Additional file 3 of Heparin-enriched plasma proteome is significantly altered in Alzheimer’s disease
Creators: name: Guo, Qi
name: Ping, Lingyan
name: Dammer, Eric B.
name: Duong, Duc M.
name: Yin, Luming
name: Xu, Kaiming
name: Shantaraman, Anantharaman
name: Fox, Edward J.
name: Golde, Todd E
name: Johnson, Erik C.B.
name: Roberts, Blaine R.
name: Lah, James J.
name: Levey, Allan I.
name: Seyfried, Nicholas T.
Publisher: name: figshare
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified
subject: Developmental Biology
subject: Mental Health
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 3: Supplemental Figure 3. Comparison of immunodepleted and heparin-enriched plasma proteomes. A) The Set 1 (control = 18, AD = 18) underwent top 14 removal and the same TMT-MS analysis as performed on the Hp-enriched Set 1. B) The volcano plot illustrates the differential abundance of 1,129 proteins between the control and AD groups. The x-axis represents the log2 fold-change (AD vs CTL), while the y-axis represents the Student’s t-statistic (-log10 p-value) calculated for all proteins in the pairwise comparison. Proteins significantly increased in AD (N = 432) are highlighted in red (p &lt; 0.05), whereas those significantly decreased in AD (N = 383) are depicted in blue. Grey dots represent proteins with insignificant changes. C) The number and overlap of proteins quantified in the top 14 (N = 1,129) and Hp-enriched (N = 2,077) datasets with less than 50% missing values are shown. There are 1,273 proteins only detected by heparin enrichment, while the top 14 method identifies only 325 specific proteins. D) The volcano plot illustrates the differential abundance of 1,273 proteins (AD vs Control) uniquely identified in the Hp-enriched dataset. The x-axis represents the log2 fold-change (AD vs CTL), while the y-axis represents the Student’s t-statistic (-log10 p-value) calculated for all proteins in the pairwise comparison. Proteins significantly increased in AD (N = 339) are highlighted in red (p &lt; 0.05), whereas those significantly decreased in AD (N = 409) are depicted in blue. Grey dots represent proteins with insignificant changes. E) A scatter plot shows the Pearson correlation between log2 fold-change (AD vs CTL) of significantly altered proteins in both the top 14 and Hp-enriched datasets. There are 380 proteins overlapping between the two sets, showing significant changes in AD with a BH FDR-corrected p-value&lt; 0.05 in both datasets. Only 5 out of 380 proteins exhibited discordant changes in AD vs Control, demonstrating a high degree of concordance (cor = 0.93, p &lt; 2.2e-166). All 215 overlapping proteins selected with a BH FDR-corrected p-value &lt; 0.01 displayed consistent changes in both datasets when comparing AD and control samples, with a remarkable correlation of 0.96 (p &lt; 1e-119). The significance of the Pearson correlation was determined by Student’s t-test. CTL, control; cor, Pearson correlation coefficient.