Characterization of the E. coli proteome and its modifications during growth and ethanol stress.

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To this end, we generated a comprehensive dataset monitoring the changes in protein expression, copy number, and post translational modifications in a systematic fashion during growth and ethanol stress in E. coli. We utilized high-resolution mass spectrometry (MS) combined with the Super-SILAC approach. In a single experiment, we have identified over 2300 proteins, which represent approximately 88% of the estimated expressed proteome of E. coli and estimated protein copy numbers using the Intensity Based Absolute Quantitation (iBAQ). The dynamic range of protein expression spanned up to six orders of magnitude, with the highest protein copy per cell estimated at approximately 300,000. We focused on the proteome dynamics involved during stationary phase growth. A global up-regulation of proteins related to stress response was detected in later stages of growth. We observed the down-regulation of the methyl directed mismatch repair system containing MutS and MutL of E. coli growing in long term growth cultures, confirming that higher incidence of mutations presents an important mechanism in the increase in genetic diversity and stationary phase survival in E. coli. During ethanol stress, known markers such as alcohol dehydrogenase and aldehyde dehydrogenase were induced, further validating the dataset. Finally, we performed unbiased protein modification detection and revealed changes of many known and unknown protein modifications in both experimental conditions. Data are available via ProteomeXchange with identifier PXD001648.", "claims": [{"id": "claim-method", "statement": "To test whether specific annotation terms are enriched or depleted within a set of proteins of interest we applied Fisher's exact test using the theoretical E. coli proteome as background. 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Derived p-values were further adjusted to address multiple hypothesis testing using the method proposed by Benjamini and Hochberg (1995)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001648.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25741329", "locator": "sections[25] \"ack\" paragraph 1", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001648."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using high-resolution mass spectrometry with Super-SILAC and iBAQ, the study identified over 2300 E. coli proteins—approximately 88% of the estimated expressed proteome—and made the source data available through ProteomeXchange under identifier PXD001648.", "kind": "quantitative", "target": {"value": 88.0, "unit": "per cent", "tolerance": null, "source": "In a single experiment, we have identified over 2300 proteins, which represent approximately 88% of the estimated expressed proteome of E. coli and estimated protein copy numbers using the Intensity Based Absolute Quantitation (iBAQ)."}, "evidence": [{"asset": "source:pmid:25741329", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In a single experiment, we have identified over 2300 proteins, which represent approximately 88% of the estimated expressed proteome of E. coli and estimated protein copy numbers using the Intensity Based Absolute Quantitation (iBAQ)."}, {"asset": "source:pmid:25741329", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD001648."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using high-resolution mass spectrometry with Super-SILAC and iBAQ, the study identified over 2300 E. coli proteins—approximately 88% of the estimated expressed proteome—and made the source data available through ProteomeXchange under identifier PXD001648.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:25741329"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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