PXD014948-1

PXD014948 is an original dataset announced via ProteomeXchange.

Title	Data independent acquisition-based proteomics reveals a multi-scale picture of proteome regulation in Escherichia coli
Description	The study of gene expression is fundamental to systems biology, and reproducible and accurate measurements of relative and absolute protein concentrations are increasingly required for computational modelling and network-based analyses. In this work, we generated a library resource of peptide query parameters (PQPs) for the selective and reproducible quantitation of 2770 E. coli proteins, which we applied to quantify the absolute abundance of the proteome of E. coli across a broad spectrum of growth conditions using data-independent acquisition (DIA)-based SWATH mass spectrometry. A comparison of the obtained label-free peptide intensities with previously published protein synthesis rates measured by ribosome profiling allowed us to establish an optimized quantitative protein inference algorithm, termed xTop, and to determine protein mass fractions for thousands of E. coli proteins with concentrations as low as 50 copies per cell. We applied this workflow, which requires minimal investment in terms of sample amount and mass spectrometric measurement time (1 hour per sample), to study carbon and nitrogen starvation, translational limitation, as well as a variety of nutrient sources, growth conditions and stresses. This analysis allowed us to explore the hierarchical nature of regulation of the E. coli proteome across different scales: from “sectors” of proteins with similar response to nutritional or translational stresses, to clusters of proteins whose expression is strongly correlated across conditions, down to the detailed behaviour of individual proteins. In particular, we unveiled two large clusters of proteins associated to protein synthesis and general stress response.
HostingRepository	PRIDE
AnnounceDate	2021-03-11
AnnouncementXML	Submission_2021-03-11_07:04:36.514.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: DIA, SWATH, spectral library, peptide query parameters, absolute protein quantification, protein inference, correlation to ribosome profiling, protein sectors

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: Data independent acquisition-based proteomics reveals a multi-scale picture of proteome regulation in Escherichia coli