A ubiquitin and ubiquitin-like protein spectral library.

We have developed and validated a ubiquitin (Ub) and ubiquitin-like protein (Ubl) spectral library, consisting of 467 consensus spectra (320 unique peptides derived from autophagy-related protein 8, F-adjacent transcript 10, interferon-stimulated gene 15 kDa protein, neural precursor cell expressed developmentally down-regulated protein 8, small ubiquitin-related modifiers 1-3 and Ub, and nine of the most commonly observed Ub/Ubl chain linkages). The use of the Ub/Ubl library with a spectral matching tool (SpectraST) yields improved performance over database search engines, and can successfully identify many types of Ub/Ubl chain-derived peptides that cannot be identified by standard database search algorithms.