Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins

The Long and Short of MicroRNA

(2013) Luke A. Yates et al.   CELL

Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae

(2013) D. M. Klass et al.   GENOME RESEARCH

Dogma Derailed: The Many Influences of RNA on the Genome

(2013) Leah R. Sabin et al.   MOLECULAR CELL

System-wide identification of RNA-binding proteins by interactome capture

(2013) Alfredo Castello et al.   Nature Protocols

Structure and function of long noncoding RNAs in epigenetic regulation

(2013) Tim R Mercer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Architecture of the Spliceosome

(2012) Clarisse van der Feltz et al.   BIOCHEMISTRY

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

Crystal structure of Cwc2 reveals a novel architecture of a multipartite RNA-binding protein

(2012) Jana Schmitzová et al.   EMBO JOURNAL

The Prp8 RNase H-like domain inhibits Brr2-mediated U4/U6 snRNA unwinding by blocking Brr2 loading onto the U4 snRNA

(2012) S. Mozaffari-Jovin et al.   GENES & DEVELOPMENT

A Systematic Investigation into the Nature of Tryptic HCD Spectra

(2012) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

Investigation of protein–RNA interactions by mass spectrometry—Techniques and applications

(2012) Carla Schmidt et al.   Journal of Proteomics

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

Structural characterization of a eukaryotic chaperone—the ribosome-associated complex

(2012) Christoph Leidig et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Global analysis of yeast mRNPs

(2012) Sarah F Mitchell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Targeted Mass Spectrometric Approach for Biomarker Discovery and Validation with Nonglycosylated Tryptic Peptides from N-linked Glycoproteins in Human Plasma

(2011) Ju Yeon Lee et al.   MOLECULAR & CELLULAR PROTEOMICS

Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF

(2011) Cameron D. Mackereth et al.   NATURE

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

The Structure of the Eukaryotic Ribosome at 3.0 A Resolution

(2011) A. Ben-Shem et al.   SCIENCE

A Cytoplasmic Complex Mediates Specific mRNA Recognition and Localization in Yeast

(2011) Marisa Müller et al.   PLOS BIOLOGY

Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1

(2011) Tyler J. Creamer et al.   PLoS Genetics

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Mass-spectrometric analysis of proteins cross-linked to 4-thio-uracil- and 5-bromo-uracil-substituted RNA

(2010) Katharina Kramer et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

Mapping the binding site of snurportin 1 on native U1 snRNP by cross-linking and mass spectrometry

(2010) E. Kuhn-Holsken et al.   NUCLEIC ACIDS RESEARCH

A novel Nop5-sRNA interaction that is required for efficient archaeal box C/D sRNP formation

(2010) H. Ghalei et al.   RNA

TOPPView: An Open-Source Viewer for Mass Spectrometry Data

(2009) Marc Sturm et al.   JOURNAL OF PROTEOME RESEARCH

A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs

(2009) D. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OpenMS – An open-source software framework for mass spectrometry

(2008) Marc Sturm et al.   BMC BIOINFORMATICS

RNA-binding proteins and post-transcriptional gene regulation

(2008) Tina Glisovic et al.   FEBS LETTERS

Application of fractional mass for the identification of peptide-oligonucleotide cross-links by mass spectrometry

(2008) Soheil Pourshahian et al.   JOURNAL OF MASS SPECTROMETRY

Structural and Functional Analysis of the E. coli NusB-S10 Transcription Antitermination Complex

(2008) Xiao Luo et al.   MOLECULAR CELL

Isolation of an active step I spliceosome and composition of its RNP core

(2008) Sergey Bessonov et al.   NATURE

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY