PXD018033

PXD018033 is an original dataset announced via ProteomeXchange.

Title	System-wide profiling of protein-complexes via size exclusion chromatography– mass spectrometry (SEC-MS)
Description	In living cells most proteins are organized in stable or transient functional assemblies known as protein complexes, which control a multitude of vital cellular processes such as cell cycle progression, metabolism, and signal transduction. System-wide workflows for analysis of protein complexes using mass spectrometry based proteomics consists of a biochemical fractionation methods which take advantage of biophysical features such as charge or mass of protein complexes. In this project, we apply size exclusion chromatography to investigate protein assemblies from a Jurkat whole cell lysate. We introduced a fast and robust in-plate sample preparation workflow which allows for replicates to be performed with fewer technical hurdles and with a high degree of reproducibility) We acquired the data in SWATH-mode in combination with a high-throughput LC-system (EVOSEP one). The bioinformatics pipeline builds on the OpenSWATH workflow combined with CCprofiler, a tool for statistical scoring of protein co-elution profiles. This method enabled us to identify more than 100 protein complexes from mammalian cells within one day of measurement.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:37:18.686.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fabian Frommelt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-13 00:59:50	ID requested
1	2022-05-30 08:06:58	announced
2	2023-11-14 08:50:51	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:37:19	announced	2024-10-22: Updated project metadata.

10.1007/978-1-0716-1178-4_18;

submitter keyword: protein complex analysis,SEC-MS, protein co-elution profiling

, Ruedi Aebersold
contact affiliation	Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Switzerland.
contact email	aebersold@imsb.biol.ethz.ch
lab head
Fabian Frommelt
contact affiliation	ETH Zurich
contact email	frommelt@imsb.biol.ethz.ch
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/2022/05/PXD018033

PRIDE project URI

• PRIDE
  1. PXD018033
     1. Label: PRIDE project
     2. Name: System-wide profiling of protein-complexes via size exclusion chromatography– mass spectrometry (SEC-MS)