Figure 1.

PROTEOFORMER integrates RIBO-seq and MS data. This schematic overview presents the different steps in the PROTEOFORMER workflow together with the used tools and file formats. The reads produced by a ribosome profiling experiment are first checked for their quality and subsequently mapped to the appropriate genome, using the STAR or TopHat transcriptome mapper and different species-specific annotation sources. Next, a SNP calling and a TIS prediction step are performed in order to accurately delineate the proteoforms. These RIBO-seq-derived proteoforms are then translated and mapped to a public protein database, creating a custom search space for an MS-based proteomics or peptidomics experiment. This protein sequence database created by PROTEOFORMER can then be used as a search space together with the SearchGUI and PeptideShaker tools (see Supplementary Methods S1) to identify proteoforms based on MS/MS spectra. The complete process of transforming RIBO-seq data into a custom search space is available as a stand-alone or Galaxy instance implementation.