Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer's disease

• Type of Material: Article
• Authors: Lingyan Ping, Emory University; Sean R. Kundinger, Emory University; Duc M. Duong, Emory University; Luming Yin, Emory University; Marla Gearing, Emory University; James Lah, Emory University; Allan Levey, Emory University; Nicholas Seyfried, Emory University
• Language: English
• Date: 2020-09-28
• Publisher: NATURE RESEARCH
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2020
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1038/s41597-020-00650-8
• Title of Journal or Parent Work: SCIENTIFIC DATA
• Volume: 7
• Issue: 1
• Start Page: 315
• End Page: 315
• Grant/Funding Information: We are grateful to the patients and families that donate tissue samples to the Emory University brain bank and for their contributions to this study. Support for this research was provided by funding from the National Institute on Aging (R01AG053960, R01AG061800, RF1AG057471, RF1AG057470, R01AG057339, RF1AG062181), the Accelerating Medicine Partnership for AD (U01AG046161 and U01AG061357) and the Emory Alzheimer’s Disease Research Center (P50AG025688).
• Keywords: NETWORKS; PATHWAYS; Multidisciplinary Sciences; AMYLOID-BETA; Science & Technology - Other Topics; Science & Technology; TAU; PHOSPHORYLATION; MOUSE; CHROMATOGRAPHY

Abstract

Alzheimer’s disease (AD) is characterized by an early, asymptomatic phase (AsymAD) in which individuals exhibit amyloid-beta (Aβ) plaque accumulation in the absence of clinically detectable cognitive decline. Here we report an unbiased multiplex quantitative proteomic and phosphoproteomic analysis using tandem mass tag (TMT) isobaric labeling of human post-mortem cortex (n = 27) across pathology-free controls, AsymAD and symptomatic AD individuals. With off-line high-pH fractionation and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) on an Orbitrap Lumos mass spectrometer, we identified 11,378 protein groups across three TMT 11-plex batches. Immobilized metal affinity chromatography (IMAC) was used to enrich for phosphopeptides from the same TMT-labeled cases and 51,736 phosphopeptides were identified. Of these, 48,992 were quantified by TMT reporter ions representing 33,652 unique phosphosites. Two reference standards in each TMT 11-plex were included to assess intra- and inter-batch variance at the protein and peptide level. This comprehensive human brain proteome and phosphoproteome dataset will serve as a valuable resource for the identification of biochemical, cellular and signaling pathways altered during AD progression.