ArticleRNA (New York, N.Y.)2005
Complete MALDI-ToF MS analysis of cross-linked peptide-RNA oligonucleotides derived from nonlabeled UV-irradiated ribonucleoprotein particles.
Article in RNA (New York, N.Y.), 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
16 citing papers in PubMed, 43 citations in OpenAlex.
- Article
- Lithium Hydroxide Hydrolysis Combined with MALDI TOF Mass Spectrometry for Rapid Sphingolipid Detection.Journal of the American Society for Mass Spectrometry · 2021Article
- Hekate: software suite for the mass spectrometric analysis and three-dimensional visualization of cross-linked protein samples.Journal of proteome research · 2013Article
- Analysis of RNA cleavage by MALDI-TOF mass spectrometry.Nucleic acids research · 2013Article
- Selective detection of peptide-oligonucleotide heteroconjugates utilizing capillary HPLC-ICPMS.Journal of the American Society for Mass Spectrometry · 2012Article
- Structural basis for the dual U4 and U4atac snRNA-binding specificity of spliceosomal protein hPrp31.RNA (New York, N.Y.) · 2011Article
- A novel Nop5-sRNA interaction that is required for efficient archaeal box C/D sRNP formation.RNA (New York, N.Y.) · 2010Article
- A bird's-eye view of post-translational modifications in the spliceosome and their roles in spliceosome dynamics.Molecular bioSystems · 2010Article
- Mapping the binding site of snurportin 1 on native U1 snRNP by cross-linking and mass spectrometry.Nucleic acids research · 2010Article
- Sequence analysis of peptide:oligonucleotide heteroconjugates by electron capture dissociation and electron transfer dissociation.Journal of the American Society for Mass Spectrometry · 2010Article
- Collision induced dissociation-based characterization of nucleotide peptides: fragmentation patterns of microcin C7-C51, an antimicrobial peptide produced by Escherichia coli.Journal of the American Society for Mass Spectrometry · 2008Article
- Application of fractional mass for the identification of peptide-oligonucleotide cross-links by mass spectrometry.Journal of mass spectrometry : JMS · 2008Article
- Protein folding by domain V of Escherichia coli 23S rRNA: specificity of RNA-protein interactions.Journal of bacteriology · 2008Article
- Detection of protein-RNA crosslinks by NanoLC-ESI-MS/MS using precursor ion scanning and multiple reaction monitoring (MRM) experiments.Journal of the American Society for Mass Spectrometry · 2007Article
- Improved identification of enriched peptide RNA cross-links from ribonucleoprotein particles (RNPs) by mass spectrometry.Nucleic acids research · 2007Article
- Residues in two homology blocks on the amino side of the tRNase Z His domain contribute unexpectedly to pre-tRNA 3' end processing.RNA (New York, N.Y.) · 2006Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-RNA cross-linking combined with mass spectrometry is a powerful tool to elucidate hitherto non-characterized protein-RNA contacts in ribonucleoprotein particles, as, for example, within spliceosomes. Here, we describe an improved methodology for the sequence analysis of purified peptide-RNA oligonucleotide cross-links that is based solely on MALDI-ToF mass spectrometry. The utility of this methodology is demonstrated on cross-links isolated from UV-irradiated spliceosomal particles; these were (1) [15.5K-61 K-U4 atac] small nuclear ribonucleoprotein (snRNP) particles prepared by reconstitution in vitro, and (2) U1 snRNP particles purified from HeLa cells. We show that the use of 2',4',6'-trihydroxyacetophenone (THAP) as MALDI matrix allows analysis of cross-linked peptide-RNA oligonucleotides in the reflectron mode at high resolution, enabling sufficient accuracy to assign unambiguously cross-linked RNA sequences. Most important, post-source decay (PSD) analysis under these conditions was successfully applied to obtain sequence information about the cross-linked peptide and RNA moieties within a single spectrum, including the identification of the actual cross-linking site. Thus, in U4 atac snRNA we identified His 270 in the spliceosomal U4/U6 snRNP-specific protein 61 K (hPrp31p) cross-linked to U 44; in the U1 snRNP we show that Leu175 of the U1 snRNP-specific 70K protein is cross-linked to U 30 of U1 snRNA. This type of analysis is applicable to any type of RNP complex and may be expected to pave the way for the further analysis of protein-RNA complexes in much lower abundance and/or of cross-links that are obtained in low yield.
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