| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and Virus Strains | ||
| Pseudomonas putida KT2440 | German collection of microorganisms and cell cultures (DSMZ) | DSM 6125 |
| Thauera aromatica K172 | German collection of microorganisms and cell cultures (DSMZ) | DSM 6984 |
| Escherichia coli BL21(DE3) | Thermo Scientific | Cat#EC0114 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| α-13C-benzoic acid | Eurisotop | CAS 3880-99-7 |
| 2-Iodoacetamide | Merck | CAS 144-48-9 |
| Ammonium bicarbonate | Bernd Kraft | CAS 1066-33-7 |
| Bovine serum albumin | Thermo Scientific | Cat#23209 |
| Dithiothreitol | ITW Reagents | CAS 3483-12-3 |
| Sequencing-grade modified trypsin | Promega | Cat#V5111 |
| Sodium acetate | Sigma-Aldrich | CAS 127-09-3 |
| Sodium benzoate | Sigma-Aldrich | CAS 532-32-1 |
| Critical Commercial Assays | ||
| Pierce BCA protein assay kits | Thermo Scientific | Cat#23225 |
| Deposited Data | ||
| Metaproteome data from an in vitro model of the human distal gut15,49 | PRIDE repository | PRIDE: PXD024291 |
| Metaproteome data generated in this study | This paper | PRIDE: PXD048255 |
| Software and Algorithms | ||
| Galaxy (UFZ instance) | The Galaxy Community, 202457 | https://galaxy.intranet.ufz.de/ |
| GroEL-proteotyping script v2.0 | This paper | https://doi.org/10.5281/zenodo.13965049 |
| MS-GF + v2023.01.12 | Kim and Pevzner, 201458 | https://github.com/MSGFPlus/msgfplus |
| ProteoWizard v3.0.19046 | Kessner et al., 200859 | https://proteowizard.sourceforge.io/ |
| OpenMS 2.8 | Röst et al., 201660 | https://openms.de/ |
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