An optimized quantitative proteomics method establishes the cell type‐resolved mouse brain secretome

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

(2020) Bing Bai et al.   NEURON

Biomarkers for Alzheimer’s disease—preparing for a new era of disease-modifying therapies

(2020) Henrik Zetterberg et al.   MOLECULAR PSYCHIATRY

Large-scale proteomic analysis of Alzheimer’s disease brain and cerebrospinal fluid reveals early changes in energy metabolism associated with microglia and astrocyte activation

(2020) Erik C. B. Johnson et al.   NATURE MEDICINE

Fibrillar Aβ triggers microglial proteome alterations and dysfunction in Alzheimer mouse models

(2020) Laura Sebastian Monasor et al.   eLife

Transmembrane protein 108 involves in adult neurogenesis in the hippocampal dentate gyrus

(2019) Zheng Yu et al.   Cell and Bioscience

Emerging cerebrospinal fluid biomarkers in autosomal dominant Alzheimer's disease

(2019) Suzanne E. Schindler et al.   Alzheimers & Dementia

Pitfalls and opportunities in the characterization of unconventionally secreted proteins by secretome analysis

(2019) Jessica Schira-Heinen et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Differential Signaling Mediated by ApoE2, ApoE3, and ApoE4 in Human Neurons Parallels Alzheimer's Disease Risk

(2019) Yu-Wen Alvin Huang et al.   JOURNAL OF NEUROSCIENCE

Increased soluble TREM2 in cerebrospinal fluid is associated with reduced cognitive and clinical decline in Alzheimer’s disease

(2019) Michael Ewers et al.   Science Translational Medicine

The Novel Perspectives of Adipokines on Brain Health

(2019) Thomas Ho-yin Lee et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

UMAP reveals cryptic population structure and phenotype heterogeneity in large genomic cohorts

(2019) Alex Diaz-Papkovich et al.   PLoS Genetics

Proteolytic ectodomain shedding of membrane proteins in mammals—hardware, concepts, and recent developments

(2018) Stefan F Lichtenthaler et al.   EMBO JOURNAL

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial

(2018) Christina Ludwig et al.   Molecular Systems Biology

The Role of APOE and TREM2 in Alzheimer′s Disease—Current Understanding and Perspectives

(2018) Cody Wolfe et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Cab45—Unraveling key features of a novel secretory cargo sorter at the trans-Golgi network

(2017) Birgit Blank et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

GlycoDomainViewer: a bioinformatics tool for contextual exploration of glycoproteomes

(2017) Hiren J Joshi et al.   GLYCOBIOLOGY

An environment-dependent transcriptional network specifies human microglia identity

(2017) David Gosselin et al.   SCIENCE

pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification

(2017) Ming-Qi Liu et al.   Nature Communications

Young microglia restore amyloid plaque clearance of aged microglia

(2016) Anna Daria et al.   EMBO JOURNAL

CSF and blood biomarkers for the diagnosis of Alzheimer's disease: a systematic review and meta-analysis

(2016) Bob Olsson et al.   LANCET NEUROLOGY

Seizure protein 6 and its homolog seizure 6-like protein are physiological substrates of BACE1 in neurons

(2016) Martina Pigoni et al.   Molecular Neurodegeneration

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

(2016) Janet Piñero et al.   NUCLEIC ACIDS RESEARCH

Early changes in CSF sTREM2 in dominantly inherited Alzheimers disease occur after amyloid deposition and neuronal injury

(2016) M. Suarez-Calvet et al.   Science Translational Medicine

In-depth mapping of the mouse brain N-glycoproteome reveals widespread N-glycosylation of diverse brain proteins

(2016) Pan Fang et al.   Oncotarget

CD200R/Foxp3-mediated signalling regulates microglial activation

(2016) Min-Hee Yi et al.   Scientific Reports

Systematic substrate identification indicates a central role for the metalloprotease ADAM10 in axon targeting and synapse function

(2016) Peer-Hendrik Kuhn et al.   eLife

Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow

(2015) Atul S. Deshmukh et al.   JOURNAL OF PROTEOME RESEARCH

A Dual SILAC Proteomic Labeling Strategy for Quantifying Constitutive and Cell–Cell Induced Protein Secretion

(2015) Michael Stiess et al.   JOURNAL OF PROTEOME RESEARCH

Label-free Quantitative Proteomics of Mouse Cerebrospinal Fluid Detects β-Site APP Cleaving Enzyme (BACE1) Protease Substrates In Vivo

(2015) Bastian Dislich et al.   MOLECULAR & CELLULAR PROTEOMICS

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

(2015) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

Cell type– and brain region–resolved mouse brain proteome

(2015) Kirti Sharma et al.   NATURE NEUROSCIENCE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Monitoring matrix metalloproteinase activity at the epidermal-dermal interface by SILAC-iTRAQ-TAILS

(2015) Pascal Schlage et al.   PROTEOMICS

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

(2014) Y. Zhang et al.   JOURNAL OF NEUROSCIENCE

The Role of SORL1 in Alzheimer’s Disease

(2014) Rui-Hua Yin et al.   MOLECULAR NEUROBIOLOGY

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Systematic Proteomic Analysis Identifies β-Site Amyloid Precursor Protein Cleaving Enzyme 2 and 1 (BACE2 and BACE1) Substrates in Pancreatic β-Cells

(2013) Ina Stützer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Direct Proteomic Quantification of the Secretome of Activated Immune Cells

(2013) F. Meissner et al.   SCIENCE

Secretome protein enrichment identifies physiological BACE1 protease substrates in neurons

(2012) Peer-Hendrik Kuhn et al.   EMBO JOURNAL

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Selective enrichment of newly synthesized proteins for quantitative secretome analysis

(2012) Katrin Eichelbaum et al.   NATURE BIOTECHNOLOGY

Tumor Necrosis Factor Signaling Requires iRhom2 to Promote Trafficking and Activation of TACE

(2012) C. Adrain et al.   SCIENCE

iRhom2 Regulation of TACE Controls TNF-Mediated Protection Against Listeria and Responses to LPS

(2012) D. R. McIlwain et al.   SCIENCE

Amyloid Precursor Protein Processing and Alzheimer's Disease

(2011) Richard J. O'Brien et al.   Annual Review of Neuroscience

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates

(2011) Oded Kleifeld et al.   Nature Protocols

Protein Sorting Receptors in the Early Secretory Pathway

(2010) Julia Dancourt et al.   Annual Review of Biochemistry

Precision Mapping of an In Vivo N-Glycoproteome Reveals Rigid Topological and Sequence Constraints

(2010) Dorota F. Zielinska et al.   CELL

Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products

(2010) Oded Kleifeld et al.   NATURE BIOTECHNOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH