MassIVE MSV000094879

Partial Public PXD052614

Chemical crosslinking extends and complements UV crosslinking in analysis of RNA and DNA nucleic acid protein interactions by mass spectrometry

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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. [doi:10.25345/C5TX35J14] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Crosslinking mass spectrometry ; Chemical crosslinking ; DNA ; RNA ; protein-RNA ; protein-DNA ; DDA ; Structural mass spectrometry

Contact

Principal Investigators:
(in alphabetical order) 		Prof. Henning Urlaub, Max Planck Institute for Multidisciplinary Sciences, Germany
Submitting User: LuisaMWelp
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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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