Table 4

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

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.

Srour et al. BMC Systems Biology 2011 5:129   doi:10.1186/1752-0509-5-129

Open Data