (under "ratios"). As can be seen, FIA agrees with previous results (even when the data is used without normalization). For the mutant case, better fits are achieved when allowing the supplied fluxes to change as well.

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ISSN: 1752-0509

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