Viewing proteomics data in a genome browser

Once we have mass spectrometer data and have identified the peptides and proteins the spectra describe using search engine software such as Xtandem, MSGF+, or Mascot, we may want to look at those in their genomic context alongside other important data. In this recipe, we'll look at how to extract peptides and the Uniprot IDs from a search file, find the genes those Uniprot IDs map to, and then create a genome browser track showing those genes. These can be sent to the UCSC human genome browser, and the interactive web page, which will be loaded in your local browser automatically.

Getting ready

For this recipe, you'll need the Bioconductor packages MSnID, EnsDB.Hsapiens...