PXD014759

PXD014759 is an original dataset announced via ProteomeXchange.

Title	Optimized parameter settings enhance proteome-wide formation of crosslinks on low-abundant proteins
Description	Studies using crosslinking coupled to mass spectrometry on the proteome-wide level have spurred great interest as they facilitate structural probing of protein interactions in living cells or even organisms. Here we show, by using both an in-vitro mimic of a crowded cellular environment and eukaryotic cell lysates, that current proteome-wide crosslinking protocols have a bias for high abundant proteins. We demonstrate that this bias can be explained by kinetics that govern the formation of a crosslink between two polypeptides. We further show that optimized parameter settings, in particularly an excess of crosslinker, leadto a significant overall increase in the detection of lower abundant proteins within cellular lysates on a proteome-wide scale. Our study therefore explains the cause of a major limitation in current proteome-wide crosslinking studies and demonstrates a way forward how to address a larger part of the proteome by crosslinking
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:58:43.366.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Florian Stengel
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-25 02:57:53	ID requested
1	2020-02-19 08:59:53	announced
⏵ 2	2024-10-22 04:58:51	announced	2024-10-22: Updated project metadata.

F, ü, rsch J, Kammer KM, Kreft SG, Beck M, Stengel F, Proteome-Wide Structural Probing of Low-Abundant Protein Interactions by Cross-Linking Mass Spectrometry. Anal Chem, 92(5):4016-4022(2020) [pubmed]

10.1021/acs.analchem.9b05559;

submitter keyword: Proteome-wide XL-MS, reaction kinetics

Florian Stengel
contact affiliation	University of Konstanz, Biology departement
contact email	florian.stengel@uni-konstanz.de
lab head
Florian Stengel
contact affiliation	Universität Konstanz
contact email	florian.stengel@uni-konstanz.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/2020/02/PXD014759

PRIDE project URI

• PRIDE
  1. PXD014759
     1. Label: PRIDE project
     2. Name: Optimized parameter settings enhance proteome-wide formation of crosslinks on low-abundant proteins