PXD049340

PXD049340 is an original dataset announced via ProteomeXchange.

Title	mini-Complexome Profiling, an FDR-controlled workflow for global targeted Detection of protein complexes (Hek293 data)
Description	Co-fractionation mass spectrometry experiments (CF-MS) using native-like protein separations such as Blue Native electrophoresis (BNE) or size exclusion chromatography (SEC) enable a global characterization of protein networks, and a better understanding of cellular functions. They do, however, pose significant requirements on sample amounts, on wet lab and on instrument time, which frequently renders statistically useful replication or comparative experiments between multiple biological states non-feasible. Here we present a fast workflow called mini-Complexome Profiling (mCP) for global targeted detection of annotated protein-protein complexes. It comprises mild extraction of complexes, fractionation by BNE and analysis by data independent acquisition mass spectrometry (DIA-MS). Of note, BNE fractionation into 35 fractions is achieved using commercial mini-gels, with minimal requirements on sample amounts. Complexes are detected using a novel, bespoke R package with a controlled false discovery rate (FDR) approach. The tool is available to the community on a Github repository (https://github.com/hugoagno3/mCP ). We first benchmarked our workflow using Hek293 cell lysates as a well established cell line model. We then challenged mCP by investigating changes in the complexome of mouse cardiomyocytes isolated from different heart cavities of single mice. In these challenging and limited samples we detected 48 annotated protein complexes per compartment on average and were able to perform differential inter-cavity comparisons from single animals. These reduced sample and instrument time requirements suggest the suitability of our workflow for complexome screening in sparse samples, e.g. in human patient biopsies.
HostingRepository	PRIDE
AnnounceDate	2024-07-25
AnnouncementXML	Submission_2024-07-25_14:04:49.834.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christof Lenz
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-12 09:49:50	ID requested
⏵ 1	2024-07-25 14:04:50	announced

10.3389/FRANS.2024.1425190;

submitter keyword: Protein Complexes, proteomics, Blue Native electrophoresis, protein-protein interactions, data-independent acquisition, systems biology

Christof Lenz
contact affiliation	Core Facility Proteomics, Department of Clinical Chemistry, University Medical Center Goettingen
contact email	christof.lenz@med.uni-goettingen.de
lab head
Christof Lenz
contact affiliation	Max Planck Institute for Biophysical Chemistry
contact email	christof.lenz@mpibpc.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/2024/07/PXD049340

PRIDE project URI

• PRIDE
  1. PXD049340
     1. Label: PRIDE project
     2. Name: mini-Complexome Profiling, an FDR-controlled workflow for global targeted Detection of protein complexes (Hek293 data)