PXD017258-1
PXD017258 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | From coarse to fine: The absolute Escherichia coli proteome under diverse growth conditions |
Description | Accurate measurements of cellular protein concentrations are invaluable to quantitative studies of gene expression and physiology in living cells. Here, we developed a versatile mass spectrometric workflow based on data-independent acquisition proteomics (DIA/SWATH) together with a novel protein inference algorithm (xTop). We used this workflow to accurately quantify absolute protein abundances in E. coli for >2000 proteins over >60 growth conditions, including nutrient limitations, non-metabolic stresses and non-planktonic states. The resulting high-quality dataset of protein mass fractions allowed us to characterize proteome responses from a coarse (groups of related proteins) to a fine (individual) protein level. Hereby, a plethora of novel biological findings could be elucidated, including the generic upregulation of low-abundant proteins under various metabolic limitations, the non-specificity of catabolic enzymes upregulated under carbon limitation, the lack of large-scale proteome reallocation under stress compared to nutrient limitations, as well as surprising strain-dependent effects important for biofilm formation. These results present valuable resources for the systems biology community and can be used for future multi-omics studies of gene regulation and metabolic control in E. coli. |
HostingRepository | PanoramaPublic |
AnnounceDate | 2022-01-12 |
AnnouncementXML | Submission_2022-01-12_12:08:34.867.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Christina Ludwig |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | Label:13C(6)15N(2); Label:13C(6)15N(4) |
Instrument | TripleTOF 5600 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2020-01-22 16:04:21 | ID requested | |
⏵ 1 | 2022-01-12 12:08:35 | announced |
Publication List
Mori M, Zhang Z, Banaei-Esfahani A, Lalanne JB, Okano H, Collins BC, Schmidt A, Schubert OT, Lee DS, Li GW, Aebersold R, Hwa T, Ludwig C, From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions. Mol Syst Biol, 17(5):e9536(2021) [pubmed] |
Keyword List
submitter keyword: Escherichia coli, absolute protein quantification, AQUA, xTop, DIA, SWATH, targeted proteomics |
Contact List
Christina Ludwig | |
---|---|
contact affiliation | Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany |
contact email | tina.ludwig@tum.de |
lab head | |
Christina Ludwig | |
contact affiliation | Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany |
contact email | tina.ludwig@tum.de |
dataset submitter |
Full Dataset Link List
Panorama Public dataset URI |