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ProteomicsU1 Small Nuclear Ribonucleoprotein Complex and RNA Splicing Alterations in Alzheimer Disease
Comprehensive study of the human brain-insoluble proteome in AD by mass spectrometry. Mass spectrometry analysis of detergent insoluble fractions was processed based on our optimized LC-MS/MS protocol. Protein concentration was determined by bicinchoninic acid (BCA) assay (Thermo Scientific) using b...
ORGANISM(S): Homo sapiens (Human) 
2013-08-28 | PXD000067 | Pride
Human Splicing U170k Lc-ms/ms 
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 
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
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
ProteomicsIntegrated proteomics reveals autophagy degradation landscape in neurons and receptors regulating neuronal activity
Autophagy is a constitutive process of lysosomal degradation required for maintaining the homeostasis of large molecular complexes and organelles in neurons. Here we reported a systemic investigation of neuronal autophagy targets through integrated proteomics and functional analysis. Proteomic profi...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2024-06-22 | PXD048730 | Pride
Mass spectrometry Neuron Autophagy degradation Integrated proteomics Tandem mass tag Lc-ms/ms 
OtherJUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy.
Data from authors [[http://stjuderesearch.org/site/lab/peng web site]]. Experiment: dataset3, file: pl08.mzXML. Published as part of Mol Cell Proteomics. 2014 Sep 8 . From the Abstract: {{i}} ... Here we present JUMP, a new hybrid database search program that generates amino acid tags and ranks pep...
ORGANISM(S): Homo_sapiens_viruses, Human 
GPM32320003491 | GPMDB
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 
ProteomicsGlobal Proteomic Profiling of Pediatric AML: A Pilot Study
Acute Myeloid Leukemia (AML) is a heterogeneous disease with several recurrent cytogenetic abnormalities. Despite genomics and transcriptomics profiling efforts to understand AML’s heterogeneity, studies focused on the proteomic profiles associated with pediatric AML cytogenetic features remain limi...
ORGANISM(S): Homo sapiens (Human) 
2023-09-26 | PXD043982 | Pride
Leukemic cells Pediatrics acute myeloid leukemia Transcriptomics Tandem mass tag Untargeted labeled proteomics 
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 
Proteomics29-Plex Tandem Mass Tag Mass Spectrometry Enabling Accurate Quantification by Interference Correction
Tandem mass tag (TMT) mass spectrometry is a mainstream isobaric chemical labeling strategy for profiling proteomes. Here we present a 29-plex TMT method to combine the 11-plex and 18-plex labeling strategies. The 29-plex method was examined with a pooled sample composed of 1x, 3x and 10x E. coli pe...
ORGANISM(S): Homo sapiens (Human) 
2023-03-10 | PXD033865 | Pride
Mass spectrometry  liquid chromatography  proteomics  proteome  tandem mass tag  ratio compression  interference  data processing 
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