repository of small ORFs identified by ribosome profiling

This section provides a summary on the acquisition and processing of the data. For more detailed information, feel free to consult the available literature. Use the navigation bar on the left to navigate trough the different steps.

10. PRIDE reprocessing

Mass spectrometry evidence provides proof of translation of sORFs into micropeptides. The PRIDE-ReSpin pipeline automatically rescan the PRIDE10 (proteomics data repository) database. Top-Down MS based datasets are downloaded from the PRIDE database, next, the parameters are extracted by analyzing the identified peptides and reconstructing the initial parameters. Using these parameters and searchGUI, the X! Tandem and MS-GF+ search engines are used to identify peptides. The database used for the search is a concatenation of the functional proteome with all its isoforms donwloaded from UniProt, the cRAP database containing frequent contaminants, and the translated sORF database. Finally, PeptideShaker is used to analyze and export identified peptides that originate solely from sORF micropeptides. The identified spectra can be manualy inspected on using the Lorikeet MS/MS spectrum viewer.