Informatics of protein and posttranslational modification detection via shotgun proteomics

Frequently, proteomic LC-MS/MS data may contain sets of modifications that evade identification during standard database search. For many laboratories, the standard technique to seek posttranslational modifications (PTMs) adds a short list of specified mass shifts to database search configuration. This technique provides information for only the specified PTMs, takes substantial time to run, and drives false discoveries upward through an exponential expansion of search space. This protocol describes a more structured approach to blind PTM discovery through reducing protein lists, targeting attention to a data-driven list of mass shifts, and seeking the resulting short list of modifications through targeted search.