Figure 1: Deep coverage of human brain proteome in Alzheimer’s and Parkinson’s Disease.

(a) TMT workflow. There were 40 tissue samples in both frontal cortex and anterior cingulate gyrus brain regions, which were TMT labeled across 5 individual batches per region. A total of 8 individual samples were labeled in every batch, 2 AD samples were dedicated to channels 127C and 127 N, 2 control samples were dedicated to channels 128C and 128 N, 2 PD samples were dedicated to channels 129C and 129 N, and 2 AD/PD samples were dedicated to channels 130C and 130 N. We also dedicated two TMT channels (126 and 131) to pooled global internal standards (GIS). After labeling, the samples were combined and fractionated by off-line ERLIC (n=21 total). Each fraction was analyzed and quantified by SPS-MS3 on an Orbitrap Fusion mass spectrometer. (b) There were 10 100 and 10 795 protein groups identified from frontal cortex and anterior cingulate gyrus, respectively, with 8,955 overlapping protein groups. Collectively, a total of 11 840 protein groups were identified across both brain regions. (c) Overlapping histogram comparing the degree of protein coverage for the highest and lowest expressed brain transcripts according to RNA-seq TPM bins. The open bar represents the distribution of protein coding gene numbers detected by RNA-seq, and the blue bar indicates the distribution of protein coding genes sequenced in this proteomic dataset. (d) Overlap between the proteome and RNA-seq data using identified gene symbols. This proteomic dataset covers ~58% of all detectable genes in the Human Brain Atlas RNA-seq dataset and 65% of highly expressed transcripts when considering RNA-seq TPM values above 1.