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Parallel reaction monitoring (PRM) analysis for protein expression

ABSTRACT: According to a previous study on the microscopic examination of stem barks in ramie, bast fibers from different parts of stem bark showed distinct differences at the developmental level: specifically, the barks in the top part of stem (TPS) did not initiate fiber growth, whereas barks in the middle part of stem (MPS) had a large number of fibers with thickening secondary walls. We have performed the phosphoproteome analysis for the tissues of TPS and MPS, and then carried out the comparison of phosphorylation level of proteins between two tissues, thereby to identified differentially phosphorylated proteins. These datasets represent the raw UHPLC spectra for phosphoproteome of ramie TPS and MPS.

INSTRUMENT(S): LTQ

ORGANISM(S): Boehmeria Nivea (chinese Grass) (urtica Nivea)

TISSUE(S): Bark

SUBMITTER: Zeng Zheng

LAB HEAD: Zeng Zheng

PROVIDER: PXD026598 | Pride | 2022-02-17

REPOSITORIES: Pride

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			Action	DRS
	K9031PRM101_MPS_1.raw	Raw
	K9031PRM101_MPS_2.raw	Raw
	K9031PRM101_MPS_3.raw	Raw
	K9031PRM101_TPS_1.raw	Raw
	K9031PRM101_TPS_2.raw	Raw

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Publications

Identification of proteins associated with bast fiber growth of ramie by differential proteomic analysis.

Li Fu F Zeng Zheng Z Huang Renyan R Wang Yanzhou Y Liu Touming T

BMC genomics 20211202 1

<h4>Background</h4>Ramie is an important fiber-producing crop in China, and its fibers are widely used as textile materials. Fibers contain specialized secondary cellular walls that are mainly composed of cellulose, hemicelluloses, and lignin. Understanding the mechanism underlying the secondary wall biosynthesis of fibers will benefit the improvement of fiber yield and quality in ramie.<h4>Results</h4>Here, we performed a proteomic analysis of the bark from the top and middle parts of the stem, ...[more]

PMID: 34856929

Similar Datasets

Proteome and differential proteomic analysis of ramie stem bark

Project description:According to a previous study on the microscopic examination of stem barks in ramie, bast fibers from different parts of stem bark showed distinct differences at the developmental level: specifically, the barks in the top part of stem (TPS) did not initiate fiber growth, whereas barks in the middle part of stem (MPS) had a large number of fibers with thickening secondary walls. We have performed the Proteome analysis for the tissues of TPS and MPS, and then carried out the comparison of Proteomic level of proteins between two tissues, thereby to identified differentially Proteomic proteins. These datasets represent the raw UHPLC spectra for Proteome of ramie TPS and MPS.

2022-02-17 | PXD026596 | Pride

Phosphoproteome of ramie stem barks

Project description:According to a previous study on the microscopic examination of stem barks in ramie, bast fibers from different parts of stem bark showed distinct differences at the developmental level: specifically, the barks in the top part of stem (TPS) did not initiate fiber growth, whereas barks in the middle part of stem (MPS) had a large number of fibers with thickening secondary walls. We have performed the phosphoproteome analysis for the tissues of TPS and MPS, and then carried out the comparison of phosphorylation level of proteins between two tissues, thereby to identified differentially phosphorylated proteins. These datasets represent the raw UHPLC spectra for phosphoproteome of ramie TPS and MPS.

2021-03-21 | PXD024896 |

Ubiquitylome of ramie stem bark

Project description:According to a previous study on the microscopic examination of stem barks in ramie, bast fibers from different parts of stem bark showed distinct differences at the developmental level: specifically, the barks in the top part of stem (TPS) did not initiate fiber growth, whereas barks in the middle part of stem (MPS) had a large number of fibers with thickening secondary walls. We have performed the Ubiquitylome analysis for the tissues of TPS and MPS, and then carried out the comparison of Ubiquitination level of proteins between two tissues, thereby to identified differentially Ubiquitinated proteins. These datasets represent the raw UHPLC spectra for Ubiquitylome of ramie TP S and MPS.

2021-03-21 | PXD024923 |

Proteomic and functional analyses of the periodic membrane skeleton in neurons

Project description:Actin, spectrin, and associated proteins form a membrane-associated periodic skeleton (MPS) in neurons. The molecular composition and functions of the MPS remain incompletely understood. Here, we combined co-immunoprecipitation and mass spectrometry analyses to identify candidate MPS-interacting proteins from cultured hippocampal neurons and adult mouse brains. In addition, we also used quantitative mass spectrometry analysis based on Tandem Mass Tag (TMT) isobaric labeling to determine how the expression levels of proteins are differentially regulated at the proteomic scale upon depletion of βII-spectrin, an important molecular component of the MPS. These results provide a systematic picture of the interactome of the MPS, and new insights into new functions of the MPS in neurons.

2022-05-04 | PXD030886 | Pride

Proteome of microparticles derived from Mycobacterium tuberculosis infected macrophages

Project description:Microparticles (MP) are small membranous particles (100-1000 nm) released under normal steady-state conditions and are thought to provide a communication network between host cells. Previous studies demonstrated that Mycobacterium tuberculosis (M.tb) infection of macrophages increased the release of MPs, and these MPs induced a proinflammatory response from uninfected macrophages in vitro and in vivo following their transfer into uninfected mice. To determine how M.tb infection modulates the protein composition of the MPs, and if this contributes to their proinflammatory properties, we compared the proteomes of MPs derived from M.tb-infected (TBinf-MP) and uninfected human THP-1 monocytic cells. MP proteins were analysed by GeLC-MS/MS with spectral counting revealing 68 proteins with statistically significant differential abundances. The 42 proteins increased in abundance in TBinf-MPs included proteins associated with immune function (7), lysosomal/endosomal maturation (4), vesicular formation (12), nucleosome proteins (4) and antigen processing (9). Prominent among these were the type I interferon inducible proteins, ISG15, IFIT1, IFIT2, and IFIT3. Exposure of uninfected THP-1 cells to TBinf-MPs induced increased gene expression of isg15, ifit1, ifit2, and ifit3 and the release of proinflammatory cytokines. These proteins may regulate the proinflammatory potential of the MPs and provide candidate biomarkers for M.tb infection.

2022-02-28 | PXD002026 | Pride

MPS vaccination alters long-term gene expression of antigen-presenting cells in lymph nodes

Project description:Given the importance of sustained antigen presentation in maintenance of lymph node (LN) immune responses, we hypothesized that vaccine antigen availability and antigen-presenting cell (APC) populations may affect LN expansion. Compared to LNs of mice given the full MPS vaccine, LNs of mice given an MPS vaccine without antigen became prominently less enlarged and contracted sooner.To identify potential mediators of this differential, antigen-dependent response, we next focused the analysis of our scRNA-seq dataset on LN APC populations.

2024-04-05 | E-MTAB-13698 | biostudies-arrayexpress

Proteomic analysis of mucopolysaccharidosis IIIB mouse brain

Project description:Mucopolysaccharidosis IIIB (MPS IIIB) is an inherited metabolic disease due to deficiency of ÃƒÅ½Ã‚Â±-N-Acetylglucosaminidase (NAGLU) enzyme with subsequent storage of undegradedheparan sulfate (HS). The main clinical manifestations of the disease are profound intellectual disability and neurodegeneration. To identify potential biomarkers and novel neuropathological mechanisms of MPS IIIB, a label-free quantitative proteomic approach was applied to compare the proteome profile of brains from MPS IIIB and control mice. Proteins were identified through a bottom up analysis and 130 were significantly under-represented and 74 over-represented in MPS IIIB mouse brains compared to wild type (WT). Multiple bioinformatic analyses of the differentially abundant proteins allowed to define three major clusters: proteins involved in cytoskeletal regulation, synaptic vesicle trafficking, and energy metabolism. The results highlight the involvement of these clustered proteins in the neuropathology of MPS IIIB disease. The proteins identified in this study would provide potential targets for diagnostic and therapeutic studies of MPS IIIB.

2020-02-26 | PXD017363 | Pride

Comparison of Akt activated cells and placental mesenchymal progenitors

Project description:The goal of our experiment is to compare the cytokines and membrane factors that are differentially expressed between akt-activated endothelial cells and mesenchymal progenitors. Those two cell type have previously been described as potential niche for HSC expansion in vivo and in vitro. We isolated placental mesenchymal progenitors as previously described (Raynaud CM. et al. 2012 stem cell international). HUVECs cells were also isolated from cord and transfected with E4ORF1 as previously described (Seandel M. et al. 2008 PNAS). Both cell type were grown separately 3 days in X-Vivo media complemented with TPO, Flt3 and SCF (HSc amplification media). Pl-MPs and E4+ECs RNA was isolated using Trizol reagent followed by additional purification using RNAeasy extraction kit from Qiagen (74106, QIAGEN) with RNA yields that produces satisfactory microarray data. Two quality control measures were carried out: (1) A spectrophotometric analysis (2) A size fractionation procedure using a microfluidics instrument (Agilent Technologies). 200 ng of total RNA were analyzed on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. Data were analyzed using Parteck Software (V6.09.1110-6; Affimetrix).

2013-08-30 | E-MEXP-3725 | biostudies-arrayexpress

Induced pluripotent stem cells from CINCA syndrome patients as a model for dissecting somatic mosaicism and drug discovery

Project description:Chronic infantile neurological cutaneous and articular (CINCA) syndrome is an IL-1-driven autoinflammatory disorder caused mainly by NLRP3 mutations. The pathogenesis of CINCA syndrome patients who carry NLRP3 mutations as somatic mosaicism has not been precisely described because of the difficulty in separating individual cells based on the presence or absence of the mutation. Here, we report the generation of NLRP3-mutant and non-mutant induced pluripotent stem cell (iPSC) lines from two CINCA syndrome patients with somatic mosaicism, and describe their differentiation into macrophages (iPS-MPs). We found that mutant cells are predominantly responsible for the pathogenesis in these mosaic patients because only mutant iPS-MPs showed the disease relevant phenotype of abnormal IL-1M-NM-2 secretion. We also confirmed that the existing anti-inflammatory compounds inhibited the abnormal IL-1M-NM-2 secretion, indicating that mutant iPS-MPs are applicable for drug screening for CINCA syndrome and other NLRP3-related inflammatory conditions. Our results illustrate that patient-derived iPSCs are useful for dissecting somatic mosaicism, and that NLRP3-mutant iPSCs can provide a valuable platform for drug discovery for multiple NLRP3-related disorders. To characterize iPS and differentiated cells, RNA expression profiles were evaluated by microarray analysis.We analyzed iPC cells and macrophage from healthy volunteers and CINCA syndrome patients. Human ES cella and fibroblasts were used as control.

2012-06-10 | E-GEOD-38626 | biostudies-arrayexpress

Global DNA methylation analysis of mouse totipotent potential stem cells, extended pluripotent stem cells and mouse embryonic stem cells

Project description:It is challenging to derive totipotent stem cells in vitro that functionally and molecularly resemble cells from totipotent embryos. Here, we report that a chemical cocktail enables the derivation of totipotent-like stem cells, designated as totipotent potential stem (TPS) cells, from 2-cell mouse embryos and extended pluripotent stem cells that can be stably maintained long-term in vitro. TPS cells shared features with 2-cell mouse embryos in terms of totipotency markers, transcriptome, chromatin accessibility and DNA methylation patterns. In vivo chimeric assays show that these cells have embryonic and extraembryonic developmental potentials at the single cell level. Moreover, TPS cells can be induced into blastocyst-like structures resembling preimplantation mouse blastocysts. Mechanistically, inhibition of HDAC1/2 and DOT1L activity and activation of RARγ signaling are important for inducing and maintaining totipotent features of TPS cells. Our study opens up a path toward fully capturing totipotent stem cells in vitro.

2022-05-04 | GSE201750 | GEO

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