PXD035032

PXD035032 is an original dataset announced via ProteomeXchange.

Title	Multiplexed interactome analysis reveals the molecular architecture of the human prefoldin network
Description	The majority of proteins are organized in protein complexes. Protein complexes represent an important cellular organizational layer, which regulate and catalyze most of the cellular processes. Within the field of proteomics several techniques such as Affinity Purification (AP) and co-fractionation (co-Frac) coupled to mass spectrometry (MS) were developed in order to study protein complexes. Our approach, deep interactome profiling coupled to MS (DIP-MS), is a combination of the benefits of these approaches by combining the selectivity of AP-MS together with a blue native-page size-based fractionation, in order to deconvolute the co-purified complexes, in which the bait is a constitutive subunit. To ensure high-quality quantitation along the fractionation gradient, and to keep data acquisition time limited, we developed a high-throughput (HT) sample preparation method and high-throughput data independent acquisition (DIA) method, enabling us to acquire almost one co-Frac gradient per day. Additionally, a tailored machine learning approach was devised – protein-protein interaction prophet (PPIprophet) which enabled the scoring of the co-elution proteins to retrieve PPIs respectively protein complexes. The method was employed to depict the complex modularity within the prefoldin and prefoldin-like protein complexes, allowing us to I) describe protein complex isoforms, II) derive stoichiometries and abundance distributions of co-purified complexes and III) identify reported and new client proteins and client complexes of the PAQosome, a multi-subunit co-chaperone complex, necessary for the stabilization and formation of multiple complexes such as the RNA polymerases (RNA Pol I, RNA Pol II, RNA Pol III). This study thereby demonstrates the applicability of our method and shows it strength and sensitivity by depicting the prefoldin complexes within only a single experiment.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:32:55.347.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	Q Exactive HF; LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-30 07:22:54	ID requested
1	2024-03-11 14:22:59	announced
⏵ 2	2024-10-22 06:32:55	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: co-fractionation based profiling, DIA, Affinity purification coupled to Mass Spectrometry, size-based fractionation,Protein complexes

Matthias Gstaiger
contact affiliation	Inst. f. Molekulare Systembiologie Otto-​Stern-Weg 3 8093 Zürich Switzerland
contact email	matthias.gstaiger@imsb.biol.ethz.ch
lab head
Fabian Frommelt
contact affiliation	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
contact email	fabian.frommelt@hotmail.com
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/2024/03/PXD035032

PRIDE project URI

• PRIDE
  1. PXD035032
     1. Label: PRIDE project
     2. Name: Multiplexed interactome analysis reveals the molecular architecture of the human prefoldin network