Table 1.
Number of identified peptides, as well as relative isotope abundance (RIA) and labeling ratio (LR) of identified labeled peptides from protein extracts of Thauera aromatica K172, cultivated with 5 mM α-13C-benzoate or 12C-benzoate mixed in different ratios
| Relative abundance of 13C-labeled proteins in the protein mixture [%] | Search against the whole proteome database (Requires prior knowledge of the sample’s community composition) |
Search against the GroEL database and filtering with a Top Rank Count threshold of ≥ 5 (Does not require prior knowledge of the sample’s community composition) |
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|---|---|---|---|---|---|---|---|---|
| Total identified peptides | Identified labeled peptides | Median RIA of labeled peptides [%] | Median LR of labeled peptides [%] | Total identified peptides | Identified labeled peptides | Median RIA of labeled peptides [%] | Median LR of labeled peptides [%] | |
| 0 | 2476.7 ± 254.5 | 3.7 ± 0.6 | 3.4 ± 1.2 | 50.0 ± 0.0 | 14.7 ± 0.5 | 0 ± 0 | 0 ± 0 | 0 ± 0 |
| 25 | 1746.3 ± 181.9 | 326.0 ± 32.8 | 12.6 ± 0.1 | 24.1 ± 1.3 | 15.7 ± 1.5 | 12.0 ± 2.0 | 14.1 ± 0.8 | 24.3 ± 2.1 |
| 50 | 1549.1 ± 356.5 | 743.7 ± 171.5 | 12.2 ± 0.0 | 50.9 ± 3.0 | 15.2 ± 1.2 | 13.7 ± 0.5 | 12.5 ± 0.8 | 52.3 ± 3.3 |
| 75 | 484.3 ± 287.1 | 402.3 ± 226.0 | 12.4 ± 0.3 | 73.9 ± 2.5 | 10.0 ± 2.6 | 10.0 ± 2.6 | 11.7 ± 0.4 | 74.6 ± 2.7 |
| 100 | 0 ± 0 | 0 ± 0 | 0 ± 0 | 0 ± 0 | 0 ± 0 | 0 ± 0 | 0 ± 0 | 0 ± 0 |
Peptides were identified using the whole proteome database of Thauera aromatica K172 containing 3,335 entries or the GroEL database with 72,759 non-redundant entries. Peptides were counted as labeled when at least one RIA was detected in addition to the natural RIA. If MetaProSIP reported multiple RIAs for a peptide, only the highest RIA was used to calculate the median and LR. Values represent means of biological triplicates ± standard deviations.