Sequence coverage of SNAP-25. (A) Heat map for the relative LC-MS signal intensities of individual tryptic peptides from SNAP-25B. Biochemically fractionated soluble proteins of superior parietal gyrus from controls (N = 7) and patients with Alzheimer’s disease (N = 9) were immunoprecipitated with SMI81. High resolution LC-MS ion chromatograms of all peptides identified as belonging to SNAP-25B were extracted. An increase of signal intensity is seen as a blue to red shift. (B) Amino acid sequences for SNAP-25B and SNAP-25A. Soluble endogenous forms identified by top-down LC-MS/MS analysis are indicated by arrows above the sequences. Differences between SNAP-25B and SNAP-25A are indicated by boxes. Amino acids belonging to tryptic peptides identified by LC-MS/MS are labeled bold. The two glutamines (Q) indicated “ionic 0 layer” contribute together with a syntaxin glutamine (Q), and a VAMP arginine (R) to the highly conserved 3Q:1R motif at the core of the SNARE complex.