PXD014759 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
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 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD014759
- Label: PRIDE project
- Name: Optimized parameter settings enhance proteome-wide formation of crosslinks on low-abundant proteins