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

ABSTRACT: 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).

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Brain

SUBMITTER: FNU MASIHUZZAMAN

LAB HEAD: Junmin Peng

PROVIDER: PXD038381 | Pride | 2023-10-24

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Content_template_of_TMTchannel.txt	Txt
	checksum.txt	Txt
	hTMT340_f01.pepXML	Pepxml
	hTMT340_f01.raw	Raw
	hTMT340_f02.pepXML	Pepxml

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1 - 5 of 206

Publications

Dissecting Detergent-Insoluble Proteome in Alzheimer's Disease by TMTc-Corrected Quantitative Mass Spectrometry.

Zaman Masihuz M Fu Yingxue Y Chen Ping-Chung PC Sun Huan H Yang Shu S Wu Zhiping Z Wang Zhen Z Poudel Suresh S Serrano Geidy E GE Beach Thomas G TG Li Ling L Wang Xusheng X Peng Junmin J

Molecular & cellular proteomics : MCP 20230624 8

Protein aggregation of amyloid-β 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 coaccumulate in the detergent-insoluble AD brain proteome remain understudied. Here, we comprehensively characterized key proteins and pathways in the detergent-insoluble proteome from human AD brain samples using differential extraction, tandem mass tag (TMT) labe ...[more]

PMID: 37356496

Similar Datasets

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

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

Targeted quantification of detergent-insoluble RNA-binding proteins in Alzheimer’s disease reveals disease-specific coaggregation signatures

Project description:Core spliceosome and related RNA-binding proteins aggregate in Alzheimer’s disease (AD) brain even in early asymptomatic stages (AsymAD) of disease. To assess the specificity of RNA-binding protein aggregation in AD, we developed a targeted mass spectrometry approach to quantify broad classes of RNA-binding proteins with other pathological proteins including Tau and amyloid beta (Aβ) in detergent insoluble fractions from AD brain and that of other dementias. In total, we quantified 870 peptides from 385 detergent-insoluble RNA-binding proteins across 44 cortical tissues including controls, AsymAD, AD, and Parkinson’s Disease (PD). Relative levels of specific insoluble RNA-binding proteins across different disease groups correlated with accumulation of Aβ and Tau aggregates. RNA-binding proteins, including splicing factors with homology to the basic-acidic dipeptide repeats of U1-70K, preferentially aggregated in AsymAD and AD. In contrast, PD brain aggregates were relatively depleted of many RNA-binding proteins compared to AsymAD and AD groups. Correlation network analyses resolved 29 distinct modules of co-aggregating proteins including modules linked to spliceosome assembly, nuclear speckles and RNA splicing. Modules related to spliceosome assembly and nuclear speckles progressively increased in insolubility across progressive AD stages, whereas the RNA splicing module was decreased specifically in PD. Collectively, this work identifies classes of RNA-binding proteins that distinctly co-aggregate in detergent-insoluble fractions across neurodegenerative diseases.

2021-03-17 | PXD022144 | 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

Transcriptional Response of Mycobacterium tuberculosis to Growth without Detergent

Project description:Transcriptional profiling of Mycobacterium tuberculosis H37Rv grown in minimal media with or without detergent for 5 days to investigate basis of differences in vaccine efficacy dependent on growth conditions Two condition experiment, detergent grown vs. grown without detergent. Biological replicates: 3 of each condition, independently grown and harvested. One replicate per array, third array is a dye-flip.

2016-05-31 | E-GEOD-72745 | biostudies-arrayexpress

Mtb Rv2869c mutant/WT +/- detergent

Project description:The purpose of this experiment is to examine gene expression controlled by Rv2869c in the presence or absence of detergent (Tween 80) in the culture medium. Keywords: parallel sample

2005-07-22 | GSE2561 | GEO

Amyloid-beta Citrullination in Alzheimer's Disease

Project description:Amyloid-beta peptides which aggregate and accumulate in Alzheimer’s disease (AD) brain are known to have sequential N-terminal truncations and multiple post-translational modifications (PTM) such as isomerization, pyroglutamate formation, phosphorylation, nitration and dityrosine cross-linking. Here we add to the list of PTM citrullination (deimination) of Arg5 residue in plaque-derived Abeta in sporadic AD brains, identified by tandem mass spectrometry. We quantitated the level of citrullination on multiple N-truncated Abeta isoforms present in plaque-associated fractions and found that almost 30 % of pyroGlu3-Abeta pool was citrullinated in plaques from AD temporal cortex. We also documented citrullinated Abeta peptides in the detergent insoluble fractions from AD frontal cortex with ~ 22 % citrullination in the pyroGlu3-Abeta pool. Citrullination of Abeta is a common PTM, closely associated with pyroglutamate-Abeta formation and Abeta accumulation in AD. This may have implications for Abeta toxicity, auto-antigenicity of Abeta, and may be relevant for the design of diagnostic assays and therapeutic targeting.

2021-11-24 | PXD025620 | Pride

Transcriptional Response of Mycobacterium tuberculosis to Growth without Detergent

2016-05-31 | GSE72745 | GEO

A Brucella ovis HWE histidine kinase is important for detergent resistance.

Project description:Through a system-level analysis of non-essential two-component signal transduction systems (TCS) genes in Brucella ovis, we have discovered that deletion of an HWE histidine kinase, BOV_1602, leads to significant increase in resistance to SDS detergent and other anionic or zwitterionic detergents. To better understand this detergent resistance phenotype, we performed RNA-seq experiment using both WT and ∆BOV_1602 cultured on no stress (TASB) or TSAB supplemented with 0.004% SDS.

2024-03-26 | GSE262183 | GEO

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