Dataset Information

HepG2 whole cell lysate LC-MS and 2D-LC-MS

ABSTRACT: Enchancing sensitivity of shotgun proteomics by means of offline fractionation of complex peptide sample of HepG2 by reversed phased chromatography in alkaline conditions. The aim of this study is deep human chromosome 18 proteome coverage.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Nikita Vavilov

LAB HEAD: Victor Gavrilovich Zgoda

PROVIDER: PXD019263 | Pride | 2020-11-26

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	DefaultProteinReportLC-MS.xls	Xls
	Defaultproteinreport2D-LC-MS.xlsx	Xlsx
	HepG2_1-3.raw	Raw
	HepG2_1-3_191221232043.raw	Raw
	HepG2_1-3_191222002312.raw	Raw

Items per page:

1 - 5 of 70

Publications

Proteomic Analysis of Chr 18 Proteins Using 2D Fractionation.

Vavilov Nikita E NE Zgoda Victor G VG Tikhonova Olga V OV Farafonova Tatiana E TE Shushkova Natalya A NA Novikova Svetlana E SE Yarygin Konstantin N KN Radko Sergey P SP Ilgisonis Ekaterina V EV Ponomarenko Elena A EA Lisitsa Andrey V AV Archakov Alexander I AI

Journal of proteome research 20201117 12

One of the main goals of the Chromosome-Centric Human Proteome Project (C-HPP) is detection of "missing proteins" (PE2-PE4). Using the UPS2 (Universal proteomics standard 2) set as a model to simulate the range of protein concentrations in the cell, we have previously shown that 2D fractionation enables the detection of more than 95% of UPS2 proteins in a complex biological mixture. In this study, we propose a novel experimental workflow for protein detection during the analysis of biological sa ...[more]

PMID: 33202127

Similar Datasets

Project description:Environmental enteric dysfunction (EED), a chronic diffuse inflammation of the small intestine, is associated with stunting in children in the developing world. The pathobiology of EED is poorly understood because of the lack of a method to elucidate the host response. This study utilized a novel microarray method to interrogate the host transcriptome in feces in Malawian children with EED. Our data showed that the children studied had a range of %L values, consistent a spectrum of EED from normal to severe. We identified 12 transcripts associated with the severity of EED, including chemokines that stimulate T-cell proliferation, Fc fragments of multiple immunoglobulin families, interferon-induced proteins, activators of neutrophils and B-cells, and mediators that dampen cellular responses to hormones. EED associated transcripts mapped to pathways related to cell adhesion, and responses to a broad spectrum of viral, bacterial and parasitic microbes and enhanced phagocytosis. Several mucins, regulatory factors and protein kinases associated with the maintenance of the mucous layer were expressed less in children with EED than normal children. In conclusion, EED represents the focused activation of elements of the immune system and is associated with widespread intestinal barrier disruption. The differentially expressed transcripts may be explored as potential biomarkers. This study was carried out, firstly using Affymetrix Human Transcriptome Array 2.0 (HTA2.0, data have already been deposited in the GEO database: GSE74681) to profile the transcriptome of the host stool RNAs in 259 subjects, and then using droplet digital PCR (ddPCR) assays to validate the microarray data in terms of signal correlation. The ddPCR assay was done for a total of 60 genes in 25 - 236 (median 67) of the 258 RNA samples per RNA availability (1 of 259 samples [stool_080B] was not used for any of the 60 assays due to lack of availability). The data of the first 42 assays (genes) in the matrix sheets were used in Figure 4 for signal correlation analysis, and the data of the rest 18 assays (genes) were used in Table 4 for validation of 18 significant genes identified in biological pathway analysis.