PXD014948-2

PXD014948 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 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.
HostingRepository	PRIDE
AnnounceDate	2021-04-29
AnnouncementXML	Submission_2021-04-29_08:32:01.082.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christina Ludwig
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-08 03:37:06	ID requested
1	2021-03-11 07:04:36	announced
⏵ 2	2021-04-29 08:32:01	announced	2021-04-29: Updated project metadata.
3	2022-02-14 01:59:52	announced	2022-02-14: Updated project metadata.
4	2024-10-22 05:20:00	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: absolute protein quantification, protein sectors, SWATH, correlation to ribosome profiling, spectral library,DIA, peptide query parameters, protein inference

Chrisitina Ludwig
contact affiliation	Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS) Technical University Munich Gregor-Mendel-Straße 4 85354 Freising GERMANY
contact email	tina.ludwig@tum.de
lab head
Christina Ludwig
contact affiliation	TU Munich
contact email	tina.ludwig@tum.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/03/PXD014948

PRIDE project URI

• PRIDE
  1. PXD014948
     1. Label: PRIDE project
     2. Name: From coarse to fine: The absolute Escherichia coli proteome under diverse growth conditions