This proteogenomic approach, coupled with the increased depth of proteome coverage and superior quantitation afforded by our TMT pipeline compared to our previous LFQ approach, allowed us to identify and quantify a number of alternative exon-exon splicing events in brain at the protein level, including alternative exon-exon junctions in AD risk factor proteins such as BIN1, PICALM, PTK2B, and FERMT2. Here, PICALM is linked to Alzheimer disease.