(A) Bis-Tris 4%–12% denaturing gel, stained with Colloidal Blue, enables separation of proteins before (−) and after (+) cross-linking revealed six new bands, A-F. The absence of Sem1 in this analysis is attributed to its low molecular mass and is consistent with other analyses [
(B) A MALDI-TOF/TOF spectrum of trypsin digestion of band D. Three proteins were identified within this band: Rpn3 (yellow), Rpn5 (cyan), and Rpn8 (pink). Peaks labeled by asterisks were sequenced in order to identify the peptide unambiguously. The inset shows a low-energy collision-induced dissociation of an Rpn5 peptide producing mainly C-terminal (y) sequence ions.