Mass spectra for crosslinks identified in protein multisubunit complexes.

<p>The Clp-protease multisubunit protein complex was crosslinked and the tryptic digest was separated into 192 fractions on the MALDI-target plate. The MS-data were analyzed in FINDX with search restrictions on the isotope doublet peak mass difference accuracy (7 ppm) and intensities (intensity parameter set to 0.22) and matched against >25000 theoretically possible peak masses. Only a few (12) peaks were suggested to be crosslinks, and subjected to MSMS. (A) MS-spectrum showing typical isotope doublet peaks recognized by FINDX. This crosslinked peptide has a theoretical mass MH⁺1886/1898 Da for H12/D12, and corresponds to the crosslink between subunit P₃ peptide I₁₆₉EKDTDR₁₇₅ and subunit R peptide A₁₆₄KEVLANK₁₇₁ and was detected only in 1 out of 192 wells on the MALDI target plate. (B) MSMS-spectrum acquired for crosslink validation. All the fragments containing the crosslinker (AKEx, IEKDx, KDTDRx, EKDTDx) appear as doublet peaks, further confirming the identification.