PXD052614-1

PXD052614 is an original dataset announced via ProteomeXchange.

Title	Chemical crosslinking extends and complements UV crosslinking in analysis of RNA and DNA nucleic acid protein interactions by mass spectrometry
Description	UV (ultra violet) crosslinking with mass spectrometry (XL MS) has been established for identifying RNA and DNA binding proteins along with their domains and amino acids involved. Here, we explore chemical XL MS, for RNA protein, DNA protein and nucleotide protein complexes in vitro and in vivo. We also introduce a novel nucleotide protein crosslink search engine, NuXL, for fast and robust identification of such crosslinks at amino-acid resolution. Chemical XL MS complements and extends UV XL MS by generating different crosslink species. The added spatial information facilitates integrative structural modelling of nucleic acid protein complexes. In vivo UV and chemical XL MS data from E. coli cells analysed by NuXL establish a comprehensive nucleic acid protein crosslink inventory at amino acid level. RNA crosslinks cover most RNA binding proteins DNA and RNA crosslinks are found in transcriptional repressors and activators. Our workflow adds spatial information to the RNA binding properties of enzymes, for which crosslinking sites are often observed close to their cofactor binding domains.
HostingRepository	MassIVE
AnnounceDate	2025-08-22
AnnouncementXML	Submission_2025-08-22_01:39:59.099.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Luisa Welp
SpeciesList	scientific name: Escherichia coli; common name: E. coli; NCBI TaxID: 562; scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae; common name: baker's yeast; NCBI TaxID: 4932;
ModificationList	Acetyl; L-methionine sulfoxide
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-28 00:31:29	ID requested
⏵ 1	2025-08-22 01:39:59	announced

no publication

submitter keyword: Crosslinking mass spectrometry, Chemical crosslinking, DNA, RNA, protein-RNA, protein-DNA, DDA, Structural mass spectrometry

Prof. Henning Urlaub
contact affiliation	Max Planck Institute for Multidisciplinary Sciences
contact email	henning.urlaub@mpinat.mpg.de
lab head
Luisa Welp
contact affiliation	Max Planck Institute for Multidisciplinary Sciences
contact email	luisa.welp@mpinat.mpg.de
dataset submitter

MassIVE dataset URI

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