Additional file 2 of Targeted mass spectrometry to quantify brain-derived cerebrospinal fluid biomarkers in Alzheimer’s disease
Creators: name: Maotian Zhou
name: Haque, Rafi U.
name: Dammer, Eric B.
name: Duong, Duc M.
name: Lingyan Ping
name: Johnson, Erik C. B.
name: Lah, James J.
name: Levey, Allan I.
name: Seyfried, Nicholas T.
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Neuroscience
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: FOS: Health sciences

description: Additional file 2: Figure S1. Overview of PRM targeted experiment. (A) Schematic of the workflow of the targeted PRM analyses of the replication cohort. Samples (n = 98 total) including 37 AD, 20 Controls, 31 non-AD dementia cases, and 10 pooled global internal standards (GIS) were randomized (e.g. diagnosis, age and sex) into four batches. (B) The raw and normalized peak areas (based on intensities) of reference peptides LASVSVSR, LASVSVSR, YVYVADVAAK, YVYVADVAAK, VVGGLVALR, VVGGLVALR, LLSLGAGEFK, and LLSLGAGEFK (heavy amino acids were labeled with underline) across the first and second injection of 98 samples (including 10 GIS samples). (C) The left panel shows the histogram for the coefficient of variation (CV) of all peptides quantified across the 10 GIS samples before normalization with an average coefficient of variation of 44%. The middle panel showing the coefficient of variation of all peptides quantification across 10 GIS samples after normalization with an average coefficient of variation of 27%. The right panel shows the coefficient of variation of 41 proteins quantified across 10 GIS samples after normalization with an average coefficient of variation is 25%. Figure S2. Label free versus isotope dilution peptide quantification. (A) The Pearson correlation with p value of normalized peak area based on with light/heavy peptide ratio of a (A) MAPT peptide SGYSSPGSPGTPGSR, (B) YWHAZ peptide, SVTEQGAELSNEER, (C) SPP1 peptide, AIPVAQDLNAPSDWDSR, (D) SPP1 peptide GDSVVYGLR, (E) VGF peptide, AYQGVAAPFPK, (F) VGF peptide NSEPQDEGELFQGVDPR and (G) STMN1 peptide SHEAEVLK. The X-axis showing the ratio of light peptide peak area divided with heavy peptide peak area, the Y-axis showing the label free measurement for the light peptide normalized peak area. Figure S3. Proteins reflect changes in neuronal/synaptic, glia/inflammation, myelin and metabolic group signatures in brain. The quantification showed significantly different levels in patients with early stage dementia due to AD (n = 37) from other non-AD neurological disease (n = 31) and age- and sex- matched normal controls (n = 20). YWHAZ, UCHL1, SYN1, MAP1B, STMN1, YWHAB, BASP1, GDA, GAP43, PACSIN1, and MAP2 proteins overlap with the neuronal/synaptic panel in brain (A). MAPT, SMOC1, ITGAM, CHI3L1, CHIT1, and YWHAE proteins overlap with the glia/inflammation panel in brain (B). SPP1, NEFL, NEFM, and SOD1 proteins overlap with the myelin panel in brain (C). And FABP3, ALDOA, PKM, and YWHAG proteins overlap with the metabolic panel in brain (D). The results are shown as the mean ± S.D. ***, ANOVA-p