Supplementary Figure 1

Raw peptide quantities from all brain regions and batch density. The top panel of box plots shows the distribution of log2 peptide
abundances for each individual in each brain region. The bottom panel of density plots shows the distribution of log2 peptide
abundances by batch in each brain region.

Supplementary Figure 2

Peptide quantities and batch density following MD Normalization. The top panel of box plots shows the distribution of log2 peptide
abundances after MD normalization for each individual in each brain region. The bottom panel of density plots shows the distribution
of log2 peptide abundances after MD normalization by batch in each brain region.

Supplementary Figure 3

Plot of first two principal component scores of the SMTG data set after controlling for batch factor. The scores are colored by
biological replicate, donor age, experimental batch and condition group factors. Confidence ellipses are shown for cofactors of
interest.

Supplementary Figure 4

Principal variance component analysis (PVCA) of protein group abundance from the SMTG samples. Estimated contribution of
proportional variance by age, batch condition, and sex effects are shown. The confounding batch cofactor present in unadjusted
data set (A) is “regressed out” using a simple linear regression model (B) prior to hypothesis testing. 

Supplementary Figure 5

Known Alzheimer’s disease proteins shown in a Kegg pathway.  Proteins quantified in the SMTG experiments map to protein
groups highlighted in red on pathway hsa05010.