ArticleJournal of proteome research2022
Does Data-Independent Acquisition Data Contain Hidden Gems? A Case Study Related to Alzheimer's Disease.
Article in Journal of proteome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 37 citations in OpenAlex.
- Spontaneous Isomerization of Tau is Most Prevalent in Alzheimer's Disease.NeuroMarkers · 2026Article
- Clinically relevant stereochemistry reprograms amyloid proteome for aggregation cross-talk-conferred neuroprotection.Science advances · 2026Article
- The microtubule nexus linking amyloid beta and tau: A simple and unifying theory for the underlying cause of Alzheimer's disease.PNAS nexus · 2026Article
- Site-Specific Aspartic Acid d-Isomerization in Tau R2 and R3 Peptide Seeds Attenuates Seed-Induced Fibril Formation of Full-Length Tau.Biomolecules · 2026Article
- Post-Translationally Modified Proteoforms as Biomarkers: From Discovery to Clinical Use.Clinical chemistry · 2025Review
- Deep Characterization of Isomerization in the Human Eye Lens Proteome by Crystallin-Depleted Data-Independent Acquisition.Aging cell · 2025Article
- Determination of Trends Underlying Aspartic Acid Isomerization in Intact Proteins Reveals Unusually Rapid Isomerization of Tau.ACS chemical neuroscience · 2025Article
- MLKL-USP7-UBA52 signaling is indispensable for autophagy in brain through maintaining ubiquitin homeostasis.Autophagy · 2025Article
- Unusually Rapid Isomerization of Aspartic Acid in Tau.bioRxiv : the preprint server for biology · 2024Article
- Alzheimer's disease: from early pathogenesis to novel therapeutic approaches.Metabolic brain disease · 2024Review
- Localizing Isomerized Residue Sites in Peptides with Tandem Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2024Article
- Selective recognition and discrimination of single isomeric changes in peptide strands with a host : guest sensing array.Chemical science · 2024Article
- Brain proteomic analysis implicates actin filament processes and injury response in resilience to Alzheimer's disease.Nature communications · 2023Article
- Statistical Framework for Identifying Differences in Similar Mass Spectra: Expanding Possibilities for Isomer Identification.Analytical chemistry · 2023Article
- A peptide-centric quantitative proteomics dataset for the phenotypic assessment of Alzheimer's disease.Scientific data · 2023Article
- Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA.Journal of proteome research · 2023Review
- The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.Journal of proteome research · 2023Article
- Influence of Asp Isomerization on Trypsin and Trypsin-like Proteolysis.Analytical chemistry · 2022Article
- Distinguishing post-translational modifications in dominantly inherited frontotemporal dementias: FTLD-TDP Type A (GRN) vs Type B (C9orf72).Neuropathology and applied neurobiology · 2022Article
- LC-MS Reveals Isomeric Inhibition of Proteolysis by Lysosomal Cathepsins.Analysis & sensing · 2022Article
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Authors and funding
16 authors at 9 institutions in 2 countries.
Funding
Abstract
One of the potential benefits of using data-independent acquisition (DIA) proteomics protocols is that information not originally targeted by the study may be present and discovered by subsequent analysis. Herein, we reanalyzed DIA data originally recorded for global proteomic analysis to look for isomerized peptides, which occur as a result of spontaneous chemical modifications to long-lived proteins. Examination of a large set of human brain samples revealed a striking relationship between Alzheimer's disease (AD) status and isomerization of aspartic acid in a peptide from tau. Relative to controls, a surprising increase in isomer abundance was found in both autosomal dominant and sporadic AD samples. To explore potential mechanisms that might account for these observations, quantitative analysis of proteins related to isomerization repair and autophagy was performed. Differences consistent with reduced autophagic flux in AD-related samples relative to controls were found for numerous proteins, including most notably p62, a recognized indicator of autophagic inhibition. These results suggest, but do not conclusively demonstrate, that lower autophagic flux may be strongly associated with loss of function in AD brains. This study illustrates that DIA data may contain unforeseen results of interest and may be particularly useful for pilot studies investigating new research directions. In this case, a promising target for future investigations into the therapy and prevention of AD has been identified.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.