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PXD010796

PXD010796 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleOptimized cross-linking mass spectrometry for in situ interaction proteomics
Descriptionecent development of mass spectrometer cleavable protein cross-linkers and algorithms for their spectral identification now permits large-scale cross-linking mass spectrometry (XL-MS). Here, we optimized the use of cleavable disuccinimidyl sulfoxide (DSSO) cross-linker for labeling native protein complexes in live human cells. We applied a generalized linear mixture model to calibrate cross-link peptide-spectra matching (CSM) scores to control the sensitivity and specificity of large-scale XL-MS. Using specific CSM score thresholds to control the false discovery rate, we found that higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) can both be effective for large-scale XL-MS protein interaction mapping. We found that the density and coverage of protein-protein interaction maps can be significantly improved through the use of multiple proteases. In addition, the use of sample-specific search databases can be used to improve the specificity of cross-linked peptide spectral matching. Application of this approach to human chromatin labeled in live cells recapitulated known and revealed new protein interactions of nucleosomes and other chromatin-associated complexes in situ. This optimized approach for mapping native protein interactions should be useful for a wide range of biological problems.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:54:53.314.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAlex Kentsis
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListiodoacetamide derivatized residue
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-08-16 03:43:44ID requested
12019-04-03 00:40:05announced
22019-05-16 02:48:29announcedUpdated publication reference for PubMed record(s): 31083951.
32024-10-22 04:54:56announced2024-10-22: Updated project metadata.
Publication List
10.1021/acs.jproteome.9b00085;
Ser Z, Cifani P, Kentsis A, Optimized Cross-Linking Mass Spectrometry for in Situ Interaction Proteomics. J Proteome Res, 18(6):2545-2558(2019) [pubmed]
Keyword List
submitter keyword: Human,Cross-linking Mass Spectrometry, Chromatin
Contact List
Alex Kentsis
contact affiliationMemorial Sloan Kettering Cancer Center
contact emailkentsisresearchgroup@gmail.com
lab head
Alex Kentsis
contact affiliationMemorial Sloan Kettering Cancer Center
contact emailkentsisresearchgroup@gmail.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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