Crappé et al. 2014 (PRJNA251587)

General Details

Title PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration
Organism
Number of Samples 2
Release Date 2014/06/04 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP042937
ENA SRP042937
GEO GSE58207
BioProject PRJNA251587

Publication

Title
Authors Crappé J, Ndah E, Koch A, Steyaert S, Gawron D, De Keulenaer S, De Meester E, De Meyer T, Van Criekinge W, Van Damme P, Menschaert G
Journal Nucleic acids research
Publication Date 2015 Mar 11
Abstract An increasing amount of studies integrate mRNA sequencing data into MS-based proteomics to complement the translation product search space. However, several factors, including extensive regulation of mRNA translation and the need for three- or six-frame-translation, impede the use of mRNA-seq data for the construction of a protein sequence search database. With that in mind, we developed the PROTEOFORMER tool that automatically processes data of the recently developed ribosome profiling method (sequencing of ribosome-protected mRNA fragments), resulting in genome-wide visualization of ribosome occupancy. Our tool also includes a translation initiation site calling algorithm allowing the delineation of the open reading frames (ORFs) of all translation products. A complete protein synthesis-based sequence database can thus be compiled for mass spectrometry-based identification. This approach increases the overall protein identification rates with 3% and 11% (improved and new identifications) for human and mouse, respectively, and enables proteome-wide detection of 5'-extended proteoforms, upstream ORF translation and near-cognate translation start sites. The PROTEOFORMER tool is available as a stand-alone pipeline and has been implemented in the galaxy framework for ease of use. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
PMC PMC4357689
PMID 25510491
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR1333393 PRJNA251587 Homo sapiens HCT116 Ribo-Seq Cycloheximide
SRR1333394 PRJNA251587 Homo sapiens HCT116 Ribo-Seq Lactimidomycin
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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