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ProteomicsGenetic Architecture of Protein Expression and its Regulation in the Mouse Brain
Natural variation in protein expression is common in all organisms and contribute to phenotypic differences among individuals. While variation in gene expression at the transcript level has been extensively investigated, the genetic mechanisms underlying variation in protein expression have lagged c...
ORGANISM(S): Mus musculus (Mouse) 
2021-11-01 | PXD025830 | Pride
Expression pattern Brain Proteome Mouse Protein regulation Protein expression 
ProteomicsHs_Brain_Phospho
Human brain phosphoproteome analyzed by refined phosphopeptide enrichment
ORGANISM(S): Homo Sapiens (human) 
2015-12-31 | PAe005247 | PeptideAtlas
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
ProteomicsExtensive Peptide Fractionation and y1 Ion-based Interference Detection Enable Accurate Quantification by Isobaric Labeling and Mass Spectrometry
Isobaric labeling quantification by mass spectrometry (MS) has emerged as a powerful technology for multiplexed large-scale protein profiling, but measurement accuracy in complex mixtures is confounded by the interference from co-isolated ions, resulting in ratio compression. Here we report that the...
ORGANISM(S): Escherichia coli 
2022-02-28 | PXD005797 | Pride
Isobaric labeling Proteomics Tmt Mass spectrometry And ratio compression Itraq Lc-ms/ms 
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 (Human) 
2019-11-11 | PXD007985 | Pride
Alzheimer’s disease  mass spectrometry  proteomics  proteome  phosphoproteome  transcriptome  rna-seq  genomics  genome  systems biology  disease network  aβ  tau  netrin 
ProteomicsProteomics profiling reveals regulation of immune response to Salmonella enterica serovar Typhimurium infection in mice
Regulation of the immune response to Salmonella enterica serovar Typhimurium (S. Typhimurium) infection is a complex process, influenced by the interaction between genetic and environmental factors. Different inbred strains of mice exhibit distinct levels of resistance to S. Typhimurium infection, r...
ORGANISM(S): Mus musculus (Mouse) 
2022-12-01 | PXD038436 | Pride
Proteome  proteomics  mass spectrometry  immune response  genetic regulation  salmonella  s. typhimurium  mouse 
ProteomicsIntegrative proteomics and phosphoproteomics profiling and systems biology analysis reveal dynamic signaling networks and mTORC1-dependent mitochondrial function in T cell activation
The underlying mechanisms by which naïve T cells exit from quiescence after antigen stimulation remain elusive. Using multiplex isobaric labeling proteomics technology, we report unbiased, temporal profiling of whole proteome (>8,000 proteins) and phosphoproteome (>13,000 phosphopeptides) during the...
ORGANISM(S): Mus musculus (Mouse) 
2017-03-15 | PXD004367 | Pride
System biology T cell activation Mtorc1 Mass spectrometry Rptor Proteomic Phosphoproteomics Mitochondrial function 
ProteomicsIntegrative proteomics and phosphoproteomics profiling and systems biology analysis reveal dynamic signaling networks and mTORC1-dependent mitochondrial function in T cell activation
The underlying mechanisms by which naïve T cells exit from quiescence after antigen stimulation remain elusive. Using multiplex isobaric labeling proteomics technology, we report unbiased, temporal profiling of whole proteome and phosphoproteome during the activation in the wild type and Rptor-/- T ...
ORGANISM(S): Mus musculus (Mouse) 
2017-03-29 | PXD005492 | Pride
System biology T cell activation Mtorc1 Mass spectrometry Rptor Proteomic Phosphoproteomics Mitochondrial function 
ProteomicsDeep undepleted human serum proteome profiling toward biomarker discovery for 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): Homo sapiens (Human) 
2019-04-23 | PXD011482 | Pride
Proteomics Alzheimer’s disease Human blood Mass spectrometry Plasma Serum Proteome Tandem mass tag Biomarker 
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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