PXD021559-2

PXD021559 is an original dataset announced via ProteomeXchange.

Title	DIA-based systems biology approach unveils novel E3-dependent responses to a metabolic shift
Description	Yeast Saccharomyces cerevisiae is a powerful model system for systems-wide biology screens and large-scale proteomics methods. The proteomics community has achieved nearly complete coverage for this organism owing to advances in mass spectrometry. However, it remains challenging to scale the technology for rapid and high-throughput analysis of the yeast proteome to investigate biological pathways on a global scale. Here we describe a systems biology approach employing plate-based sample preparation and rapid, single-run data independent mass spectrometry analysis (DIA). Our approach is straightforward, easy to implement and enables quantitative profiling and comparisons of hundreds of largely covered yeast proteomes in only a few days. We evaluate its capability by characterizing changes in the yeast proteome in response to a variety of stresses commonly used in yeast research, identify distinct responses to each stress, and provide a comprehensive resource of these responses. Using our facile, rapid and robust methodology, we observe many previously characterized stress responses, including carbon source dependent regulation of the GID E3 ligase, an important regulator of cellular metabolism during the switch between gluconeogenic and glycolytic growth conditions. Furthermore, we applied our methodology to search for new regulatory targets of the GID ligase during a metabolic switch. We are able to pinpoint effects of a single deletion or point mutation in the GID complex on the global proteome, and thereby identify and validate novel targets of the GID E3 ligase. Moreover, our approach allowed the identification of targets from multiple cellular pathways that display distinct patterns of regulation.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:15:44.652.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2020-09-18 03:30:26	ID requested
1	2020-11-26 02:44:57	announced
⏵ 2	2024-10-22 05:15:45	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: proteomics, DIA, GID E3 ligase, mass spectrometry, systems biology,yeast, LC-MS/MS

Matthias Mann
contact affiliation	Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.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/2020/11/PXD021559

PRIDE project URI

• PRIDE
  1. PXD021559
     1. Label: PRIDE project
     2. Name: DIA-based systems biology approach unveils novel E3-dependent responses to a metabolic shift