PXD010796

PXD010796 is an original dataset announced via ProteomeXchange.

Title	Optimized cross-linking mass spectrometry for in situ interaction proteomics
Description	ecent 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:54:53.314.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alex Kentsis
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2018-08-16 03:43:44	ID requested
1	2019-04-03 00:40:05	announced
2	2019-05-16 02:48:29	announced	Updated publication reference for PubMed record(s): 31083951.
⏵ 3	2024-10-22 04:54:56	announced	2024-10-22: Updated project metadata.

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]

submitter keyword: Human,Cross-linking Mass Spectrometry, Chromatin

Alex Kentsis
contact affiliation	Memorial Sloan Kettering Cancer Center
contact email	kentsisresearchgroup@gmail.com
lab head
Alex Kentsis
contact affiliation	Memorial Sloan Kettering Cancer Center
contact email	kentsisresearchgroup@gmail.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/2019/04/PXD010796

PRIDE project URI

• PRIDE
  1. PXD010796
     1. Label: PRIDE project
     2. Name: Optimized cross-linking mass spectrometry for in situ interaction proteomics