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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.

REANALYSED by: PAe005372PAe005452PAe005439PAe005438PAe005427PAe005421PAe005350PAe005345PAe005332PAe005390PAe005386

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung, Liver

SUBMITTER: LI Yaxing

LAB HEAD: Tong Wang

PROVIDER: PXD001694 | Pride | 2015-06-29

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	A549 _20140715_xinku_MGFPeaklist.pride.mgf.gz	Mgf
	A549.mzid.gz	Mzid
	A549.pride.mztab.gz	Mztab
	A549_1.wiff	Wiff
	A549_1.wiff.scan	Wiff

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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.

2016-07-22 | MSV000079997 | 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

Finding missing proteins from the epigenetically manipulated human cell with stringent quality criteria

Project description:There are three major epigenetic mechanisms, DNA methylation, histone modifications, and ncRNAs. The histone is a key player in epigenetics, and the acetylation and methylation are their most common post-translational modifications (PTMs). These histone modifications have important roles in transcriptional regulation, DNA repair, DNA replication, alternative splicing and chromosome condensation. For example, we previously found that H3.3 lysine 36 trimethylation (H3.3K36me3) histone and its reader protein BS69 could work together to regulate pre-mRNA process. Therefore, in this study, we established in vitro histone acetylation, demethylation and methylation models, respectively, by using human lung, liver and colorectal cancer cells.

2022-03-02 | PXD002453 | Pride

The SUMO protease SENP6 regulates the constitutive centromere-associated network by group

Project description:Project 1: Identification of SUMOylated proteins which are regulated by the SUMO protease SENP6. SENP6 knockdown was performed by two independent shRNAs and SUMOylated proteins were purified from U2OS expressing His10-tagged SUMO2 by means of Ni-NTA pulldown. Purified SUMOylated proteins were identified and quantified by label-free quantification. Project 2: Dynamics of chromatin-associated proteins influenced by SENP6. After siRNA-mediated knockdown of SENP6, chromatin fractions of U2OS cells were isolated and abundances of proteins were quantified. Project 3: Analysis of in vitro SUMOylated CENP-T for the presence of SUMOylated SUMO peptides. For this aim purified CENP-T-HA was in vitro SUMOylated with a SUMO Q87R mutant to reduce the length of the tryptic peptide and therefore to be able to identified sit-specific SUMOylation.

2019-09-13 | PXD011963 | Pride

Alzheimer Disease (AD) and AD model detergent insoluble proteomes

2019-06-25 | PXD005321 | Pride

Pitx2 positions the embryonic axis and regulates twinning

Project description:Two experiments performed as follows: One-color microarray experiment comparing the Posterior Marginal Zone (PMZ) and an equivalent anterior explant (AMZ). RNA from the pooled explants (36 of each type) was analysed in triplicate using the A-AFFY-103 array design. One-color microarray experiment comparing the cVg1-expressing site of the anterior cut halves (cVg1-like) and an equivalent cVg1-non-expressing site of the anterior cut halves (cVg1-unlike). RNA from the pooled explants (63 of each type) was analysed in triplicate using the A-AFFY-103 array design.

2014-11-18 | E-MTAB-3116 | biostudies-arrayexpress

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

Human platelet detergent resistant membranes proteome

Project description:Here we characterized the proteins associated with detergent resistant membranes (DRMs) from resting and activated human platelets. We achieved a proteomic profile of 141 DRM proteins involved in many biological pathways including 'PAR-1-mediated thrombin signal events', 'Integrin family cell surface interactions', 'Platelet activation, signalling and aggregation' and 'Platelet degranulation'. Therefore, a high level of relevant platelet signalling and trafficking proteins were identified e.g., Rap 1b, Src, SNAP-23 and syntaxin-11, implicating platelet DRMs as concentrating platforms not only in the critical platelet function of activation but also in secretion/degranulation.

2016-06-23 | PXD002554 | Pride

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

Detergent-resistant microdomains in Saprolegnia parasitica

Project description:Oomycete cells are surrounded by a polysaccharide rich cell wall matrix that, in addition to being essential for cell growth, also functions as protective ”armour”. It follows, that the enzymes responsible for the synthesis of the cell wall provide potential targets for disease management. Interestingly, the oomycete cell wall enzymes are predicted to be plasma membrane proteins. In this project, we used a quantitative (iTRAQ) mass spectrometry-based proteomics approach to characterize the plasma membrane proteome of the hyphal cells of S. parasitica, providing the first complete plasma membrane proteome of an oomycete species. Of significance, is the identification of proteins enriched in functional microdomains (Detergent-Resistant Microdomains; DRMs). In silico analysis showed that DRM-enriched proteins are mainly involved in both molecular transport and β-1,3-glucan synthesis, potentially contributing to post infection pathogenesis.

2024-06-13 | PXD010817 | Pride

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