alexa PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Phylogenetics & Evolutionary Biology

Author(s): Crapp J, Ndah E, Koch A, Steyaert S, Gawron D, , Crapp J, Ndah E, Koch A, Steyaert S, Gawron D,

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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.
This article was published in Nucleic Acids Res and referenced in Journal of Phylogenetics & Evolutionary Biology

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