Dissecting detergent-insoluble proteome in Alzheimer's disease by TMTc-corrected quantitative mass spectrometry

Large-scale deep multi-layer analysis of Alzheimer’s disease brain reveals strong proteomic disease-related changes not observed at the RNA level

(2022) Erik C. B. Johnson et al.   NATURE NEUROSCIENCE

29‐Plex tandem mass tag mass spectrometry enabling accurate quantification by interference correction

(2022) Huan Sun et al.   PROTEOMICS

Comparative Evaluation of Proteome Discoverer and FragPipe for the TMT-Based Proteome Quantification

(2022) Tianen He et al.   JOURNAL OF PROTEOME RESEARCH

Alzheimer's disease

(2021) Philip Scheltens et al.   LANCET

TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level

(2021) Alex Johnson et al.   JOURNAL OF PROTEOME RESEARCH

Clinical diagnosis of Alzheimer's disease: recommendations of the International Working Group

(2021) Bruno Dubois et al.   LANCET NEUROLOGY

Proteomic landscape of Alzheimer’s Disease: novel insights into pathogenesis and biomarker discovery

(2021) Bing Bai et al.   Molecular Neurodegeneration

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

(2021) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

A brain proteomic signature of incipient Alzheimer’s disease in young APOE ε4 carriers identifies novel drug targets

(2021) Jackson A. Roberts et al.   Science Advances

Full-featured, real-time database searching platform enables fast and accurate multiplexed quantitative proteomics.

(2020) Devin K. Schweppe et al.   JOURNAL OF PROTEOME RESEARCH

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

(2020) Dorte B. Bekker-Jensen et al.   MOLECULAR & CELLULAR PROTEOMICS

Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer’s Disease Progression

(2020) Bing Bai et al.   NEURON

27-Plex Tandem Mass Tag Mass Spectrometry for Profiling Brain Proteome in Alzheimer’s Disease

(2020) Zhen Wang et al.   ANALYTICAL CHEMISTRY

PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins

(2020) Patryk Jarnot et al.   NUCLEIC ACIDS RESEARCH

Quantitative proteomic analysis of the frontal cortex in Alzheimer’s disease

(2020) Gajanan Sathe et al.   JOURNAL OF NEUROCHEMISTRY

Integrated analysis of ultra-deep proteomes in cortex, cerebrospinal fluid and serum reveals a mitochondrial signature in Alzheimer’s disease

(2020) Hong Wang et al.   Molecular Neurodegeneration

MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets

(2020) Meena Choi et al.   NATURE METHODS

Beyond aggregation: Pathological phase transitions in neurodegenerative disease

(2020) Cécile Mathieu et al.   SCIENCE

Integrated proteomics reveals brain-based cerebrospinal fluid biomarkers in asymptomatic and symptomatic Alzheimer’s disease

(2020) Lenora Higginbotham et al.   Science Advances

Quantitative proteomics reveals distinct composition of amyloid plaques in Alzheimer's disease

(2019) Feng Xiong et al.   Alzheimers & Dementia

Limbic-predominant age-related TDP-43 encephalopathy (LATE): consensus working group report

(2019) Peter T Nelson et al.   BRAIN

Alzheimer Disease: An Update on Pathobiology and Treatment Strategies

(2019) Justin M. Long et al.   CELL

Accurate, Sensitive, and Precise Multiplexed Proteomics Using the Complement Reporter Ion Cluster

(2018) Matthew Sonnett et al.   ANALYTICAL CHEMISTRY

RNA-binding proteins with basic-acidic dipeptide (BAD) domains self-assemble and aggregate in Alzheimer's disease

(2018) Isaac Bishof et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility

(2018) Towfique Raj et al.   NATURE GENETICS

Integrative Proteomics and Phosphoproteomics Profiling Reveals Dynamic Signaling Networks and Bioenergetics Pathways Underlying T Cell Activation

(2017) Haiyan Tan et al.   IMMUNITY

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

A scored human protein–protein interaction network to catalyze genomic interpretation

(2016) Taibo Li et al.   NATURE METHODS

Changes in the detergent-insoluble brain proteome linked to amyloid and tau in Alzheimer's Disease progression

(2016) Chadwick M. Hales et al.   PROTEOMICS

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

Arizona Study of Aging and Neurodegenerative Disorders and Brain and Body Donation Program

(2015) Thomas G. Beach et al.   NEUROPATHOLOGY

Aggregates of Small Nuclear Ribonucleic Acids (snRNAs) in Alzheimer's Disease

(2014) Chadwick M. Hales et al.   BRAIN PATHOLOGY

Integrated Approaches for Analyzing U1-70K Cleavage in Alzheimer’s Disease

(2014) Bing Bai et al.   JOURNAL OF PROTEOME RESEARCH

Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics

(2014) Navin Rauniyar et al.   JOURNAL OF PROTEOME RESEARCH

JUMP: A Tag-based Database Search Tool for Peptide Identification with High Sensitivity and Accuracy

(2014) Xusheng Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

U1 small nuclear ribonucleoproteins (snRNPs) aggregate in Alzheimer’s disease due to autosomal dominant genetic mutations and trisomy 21

(2014) Chadwick M Hales et al.   Molecular Neurodegeneration

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Full-length TDP-43 forms toxic amyloid oligomers that are present in frontotemporal lobar dementia-TDP patients

(2014) Yu-Sheng Fang et al.   Nature Communications

Staging TDP-43 pathology in Alzheimer’s disease

(2013) Keith A. Josephs et al.   ACTA NEUROPATHOLOGICA

Measuring and Managing Ratio Compression for Accurate iTRAQ/TMT Quantification

(2013) Mikhail M. Savitski et al.   JOURNAL OF PROTEOME RESEARCH

U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer's disease

(2013) B. Bai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate Multiplexed Proteomics at the MS2 Level Using the Complement Reporter Ion Cluster

(2012) Martin Wühr et al.   ANALYTICAL CHEMISTRY

iTRAQ Labeling is Superior to mTRAQ for Quantitative Global Proteomics and Phosphoproteomics

(2011) Philipp Mertins et al.   MOLECULAR & CELLULAR PROTEOMICS

PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

(2011) Jing Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging

(2011) Craig D Wenger et al.   NATURE METHODS

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

(2011) Lily Ting et al.   NATURE METHODS

Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells

(2011) Yuexi Wang et al.   PROTEOMICS

Alzheimer's Disease

(2010) Henry W. Querfurth et al.   NEW ENGLAND JOURNAL OF MEDICINE

Systematical Optimization of Reverse-Phase Chromatography for Shotgun Proteomics

(2009) Ping Xu et al.   JOURNAL OF PROTEOME RESEARCH

Proteomics Analysis Reveals Novel Components in the Detergent-Insoluble Subproteome in Alzheimer’s Disease

(2009) Yair M. Gozal et al.   JOURNAL OF PROTEOME RESEARCH

Practical Implementation of 2D HPLC Scheme with Accurate Peptide Retention Prediction in Both Dimensions for High-Throughput Bottom-Up Proteomics

(2008) Ravi C. Dwivedi et al.   ANALYTICAL CHEMISTRY

Concomitant TAR-DNA-Binding Protein 43 Pathology Is Present in Alzheimer Disease and Corticobasal Degeneration but Not in Other Tauopathies

(2008) Kunihiro Uryu et al.   JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY