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PXD014759

PXD014759 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleOptimized parameter settings enhance proteome-wide formation of crosslinks on low-abundant proteins
DescriptionStudies 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
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:58:43.366.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterFlorian Stengel
SpeciesList scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListiodoacetamide derivatized residue
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-07-25 02:57:53ID requested
12020-02-19 08:59:53announced
22024-10-22 04:58:51announced2024-10-22: Updated project metadata.
Publication List
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;
Keyword List
submitter keyword: Proteome-wide XL-MS, reaction kinetics
Contact List
Florian Stengel
contact affiliationUniversity of Konstanz, Biology departement
contact emailflorian.stengel@uni-konstanz.de
lab head
Florian Stengel
contact affiliationUniversität Konstanz
contact emailflorian.stengel@uni-konstanz.de
dataset submitter
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Dataset FTP location
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PRIDE project URI
Repository Record List
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