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Mass spectrometry based detergent-insoluble proteins of human cell lysates

ABSTRACT: The PXD project contains a project which aimed to identify protein evidences (missing proteins) from insoluble proteins from cell lysate by mass spectrometry. It involves the analysis of 3 human lung cell line and 3 liver cell lines,including the identification information and quantitative information.The raw data, peak data and search data were all cataloged into this project.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Dr Tong Wang

PROVIDER: MSV000079997 | MassIVE | Fri Jul 22 16:21:00 BST 2016

SECONDARY ACCESSION(S): PXD001694

REPOSITORIES: MassIVE

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Publications

Identification of Missing Proteins Defined by Chromosome-Centric Proteome Project in the Cytoplasmic Detergent-Insoluble Proteins.

Chen Yang Y Li Yaxing Y Zhong Jiayong J Zhang Jing J Chen Zhipeng Z Yang Lijuan L Cao Xin X He Qing-Yu QY Zhang Gong G Wang Tong T

Journal of proteome research 20150710 9

Finding protein evidence (PE) for protein coding genes is a primary task of the Phase I Chromosome-Centric Human Proteome Project (C-HPP). Currently, there are 2948 PE level 2-4 coding genes per neXtProt, which are deemed missing proteins in the human proteome. As most samples prepared and analyzed in the C-HPP framework were focusing on detergent soluble proteins, we posit that as a natural composition the cytoplasmic detergent-insoluble proteins (DIPs) represent a source of finding missing pro ...[more]

PMID: 26108252

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Mass spectrometry based detergent-insoluble proteins of human cell lysates

Project description:The PXD project contains a project which aimed to identify protein evidences (missing proteins) from insoluble proteins from cell lysate by mass spectrometry. It involves the analysis of 3 human lung cell line and 3 liver cell lines,including the identification information and quantitative information.The raw data, peak data and search data were all cataloged into this project.

2015-06-29 | PXD001694 | Pride

Alzheimer Disease model detergent insoluble proteomes

Project description:Characterizing the detergent insoluble brain proteome of sporadic late-onset Alzheimer’s disease (LOAD) has identified proteins and pathways associated with disease pathogenesis. Similar studies in early onset Alzheimer’s disease cases due to presenilin-1 mutations (PS1-EOAD), along with more detailed correlations with insoluble proteomes from LOAD and AD transgenic rodents, are limited. We therefore utilized quantitative proteomics to identify proteins that were significantly changing in the PS1-EOAD insoluble proteome versus controls. Comparison with the LOAD insoluble proteome identified common pathologic AD markers in addition to unique PS1-EOAD insoluble proteins. Similarly, weighted correlation network analysis (WGCNA) identified PS1-EOAD and LOAD co-expression modules with both like and disparate expression levels. Finally, we compared the human PS1-EOAD insoluble proteome to transgenic AD mouse and rat insoluble proteomes to understand how well these models mimic the human disease. Although many common AD pathologic findings were found in the rodents, there were multiple PS1-EOAD proteome changes not well recapitulated in the animal models. These proteomic studies highlight unique PS1-EOAD proteome changes as compared to LOAD and identify limitations to using AD transgenic rodents to study some aspects of AD. This submission exclusively provides the mouse and rat model data.

2022-03-01 | PXD005347 | Pride

Alzheimer Disease (AD) and AD model detergent insoluble proteomes

2019-06-25 | PXD005321 | Pride

Profiling of the detergent-insoluble proteome of the cortical brain tissues by TMT-LC/LC-MS/MS

Project description:Mass spectrometry analysis of insoluble proteome from 5xFAD/Mdk-KO mouse brain. This study examines the insoluble protein fraction, focusing on aggregation-prone proteins including Aβ and its associated proteins. The data reveals significant accumulation of Aβ-correlated proteins and microglial components in the absence of MDK, supporting its protective role against amyloid pathology in Alzheimer's disease.

2025-07-16 | PXD061104 | Pride

Dissecting detergent-insoluble proteome in Alzheimer's disease by improved TMT-MS of high accuracy

Project description:Protein aggregation of amyloid-β (Aβ) peptides and tau are pathological hallmarks of Alzheimer's disease (AD), which are often resistant to detergent extraction and thus enriched in the insoluble proteome. However, additional proteins that co-accumulate in the detergent-insoluble AD brain proteome remain less studied. Here we comprehensively characterized key proteins and pathways in the detergent-insoluble proteome from human AD brain samples by differential extraction, coupled with tandem mass tags labeling and two-dimensional liquid chromatography tandem mass spectrometry (TMT-LC/LC-MS/MS).

2023-10-24 | PXD038381 | Pride

Quantitative proteomics of tau and Aβ amyloid in detergent insoluble fractions from Alzheimer’s disease brains

Project description:The two hallmarks of Alzheimer’s disease (AD) are A-amyloid- (A) plaques and neurofibrillary tangles marked by phosphorylated tau. There is compelling evidence that aggregating A drives tau accumulation, a process that involves synaptic degeneration leading to cognitive impairment. Conversely there is a growing realization that non-fibrillar (oligomeric) forms of Aβ mediate toxicity in AD. Using quantitative proteomics, we find that AD brain sarkosyl-insoluble pellets are greatly enriched with A at almost equimolar levels to N-terminal truncated microtubule binding region (MTBR) isoforms of tau with multiple post-translational modifications (PTMs). The extracted R3-R4 tau peptides are 100-fold higher compared to N-terminus intact tau peptides. Substantial proportions of site-specific phosphorylation at T181 (~ 22 %) and T217 (~ 16 %) along with other PTMs in the proline rich region (PRR) and MTBR indicate a regional susceptibility of PTMs in aggregated tau. Immuno-electron microscopy reveals that co-purified A and tau co-localize to globular non-filamentous aggregates.

2022-06-04 | PXD032372 | Pride

Quantitative proteomics of tau and Aβ amyloid in detergent insoluble fractions from Alzheimer’s disease brains

2022-06-04 | PXD032389 | Pride

Characterization of detergent insoluble proteome in chronic traumatic encephalopathy

Project description:Proteomic sequencing of postmortem human brain can identify dysfunctional proteins that contribute to neurodegenerative disorders like Alzheimer’s disease and frontotemporal dementia. Similar studies in chronic traumatic encephalopathy are limited, but may provide important new insights into this disorder. Given our previous success with identifying pathology associated proteins, we performed proteomic sequencing of detergent insoluble brain homogenates from frontal cortex of deceased subjects with CTE covering a range of CTE pathologic stages. We compared the insoluble proteome of CTE brain to control and AD brains to identify differentially expressed proteins. We identified over 4000 proteins in CTE brains, including significant enrichment of the microtubule associated protein tau. We also found enrichment and pathologic aggregation of RNA processing factors as seen previously in AD, supporting the previously recognized overlap between AD and CTE. In addition to these similarities, we identified CTE-specific enrichment of a number of proteins which increase with increasing severity of CTE pathology. NADPH dehydrogenase quinone 1 (NQO1) was one of the proteins which showed significant enrichment in CTE and also correlated with increasing CTE stage. NQO1 demonstrated neuropathologic correlation with hyperphosphorylated tau in glial cells, mainly astrocytes. These results demonstrate that quantitative proteomic sequencing of CTE postmortem human brain can identify disease relevant findings and novel cellular pathways involved in CTE pathogenesis.

2017-11-27 | PXD007694 | Pride

Characterization of Detergent Insoluble Proteome in Chronic Traumatic Encephalopathy.

Project description:Quantitative proteomics of postmortem human brain can identify dysfunctional proteins that contribute to neurodegenerative disorders like Alzheimer disease (AD) and frontotemporal dementia. Similar studies in chronic traumatic encephalopathy (CTE) are limited, therefore we hypothesized that proteomic sequencing of CTE frontal cortex brain homogenates from varying CTE pathologic stages may provide important new insights into this disorder. Quantitative proteomics of control, CTE and AD brains was performed to characterize differentially expressed proteins, and we identified over 4000 proteins in CTE brains, including significant enrichment of the microtubule associated protein tau. We also found enrichment and pathologic aggregation of RNA processing factors as seen previously in AD, supporting the previously recognized overlap between AD and CTE. In addition to these similarities, we identified CTE-specific enrichment of proteins which increase with increasing severity of CTE pathology. NADPH dehydrogenase quinone 1 (NQO1) was one of the proteins which showed significant enrichment in CTE and also correlated with increasing CTE stage. NQO1 demonstrated neuropathologic correlation with hyperphosphorylated tau in glial cells, mainly astrocytes. These results demonstrate that quantitative proteomic analysis of CTE postmortem human brain can identify disease relevant findings and novel cellular pathways involved in CTE pathogenesis.

| S-EPMC5939631 | biostudies-literature

Dissecting detergent-insoluble proteome in Alzheimer's disease by improved TMT-MS of high accuracy

Project description:Protein aggregation of amyloid beta peptides and tau are pathological hallmarks of Alzheimer's disease (AD), which are often resistant to detergent extraction and thus enriched in the insoluble proteome. However, additional proteins that co-accumulate in the detergent-insoluble AD brain proteome remain less studied. Here we comprehensively characterized key proteins and pathways in the detergent-insoluble proteome from human AD brain samples by differential extraction, coupled with tandem mass tags labeling and two-dimensional liquid chromatography tandem mass spectrometry (TMT-LC/LC-MS/MS).

2023-04-25 | MSV000091796 | MassIVE

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