Browse
Submit Data
Databases
API
Help

Dataset Information

165 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human intracranial tumors LC-MS/MS

ABSTRACT: We found the reality that each Coomassie blue-stained 2D gel spot contained lots of protein species in analysis of in tissue proteome.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Brain

DISEASE(S): Brain Cancer

SUBMITTER: Xianquan Zhan

LAB HEAD: Xianquan Zhan

PROVIDER: PXD004930 | Pride | 2017-12-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

How many proteins can be identified in a 2DE gel spot within an analysis of a complex human cancer tissue proteome?

Zhan Xianquan X Yang Haiyan H Peng Fang F Li Jianglin J Mu Yun Y Long Ying Y Cheng Tingting T Huang Yuda Y Li Zhao Z Lu Miaolong M Li Na N Li Maoyu M Liu Jianping J Jungblut Peter R PR

Electrophoresis 20180208 7

Two-dimensional gel electrophoresis (2DE) in proteomics is traditionally assumed to contain only one or two proteins in each 2DE spot. However, 2DE resolution is being complemented by the rapid development of high sensitivity mass spectrometers. Here we compared MALDI-MS, LC-Q-TOF MS and LC-Orbitrap Velos MS for the identification of proteins within one spot. With LC-Orbitrap Velos MS each Coomassie Blue-stained 2DE spot contained an average of at least 42 and 63 proteins/spot in an analysis of ...[more]

PMID: 29205401

Similar Datasets

Identification of Eimeria sporozoite antigens of common immunogenicity

Project description:Whole sporozoite proteins of Eimeria acervulina were prepared and analyzed by 2-dimensional gel electrophoresis (2-DE) followed by Western blotting using immune sera specific to E. tenella, E. acervulina, or E. necatrix.

2020-05-27 | PXD016418 | Pride

Labeo rohita (Rohu) plasma MALDI-TOF MS/MS

Project description:Arsenic (As) is a toxic environmental contaminant and potential human carcinogen. Chronic intake of arsenic-contaminated water leads to arsenicosis that is a major public health problem in many parts of the world, including India and Bangladesh. Thus, the early detection of arsenic toxicity will greatly benefit patients. However, the detection of arsenicosis needs to be done early before onset of severe symptoms in which case the tools used for detection have to be both sensitive and reliable. In this context, the present study investigated plasma proteome changes in arsenic-exposed Labeo rohita, with the aim of identifying biomarkers for arsenicosis. Changes in the plasma proteome were investigated using gel-based proteomics technology. Using quantitative image analysis of the 2D protein profiles, unique protein spots were identified from the plasma proteome by MALDI-TOF-TOF-MS. Unique proteins identified included Apolipoprotein-A1 (Apo-A1), α-2 macroglobulin-like protein (A2ML), and transferrin. Highly up-regulated protein spots identified in plasma from arsenic-exposed fish were liver-specific, including Apo-A1, and A2ML consistent with liver damage. It is proposed that a combination of these proteins could serve as useful biomarkers of hepatotoxicity and chronic liver disease due to arsenic exposure.

2017-05-11 | PXD003404 | Pride

Identification of immunodominant antigen among Brucella species (B. abortus and B. melitensis) using hyper immune serum from naturally infected hosts

Project description:In the present study, the whole cell protein extracts of B. abortus and B. melitensis were separated using SDS-PAGE and western blotting was carried out with the antiserum from naturally infected host animals (cow, buffalo, goat and sheep). The proteins bands that matched with western blot signals were excised, trypsin digested and subjected to MALDI identification.

2014-12-01 | PXD001270 | Pride

Proteome analysis of testis from infertile protein C inhibitor deficient mice reveals predominant changes in serpin processing and prostaglandin metabolism

Project description:Serine protease inhibitors have therapeutic potential in a variety of pathogenic processes, ranging from thrombosis, altered immune response to liver cirrhosis. To investigate the physiological effects of protein C inhibitor (PCI, serpinA5) this gene was inactivated in a mouse model with the resulting phenotype of male infertility. In the actual report 2D-DIGE analysis was utilized to investigate the molecular mechanisms for PCI in male reproduction. Comparing the testes proteome of three PCI knockout-mice with the three wild-types- demonstrated similar pattern with the exception of a massive upregulation of prostaglandin reductase 1 (10-fold; P < 0.002) and complete shifts in the molecular weights of serpinA1C and serpinA3K. All these PCI-dependent proteome changes were immunologically verified. Unbiased proteome analysis indicated that the inactivation of serpinA5 strongly influenced both the protein species pattern of other A-clade serpins as well as the prostaglandin metabolism in the testes.

2015-12-07 | PXD002944 | Pride

Tissue Proteome Profiling of Ovarian cancer.

Project description:Ovarian cancer is one of the leading causes of death from cancer in females, worldwide. An early diagnosis of ovarian carcinoma is likely to improve clinical outcome of patients in terms of reduced morbidity and mortality. The objective of our project is the proteomic analysis of ovarian malignant and non-malignant tissue samples to find potential biomarkers of disease diagnosis and prognosis that can be assessed non-invasively through patient plasma/serum screening. In this project, we have used a methodical approach involving 2-dimensional gel electrophoresis in conjunction with MALDI-TOF MS analysis followed by immunological validation of the selected markers by western blotting and ELISA for identification of biomarkers of ovarian cancer. The associated research paper is in preparation.

2021-09-08 | PXD014352 | Pride

Tissue Proteome Profiling of Ovarian cancer in Pakistani Population.

Project description:Ovarian cancer is the 5th main cause of death from cancer in females, worldwide. An early and accurate diagnosis of ovarian carcinoma is likely to improve clinical outcome of patients in terms of reduced morbidity and mortality. The objective of our project is the proteome profiling of ovarian malignant and non-malignant tissue samples to find potential biomarkers of disease diagnosis and prognosis. In this project, we have used a systematic protein profiling approach involving 2-dimensional gel electrophoresis coupled with MALDI-TOF MS analysis for identification of biomarkers of ovarian cancer. The associated research paper is in preparation.

2019-11-27 | PXD013827 | Pride

Human mitochondria hub of small RNAs: Analysis by deep Sequencing

Project description:We report here that human mitochondria contain small RNA including microRNA, piRNA, tRNA, rRNA, and RNA repeats. Mitochondria from human cells were purified and RNA isolated. Small RNAs were purified, library generated and analyzed by Illumina Hiseq 2000 system. The sequencing generated 19.5 and 17.7 million reads from HEK-293 and HeLa respectively. 91% and 97% sequences of HEK293 and HeLa respectively were annotated to various classes of small RNA. The total percentage of 4.21 and 2.58 sequences from HEK293 and HeLa respectively was found to be of miRNA. Further, we found only 1.2 % sequences from both the libraries aligned to mitochondrial genome. These results suggest that there is efficient transport of nuclear encoded small RNA to mitochondria. The small RNA in mitochondria may regulate critical cellular processes. Analyzing the smallRNA in human mitochondria from two human cell lines (HEK-293 and HeLa).

2013-03-05 | E-GEOD-32185 | biostudies-arrayexpress

Mouse Skin LC-MS/MS

Project description:Previously, we reported that a null mutation of the Zdhhc13 gene caused by ethylnitrosourea (ENU) mutagenesis in mice resulted in severe systematic phenotypes with amyloidosis, alopecia, dermatitis and osteoporosis. In this study we continued to delineate the pathological mechanism for the dermatitis phenotype and to explore potential palmitoylation substrates of ZDHHC13, which potentially explain the loss-of-function phenotype of ZDHHC13 in skin. Our data clearly suggested that protein S-palmitoylation of a constellation of skin barrier components by ZDHHC13 is crucial for their protein stability, functions, and overall barrier integrity.

2022-02-25 | PXD002958 | Pride

Dietary effect on the proteome of the common octopus (Octopus vulgaris) paralarvae, 2D-DIGE gel data

Project description:Nowadays, the common octopus (Octopus vulgaris) culture is hampered by massive mortalities occurring during early life-cycle stages (paralarvae). Despite the causes of the high paralarvae mortality are not yet well defined and understood, the nutritional stress caused by inadequate diets is pointed out as one of the main factors. In this study the effects of diet on paralarvae is analyzed through a proteomic approach, to search for novel biomarkers of nutritional stress. A total of 43 proteins showing differential expression in the different conditions studied have been identified. The analysis highlights proteins related with the carbohydrate metabolism: glyceraldehyde-3-phosphate-dedydrogenase (GAPDH), triosephosphate isomerase; other ways of energetic metabolism: NADP+-specific isocitrate dehydrogenase, arginine kinase; detoxification: glutathione-S-transferase (GST); stress: heat shock proteins (HSP70); structural constituent of eye lens: S-crystallin 3; and cytoskeleton: actin, actin-beta/gamma1, beta actin. These results allow defining characteristic proteomes of paralarvae depending on the diet; as well as the use of several of these proteins as novel biomarkers to evaluate their welfare linked to nutritional stress. Notably, the changes of proteins like S-crystallin 3, arginine kinase and NAD+ specific isocitrate dehydrogenase, may be related to fed versus starving paralarvae, particularly in the first 4 days of development.

2022-03-01 | PXD006242 | Pride

Impact of glycan positioning on HIV-1 Env glycan shield density, function, and antibody recognition

Project description:N-glycans, which represent >50% mass of the HIV-1 envelope (Env) trimer, play important roles for virus-cell entry and immune evasion. How each glycan unit interacts to shape the Env protein-sugar complex and affects Env function is not well understood. Here, high-resolution glycomics analysis of two Env variants from the same donor, with differing functional characteristics and N-glycosylation-site composition, revealed that changes to key N-glycosylation-site not only affected the Env structure at distant locations, but also had a ripple effect on Env-wide glycan processing, virus infectivity, and antibody recognition and virus neutralization. Specifically, the N262 glycan, although not located in the CD4-binding site, controlled Env binding to the CD4 receptor, affected the recognition of Env by several glycan-dependent broadly neutralizing antibodies, and altered heterogeneity of glycosylation at several sites, with N156, N160, and N448 displaying limited glycan processing. Molecular dynamic simulations visualized how specific oligosaccharide positions can move to compensate for loss of a glycan. This study demonstrates how changes in individual glycan units can alter molecular dynamics and processing of the Env-glycan shield and, consequently, Env function.

2021-09-09 | PXD017941 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data