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ProteomicsDeep Multilayer Tissue Proteomics Identifies Molecular Networks in Alzheimer’s Disease Progression, human data
The molecular networks underlying Alzheimer’s disease (AD) are not well-defined. We present temporal profiling of >14,000 proteins and >34,000 phosphosites at the asymptomatic and symptomatic stages of AD, deep proteomics analysis of transgenic mouse models.
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-10-17 | MSV000096123 | MassIVE
UnknownFGF22 deletion causes hidden hearing loss by affecting the function of inner hair cell ribbon synapses.
Not available
S-EPMC9366910 | biostudies-literature
ProteomicsUltra Deep Mouse cerebrospinal fluid (CSF) profiling in Alzheimer’s disease
Alzheimer's disease (AD) is a neurodegenerative disease, the most common cause of dementia in elderly persons. Accumulation of amyloid plaques in the brain is a characteristic of AD. The requirements for a biomarker include the ability to measure a pathologic process, predict outcome, distinguish di...
ORGANISM(S): Mus musculus (Mouse) 
2021-09-09 | PXD018658 | Pride
Proteomics Alzheimer’s disease Mass spectrometry Mouse Csf Proteome Tandem mass tag Biomarker 
ProteomicsDisruption of LRRK2 Activator RAB12 Facilitates Neurotransmission and Causes Hyperactivity in Mice
RAB12 is a family member of small GTPases best known as a physiological substrate of LRRK2 kinase, the variants of which cause Parkinson’s disease (PD). RAB12 - LRRK2 interaction is crucial for the activation of LRRK2 kinase activity and pathogenic signaling in ciliogenesis and immune response. Howe...
ORGANISM(S): Mus musculus (Mouse) 
2026-04-29 | PXD075183 | Pride
Parkinson’s disease  lrrk2  rab12 ko  mouse  proteomics striatal synaptosome 
ProteomicsJUMPg: an Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells
Proteogenomics is an emerging approach to improve gene annotation and interpretation of proteomics data. Here we present JUMPg, an integrative proteogenomics pipeline including customized database construction, tag-based database search, peptide-spectrum match filtering, and data visualization. JUMP...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-16 | MSV000080641 | MassIVE
TranscriptomicsChromatin immunoprecipitation of wild type and Foxa2 knock-out mouse liver using anti-HNF6 anitbodies to test whether Foxa2 inhibits HNF6-mediated transcription in the liver
The aim of this study was to test, in vivo, if Foxa2 inhibits HNF6-mediated transcription in the liver. We utilized hepatocyte-specific gene ablation of Foxa2 and the Mouse PromoterChip BCBC 3.0 and Mouse PancChip 5.0 cDNA microarrays to investigate HNF6 binding to its target promoters in vivo in t...
ORGANISM(S): Mus musculus 
2007-09-14 | E-CBIL-36 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of wild type and PGC-1alpha knock-out liver and skeletal muscle
PGC-1alpha; is a coactivator of nuclear receptors and other transcription factors that regulates several metabolic processes, including mitochondrial biogenesis and respiration, hepatic gluconeogenesis, and muscle fiber-type switching. We show here that, while hepatocytes lacking PGC-1alpha; are def...
ORGANISM(S): Mus musculus 
2007-04-06 | E-CBIL-22 | biostudies-arrayexpress
ProteomicsGlobal Profiling of Lysine Accessibility to Evaluate Protein Structure Changes in Alzheimer’s Disease
The linear sequence of amino acids in a protein folds into a 3D structure to execute protein activity and function, but it is still challenging to profile the 3D structure at the proteome scale. Here, we present a method of native protein tandem mass tag (TMT) profiling of Lys accessibility and its ...
ORGANISM(S): Homo sapiens (Human) 
2021-03-23 | PXD024914 | Pride
Structural mass spectrometry Alzheimer’s disease Proteomics Structuromics And tau Tandem mass tag 
ProteomicsEvaluation of a Pooling Chemoproteomics Strategy with an FDA-approved Drug Library
Chemoproteomics is a key platform for characterizing the mode of action (MoA) for compounds, especially for targeted protein degraders such as proteolysis targeting chimerics (PROTACs) and molecular glues. With deep proteome coverage, multiplexed tandem mass tag-mass spectrometry (TMT-MS) can tackle...
ORGANISM(S): Homo sapiens (Human) 
2023-03-11 | PXD033780 | Pride
Mass spectrometry  proteomics  chemoproteomics  tandem mass tag  pooling strategy  protac  molecular glue  targeted protein degeneration  fda library 
ProteomicsJUMPg: an Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells
Proteogenomics is an emerging approach to improve gene annotation and interpretation of proteomics data. Here we present JUMPg, an integrative proteogenomics pipeline including customized database construction, tag-based database search, peptide-spectrum match filtering, and data visualization. JUMP...
ORGANISM(S): Homo sapiens (Human) 
2017-02-20 | PXD004010 | Pride
Proteomics Proteogenomics Database search Mass spectrometry Genomics Multistage analysis Rna-seq Spectrum quality control 
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