PXD017258

PXD017258 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-22 16:04:21	ID requested
⏵ 1	2022-01-12 12:08:35	announced

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]

submitter keyword: Escherichia coli, absolute protein quantification, AQUA, xTop, DIA, SWATH, targeted proteomics

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

Panorama Public dataset URI