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

Matteo Mori, Zhongge Zhang, Amir Banaei‐Esfahani, Jean‐Benoît Lalanne, Hiroyuki Okano, Ben C Collins, Alexander Schmidt, Olga T Schubert, Deok‐Sun Lee, Gene‐Wei Li, Ruedi Aebersold, Terence Hwa, Christina Ludwig

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)
95 Downloads (Pure)


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 Escherichia coli for > 2,000 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.
Original languageEnglish
Article numbere9536
JournalMolecular systems biology
Issue number5
Publication statusPublished - 01 May 2021


Dive into the research topics of 'From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions'. Together they form a unique fingerprint.

Cite this