Table 1.
Size of experimental data sets and models. (A) Three experimental datasets under different conditions were collected for the CHO cell, and two for the gut microbiota sample. (B) The size of the metabolic model: number of reactions, metabolites, and unique masses. (C) The size of the expanded metabolic model: number of operators derived using PROXIMAL, unique derivatives generated by PROXIMAL, unique derivative masses due to PROXIMAL. For comparison purposes, the numbers of derivatives and derivative masses exclude those in the metabolic model. (D) Fold increase in number of metabolites and masses when comparing the size of these sets for EMM against the metabolic model.
| (A) Experimental Data |
(B) Metabolic Model |
(C) Expanded Metabolic Model Using PROXIMAL |
(D) Fold Change for EMM Relative to Metabolic Model |
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|---|---|---|---|---|---|---|---|---|---|---|---|
| Biological Sample | Dataset | MS Mode | Number of Measured Masses | Number of Reactions | Number of Metabolites | Number of Unique Masses | Number of Unique Operators | Number of Unique Derivatives | Number of Unique Derivative Masses | Number of Metabolites | Number of Unique Masses |
| CHO cell | HilNeg | negative | 2502 | 1619 | 1353 | 775 | 2392 | 76745 | 17930 | 56.72 | 23.14 |
| HilPos | positive | 3856 | |||||||||
| SynNeg | negative | 5336 | |||||||||
| gut microbiota | Neg | negative | 1651 | 1381 | 1307 | 779 | 2756 | 94186 | 23356 | 72.06 | 29.98 |
| Pos | positive | 1657 | |||||||||