CoChat
Sign Up
Cited by 127Advanced Proteomics Techniques and ApplicationsAlzheimer's disease research and treatmentsDementia and Cognitive Impairment Research

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

Open access
Ping, Lingyan, Kundinger, Sean R., Duong, Duc M., Yin, Luming, Gearing, Marla, Lah, James J., Levey, Allan I., Seyfried, Nicholas T.·2020·Scientific Data
DOI 10.1038/s41597-020-00650-8PMC PMC7522715

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

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.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41597-020-00650-8

Cites

8 of 8 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Proteomic approaches have revealed dysregulation in synaptic proteins, immune modulators, and metabolic enzymes that extend beyond the classical amyloid and tau pathways.

    “These approaches have revealed dysregulation in synaptic proteins, immune modulators, and metabolic enzymes that extend beyond the classical amyloid and tau pathways134,160,170, 171, 172, 173.”

    From Artificial intelligence-driven multi-omics approaches in Alzheimer's disease: Progress, challenges, and future directions (2025) · cites this paper as [134]

    The Usage Notes (‘AD stage-specific differential protein expression’; page not provided) report substantial peptide-level differences between Alzheimer’s disease and controls, beyond the paper’s separate measurements of amyloid and tau. The passages do not identify the altered proteins as synaptic proteins, immune modulators, or metabolic enzymes, so those specific parts of the claim are not supported by this copy. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 64

  1. [2]Guo T Molecular and cellular mechanisms underlying the pathogenesis of Alzheimer’s disease Molecular neurodegeneration 2020 15 40 32677986 PMC7364557
  2. [3]Sperling RA Toward defining the preclinical stages of Alzheimer’s disease: recommendations from the National Institute on Aging-Alzheimer’s Association workgroups on diagnostic guidelines for Alzheimer’s disease Alzheimer’s & dementia: the journal of the Alzheimer’s Association 2011 7 280 292 PMC3220946 21514248
  3. [5]Seyfried NT A Multi-network Approach Identifies Protein-Specific Co-expression in Asymptomatic and Symptomatic Alzheimer’s Disease Cell systems 2017 4 60 72.e64 27989508 PMC5269514
  4. [6]Bush, S. J., Chen, L., Tovar-Corona, J. M. & Urrutia, A. O. Alternative splicing and the evolution of phenotypic novelty. Philos Trans R Soc Lond B Biol Sci372, 1–7 (2017). PMC5182408 27994117
  5. [7]Li HD Menon R Omenn GS Guan Y The emerging era of genomic data integration for analyzing splice isoform function Trends Genet 2014 30 340 347 24951248 PMC4112133
  6. [8]Cox J Mann M Quantitative, high-resolution proteomics for data-driven systems biology Annual review of biochemistry 2011 80 273 299 21548781
  7. [9]Maiolica A Junger MA Ezkurdia I Aebersold R Targeted proteome investigation via selected reaction monitoring mass spectrometry Journal of proteomics 2012 75 3495 3513 22579752
  8. [10]Oliveira J Costa M de Almeida MSC da Cruz ESOAB Henriques AG Protein Phosphorylation is a Key Mechanism in Alzheimer’s Disease Journal of Alzheimer’s disease: JAD 2017 58 953 978 28527217
  9. [11]Sathe G Multiplexed Phosphoproteomic Study of Brain in Patients with Alzheimer’s Disease and Age-Matched Cognitively Healthy Controls Omics: a journal of integrative biology 2020 24 216 227 32182160 PMC7366319
  10. [12]Herskowitz JH Pharmacologic inhibition of ROCK2 suppresses amyloid-beta production in an Alzheimer’s disease mouse model. The Journal of neuroscience: the official journal of the Society for Neuroscience 2013 33 19086 19098 PMC3850036 24305806
  11. [13]Hanger DP Hughes K Woodgett JR Brion J-P Anderton BH Glycogen synthase kinase-3 induces Alzheimer’s disease-like phosphorylation of tau: Generation of paired helical filament epitopes and neuronal localisation of the kinase Neuroscience Letters 1992 147 58 62 1336152
  12. [14]Noble, W. et al. Cdk5 Is a Key Factor in Tau Aggregation and Tangle Formation In Vivo. Neuron38, 555–565 (2003). 12765608
  13. [15]Cole G Dobkins KR Hansen LA Terry RD Saitoh T Decreased levels of protein kinase C in Alzheimer brain Brain Research 1988 452 165 174 3165303
  14. [16]Chin JY Microtubule-Affinity Regulating Kinase (MARK) Is Tightly Associated with Neurofibrillary Tangles in Alzheimer Brain: A Fluorescence Resonance Energy Transfer Study Journal of Neuropathology & Experimental Neurology 2000 59 966 971 11089574
  15. [17]Gong CX Singh TJ Grundke-Iqbal I Iqbal K Phosphoprotein phosphatase activities in Alzheimer disease brain J Neurochem 1993 61 921 927 8395566
  16. [19]O’Connell JD Paulo JA O’Brien JJ Gygi SP Proteome-Wide Evaluation of Two Common Protein Quantification Methods Journal of proteome research 2018 17 1934 1942 29635916 PMC5984592
  17. [20]Lim H Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry Journal of the American Society for Mass Spectrometry 2003 14 957 970 12954164
  18. [21]Gygi SP Corthals GL Zhang Y Rochon Y Aebersold R Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology Proceedings of the National Academy of Sciences of the United States of America 2000 97 9390 9395 10920198 PMC16874
  19. [22]Ping L Global quantitative analysis of the human brain proteome in Alzheimer’s and Parkinson’s Disease Scientific data 2018 5 180036 29533394 PMC5848788
  20. [23]Mertins P Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry Nature protocols 2018 13 1632 1661 29988108 PMC6211289
  21. [24]Tan A Fanaras JC Use of high-pH (basic/alkaline) mobile phases for LC-MS or LC-MS/MS bioanalysis Biomedical chromatography: BMC 2019 33 e4409 30315658
  22. [25]Horvatovich P Hoekman B Govorukhina N Bischoff R Multidimensional chromatography coupled to mass spectrometry in analysing complex proteomics samples Journal of separation science 2010 33 1421 1437 20486207
  23. [26]Bai B Deep Profiling of Proteome and Phosphoproteome by Isobaric Labeling, Extensive Liquid Chromatography, and Mass Spectrometry Methods in enzymology 2017 585 377 395 28109439 PMC5441839
  24. [27]Mirra SS The Consortium to Establish a Registry for Alzheimer’s Disease (CERAD). Part II. Standardization of the neuropathologic assessment of Alzheimer’s disease Neurology 1991 41 479 486 2011243
  25. [29]Ping L Duong DM Seyfried NT 2020 Sample traits. Synapse 10.7303/syn20820456 · DOI
  26. [30]Ping L Duong DM Seyfried NT 2020 RAW files. Synapse 10.7303/syn20820454 · DOI
  27. [31]UniProt: a worldwide hub of protein knowledge. Nucleic acids research 47, D506–d515 (2019). PMC6323992 30395287
  28. [32]Müller JB The proteome landscape of the kingdoms of life Nature 2020 582 592 596 32555458
  29. [33]Breuza, L. et al. The UniProtKB guide to the human proteome. Database: the journal of biological databases and curation 2016 (2016). PMC4761109 26896845
  30. [34]Ping L Duong DM Seyfried NT 2020 Database. Synapse 10.7303/syn20820455 · DOI
  31. [36]Johnson, E. C. B. et al. Large-scale proteomic analysis of Alzheimer’s disease brain and cerebrospinal fluid reveals early changes in energy metabolism associated with microglia and astrocyte activation. Nature medicine 26, 769–780 (2020). PMC7405761 32284590
  32. [37]Wiese H Comparison of alternative MS/MS and bioinformatics approaches for confident phosphorylation site localization J Proteome Res 2014 13 1128 1137 24364495
  33. [38]Ping L Duong DM Seyfried NT 2020 Search result. Synapse 10.7303/syn20820472 · DOI
  34. [39]Ping L 2020 Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer’s disease. Synapse 10.7303/syn20820053 PMC7522715 32985496 · DOI
  35. [40]Ping L Duong DM Seyfried NT 2020 Anova analysis. Synapse 10.7303/syn21986491 · DOI
  36. [41]Ping L 2020 Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer’s disease PRIDE Archive PXD020296 PMC7522715 32985496
  37. [42]Zhang H Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell 2016 166 755 765 PMC4967013 27372738
  38. [43]Clark DJ Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics Journal of proteome research 2018 17 2205 2215 29718670 PMC6670293
  39. [44]Mertins P Proteogenomics connects somatic mutations to signalling in breast cancer Nature 2016 534 55 62 27251275 PMC5102256
  40. [46]Higginbotham, L. et al. Integrated Proteomics Reveals Brain-Based Cerebrospinal Fluid Biomarkers in Asymptomatic and Symptomatic Alzheimer’s Disease. bioRxiv, 806752 (2019). PMC7577712 33087358
  41. [47]Seyfried NT Multiplex SILAC analysis of a cellular TDP-43 proteinopathy model reveals protein inclusions associated with SUMOylation and diverse polyubiquitin chains Molecular & cellular proteomics: MCP 2010 9 705 718 20047951 PMC2860236
  42. [48]Dammer EB Quantitative phosphoproteomics of Alzheimer’s disease reveals cross-talk between kinases and small heat shock proteins Proteomics 2015 15 508 519 25332170 PMC4404162
  43. [49]Brenes A Hukelmann J Bensaddek D Lamond AI Multibatch TMT Reveals False Positives, Batch Effects and Missing Values Molecular & cellular proteomics: MCP 2019 18 1967 1980 31332098 PMC6773557
  44. [50]Glenner GG Wong CW Alzheimer’s disease: initial report of the purification and characterization of a novel cerebrovascular amyloid protein Biochemical and biophysical research communications 1984 120 885 890 6375662
  45. [51]Grundke-Iqbal I Abnormal phosphorylation of the microtubule-associated protein tau (tau) in Alzheimer cytoskeletal pathology Proc Natl Acad Sci USA 1986 83 4913 4917 3088567 PMC323854
  46. [52]Hampel H Core candidate neurochemical and imaging biomarkers of Alzheimer’s disease Alzheimers Dement 2008 4 38 48 18631949
  47. [53]Kolarova M Garcia-Sierra F Bartos A Ricny J Ripova D Structure and pathology of tau protein in Alzheimer disease International journal of Alzheimer’s disease 2012 2012 731526 22690349 PMC3368361
  48. [54]Falcon B Conformation determines the seeding potencies of native and recombinant Tau aggregates. The Journal of biological chemistry 2015 290 1049 1065 25406315 PMC4294473
  49. [56]Zhou X Su Z EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species BMC genomics 2007 8 246 17645808 PMC1940007
  50. [57]Huang da W Sherman BT Lempicki RA Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists Nucleic acids research 2009 37 1 13 19033363 PMC2615629
  51. [58]Franceschini A STRING v9.1: protein-protein interaction networks, with increased coverage and integration Nucleic acids research 2013 41 D808 815 23203871 PMC3531103
  52. [59]Poulopoulos A Subcellular transcriptomes and proteomes of developing axon projections in the cerebral cortex Nature 2019 565 356 360 30626971 PMC6484835
  53. [60]Dix MM Functional interplay between caspase cleavage and phosphorylation sculpts the apoptotic proteome Cell 2012 150 426 440 22817901 PMC3569040
  54. [61]Kolch W Pitt A Functional proteomics to dissect tyrosine kinase signalling pathways in cancer Nature reviews. Cancer 2010 10 618 629 20720570
  55. [62]Koomen JM Proteomic contributions to personalized cancer care Molecular & cellular proteomics: MCP 2008 7 1780 1794 18664563 PMC2559938
  56. [63]Blagoev B Ong SE Kratchmarova I Mann M Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics Nature biotechnology 2004 22 1139 1145 15314609
  57. [64]Lopez-Villar E A proteomic approach to obesity and type 2 diabetes Journal of cellular and molecular medicine 2015 19 1455 1470 25960181 PMC4511345
  58. [65]Inestrosa NC Toledo EM The role of Wnt signaling in neuronal dysfunction in Alzheimer’s Disease Molecular neurodegeneration 2008 3 9 18652670 PMC2515306
  59. [67]Zhu X Lee HG Raina AK Perry G Smith MA The role of mitogen-activated protein kinase pathways in Alzheimer’s disease Neuro-Signals 2002 11 270 281 12566928
  60. [68]Tompa P Davey NE Gibson TJ Babu MM A million peptide motifs for the molecular biologist Molecular cell 2014 55 161 169 25038412
  61. [69]Makalowski W Zhang J Boguski MS Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences Genome research 1996 6 846 857 8889551
  62. [70]Krystkowiak I Manguy J Davey NE PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants Nucleic acids research 2018 46 W235 w241 29873773 PMC6030969
  63. [71]Bidin, S., Vujaklija, I., Paradzik, T., Bielen, A. & Vujaklija, D. Leitmotif: protein motif scanning 2.0. Bioinformatics (Oxford, England) (2020). 32154834
  64. [72]Rose CM TomahaqCompanion: A Tool for the Creation and Analysis of Isobaric Label Based Multiplexed Targeted Assays Journal of proteome research 2019 18 594 605 30501201 PMC7315617

Cited by

Sorted by citations

Authors
Ping, L., Kundinger, S. R., Duong, D. M., Yin, L., Gearing, M., Lah, J. J., Levey, A. I., & Seyfried, N. T.
Affiliations
Emory University (US)
Corresponding author
Seyfried, Nicholas T.
ORCID
Venue
Scientific Data
Publisher
Springer Science and Business Media LLC
Published
2020-09-28
Volume
7
Issue
1
Pages
315-315
ISSN
2052-4463 (ISSN-L)
DOI
10.1038/s41597-020-00650-8
PMC
PMC7522715
OpenAlex
W3088072832
Cited by
127
References
8
Citations by year
2026: 21 · 2025: 22 · 2024: 17 · 2023: 30 · 2022: 20 · 2021: 12 · 2020: 4
Type
data paper
Language
en
Open access
Licence
Locations
  • Scientific Data (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Emory University (R01AG061800, RF1AG057471, R01AG053960, P50AG025688, U01AG061357, R01AG057339, RF1AG057470)
  • Alzheimer's Disease Research Center, Emory University (P50 AG025688)
  • National Institute on Aging (RF1AG057470, U01AG061357, RF1AG062181, U01AG046161, RF1AG057471, P50AG025688, R01AG057339, R01AG053960, R01AG061800)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
Keywords
Alzheimer's disease, human brain proteome, amyloid plaques, phosphopeptides, phosphosites, protein quantification, disease progression
MeSH terms
Alzheimer Disease, Brain, Chromatography, Liquid, Humans, Phosphoproteins, Proteome, Tandem Mass Spectrometry

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review