Using quantitative metabolomics, proteomics, and lipidomics methods to analyze plasma and cerebrospinal fluid (CSF) indicated specific and close association of amino acids (including homocysteine, a non-proteinogenic amino acid) and tryptophan metabolites (kynurenic acid and quinolinic acid) with AD biomarkers: Aβ42, Tau, and phospho-Tau (Thr181). Here, MAPT is linked to Alzheimer disease.