Proteomics

Dataset Information

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From coarse to fine: The absolute Escherichia coli proteome under diverse growth conditions


ABSTRACT: 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 larg e-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.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Escherichia Coli

SUBMITTER: Christina Ludwig  

LAB HEAD: Chrisitina Ludwig

PROVIDER: PXD014948 | Pride | 2021-03-11

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
Ecoli_DDA_search_results.zip Other
Ecoli_PQP_library_formats.zip Other
Ecoli_SWATH_quant_results.zip Other
chludwig_K150203_001_IDA_ecoli_1243_1.wiff Wiff
chludwig_K150203_001_IDA_ecoli_1243_1.wiff.scan Wiff
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