1D-DDA of human diploid fibroblasts, TIG-3 cells
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Lung, Fibroblast
SUBMITTER: 
Masaki Matsumoto
LAB HEAD: Keiichi I. Nakayama
PROVIDER: PXD001499 | Pride | 2016-12-06
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 20130402_IDA_TIG3 2ug_240min.pride.mgf.gz | Mgf | |||
| 20130402_IDA_TIG32ug_240min.mgf | Mgf | |||
| 20130402_IDA_TIG32ug_240min.wiff | Wiff | |||
| 20130402_IDA_TIG32ug_240min.wiff.scan | Wiff | |||
| F009576.mzid.gz | Mzid |
Items per page: 5 1 - 5 of 6 |
Similar Datasets
Project description:Joint diseases are often characterized by inflammatory processes resulting in pathological changes in joint tissues, including cartilage degradation and release of components to the synovial fluid. The complement system plays a central role in promoting the inflammation. Since several cartilage proteins are known to interact with complement, causing either activation or inhibition of the system, we aimed to investigate these interactions comprehensively. Bovine cartilage explants were cultured with interleukin-1alpha (IL-1a) to induce cartilage degradation, followed by incubation with human serum to allow interactions with complement. Label-free selected reaction monitoring (SRM) mass spectrometry (MS) was then used to specifically quantify complement proteins interacting with the cartilage explant. In parallel, the time-dependent degradation of cartilage was detected using tandem MS (MS/MS). Complement proteins resulting from activation of the classical and alternative pathway as well as the terminal pathway were detected on IL-1a stimulated cartilage at time points when clear alterations in the extracellular matrix composition had occurred. To confirm SRM results indicating complement activation, increased levels of the complement activation product C4d were detected by ELISA in serum after incubation with IL-1a stimulated cartilage. Further, typical activated (cleaved) C3 fragments were detected by western blotting of urea extracts of IL-1a stimulated cartilage. No complement activation was triggered by cartilage cultured in the absence of IL-1a. Components released from IL-1a stimulated cartilage during culture had an inhibitory effect on complement activation. These were released after a longer incubation period with IL-1a and may represent a feedback reaction to cartilage-triggered complement activation observed after a shorter incubation period.
2016-09-27 | PXD004158 | Pride
Project description:The data includes a transcriptome analysis of K562 cell lines in which the gene N-glycanase 1 (NGLY1) was mutated in exon 1 and/or exon 3 to include loss of function mutations as described in Mueller and Jakob et al, 2020. The data were used in conjunction with whole proteome MS/MS experiments to show a gene expression profile consistent with NGLY1 deficiency, a human disease. The experiments demonstrate the wide ranging effect of the loss of NGLY1 on a cellular system.
2020-04-20 | E-MTAB-8876 | biostudies-arrayexpress
Project description:The neuroblastoma-derived cell line N2a is permissive to certain prion strains but resistant sublines unable to accumulate the pathological proteinase-K resistant form of the prion protein can be isolated. We compared for gene expression and phenotypes different N2a sublines that were susceptible or resistant to the 22L prion strain. Karyotypes and comparative genomic hybridization arrays revealed chromosomal imbalances but did not demonstrate a characteristic profile of genomic alterations linked to prion susceptibility. Likewise, we showed that this phenotype was not dependent on the binding of PrPres, the expression of the prion protein gene, or on its primary sequence. We completed this analysis by looking using real-time quantitative PCR at the expression of a set of genes encoding proteins linked to prion biology. None of the candidates could account by itself for the infection phenotype, nevertheless sublines had distinct transcriptional profiles. Taken together, our results do not support a role for specific genomic abnormalities and possible candidate proteins in N2a prion susceptibility. They also reveal genetic heterogeneity among the sublines and serve as a guidance for further investigation into the molecular mechanisms of prion infection. In a first approach, CGHa profiles were established for the parental cell line N2apcl, a sensitive (G9) and a resistant (F1) sublines, as compared to A/HeJ mouse strain normal DNA. To allow a more precise description of the differences between N2apcl and six of its derived sub-lines (58, D11, F1, G9, R4, R10), N2apcl DNA was used as reference DNA in a series of CGHa experiments, avoiding the potential copy number polymorphisms between the cell lines and A/HeJ murine DNAs.
2010-06-19 | E-GEOD-5374 | biostudies-arrayexpress
Project description:Ribosome assembly is a complex process involving the coordination of multiple enzymes. A recently discovered endoribonuclease (RNase), Las1, and the poly-nucleotide kinase (PNK), Grc3, assemble into a complex. To attempt to understand the coordination of the two enzymes in this complex, we performed chemical crosslinking and mass spectrometry and also solved a series of cryo-electron microscopy structures of RNase PNK in multiple conformational states.
2019-09-11 | PXD014738 | Pride
Project description:To estimate the amount of proteins in HeLa, whole cell digests were subjected to fractionation by off line reverse phase chromatography at basic pH followed by LC-MS/MS analysis
2016-12-07 | PXD001441 | Pride
Project description:Neuropathic pain is a major clinic probelm as it is very difficult to treat and mechanism remain unknown. Here, we investigated the differential expression of proteins in the central nuecleus of amygdala (CeA) in neuropathic pain moldel spinal nerve transection (SNT)in rats. CeA was excised from naive, sham, SNTmodels at days 3, 7, 14 and 21 rats. The aim was to quatify the differential proteins in CeA including memebrane proteins. We used gel- and mass spectrometry- based proteomics. For gel-proteomics, total tissue lysate proteins were separated by 2D-PAGE. The 2D gels from different SNT time points against Sham and control rats were compared using Progenesis SameSpot software. The spots with fold change greater then 2 excised for the proteins IDs by LC-MS/MS. Protein spots were digested using trypsin. Extracted peptides were injected on the nano C18 column and measured by a LTQ Orbitrap XL or a LTQ Orbitrap Velos mass spectrometers. For the identification of membrane proteins in CeA, we used 1-SDS-PAGE and cut the gel region of MW 80 kDa and higher for nano-LC-MS/MS analysis. We also quantified membrane proteins by utilising triplex stabel isotope dimethyl labelling at the peptide level. Sham, control and day 3, 7 and 21 after SNT surgery rats CeA membrane proteins were purified and digested by trypsin and labelled with "light", "medium" and "heavy" dimethyl labelling reagents. The resulting peptides were analysed by a nano LC connected to the Q Exactive mass spectrometer. Quantification of peptide was processed using Proteome Discoverer 1.3.
2020-02-21 | PXD017473 | Pride
Project description:The standard proteomics database search strategy involves searching spectra against a peptide database and estimating the false discovery rate (FDR) of the resulting set of peptide-spectrum matches. One assumption of this protocol is that all the peptides in the database are reDR control strategies are needed. Recently, two methods were proposed to address this problem: subset-search and all-sub. We show that both methods fail to control the FDR. For subset-search, this failure is due to the presence of “neighbor” peptides, which are defined as irrelevant peptides with a similar precursor mass and fragmentation spectrum as a relevant peptide. Not considering neighbors compromises the FDR estimate because a spectrum generated by an irrelevant peptide can incorrectly match well to a relevant peptide. Therefore, we have developed a new method, “filter then subset-neighbor search” (FSNS), that accounts for neighbor peptides. We show evidence that FSNS properly controls the FDR when neighbors are present and that FSNS outperforms group-FDR, the only other method able to control the FDR relative to a subset of relevant peptides
2021-06-17 | PXD022778 | Pride
Project description:Hepatic cell lines serve as economical and reproducible alternatives for primary human hepatocytes. However, the utility of hepatic cell lines to examine bile acid homeostasis and cholestatic toxicity is limited due to abnormal expression and function of bile acid-metabolizing enzymes, transporters, and the absence of canalicular formation. Previously, addition of dexamethasone (DEX) and Matrigel™ overlay restored expression, localization, and function of the bile salt export pump (BSEP), and formation of bile canalicular-like structures in four-week cultures of HuH-7 human hepatoma cells. We present here an improved differentiation process with the addition of 0.5% dimethyl sulfoxide (DMSO), which increased the expression and function of the major bile acid uptake and efflux transporters, sodium taurocholate co-transporting polypeptide (NTCP) and BSEP, respectively, in two-week HuH-7 cell cultures. This in vitro model was further characterized for expression of cytochrome P450 enzymes (CYP450s), uridine 5'-diphospho-glucuronosyltransferase (UGTs) and transporters using quantitative targeted proteomics.
2022-10-14 | PXD031731 | Pride
Project description:Campylobacter jejuni (C. jejuni) protein microarrays were used to identify immunogenic C. jejuni proteins that may be useful in the development of biomarkers, diagnostic assays, or subunit vaccines for humans or livestock. A native protein microarray with over 1400 individually purified GST-tagged C. jejuni proteins (86 % of the proteome), was constructed and screened for antibody titers present in test sera. The protein arrays were screened with antisera from rabbits inoculated with whole C. jejuni or various serotypes of E. coli or Salmonella, with antisera from mice infected with C. jejuni, and sera from healthy humans. Dual detection of GST signals was incorporated as a way of normalizing the variation of protein concentrations contributing to the antibody staining intensities.
2018-12-29 | E-MTAB-7535 | biostudies-arrayexpress
Project description:The HIV-1 Trans-Activator of Transcription (Tat) protein binds to multiple host cellular factors and greatly enhances the level of transcription of the HIV genome. Here, we report the genome-wide binding map of Tat to the human genome in Jurkat T cells (Jurkat-Tat cells) using chromatin immunoprecipitation combined with next-generation sequencing. cDNA microarray was used to monitor gene expression changes between Jurkat and Jurkat-Tat cells. Additionally, we compared distribution of H3K9ac near gene promoters between Jurkat and Jurkat-Tat cells using ChIP-chip method and hybridized onto Agilent promoter array. Our data reveal that TatM-CM-"M-BM-^@M-BM-^Ys interaction with the host genome is more extensive than previously thought, with potentially important implications for the viral life cycle. Expression profiles on Jurkat-Tat cells versus Jurkat cells. ChIP on chip for H3K9ac in Jurkat-Tat versus Jurkat cells. ChIP-seq for HIV-1 Tat protein in Jurkat-Tat cells.
2011-11-06 | E-GEOD-30738 | biostudies-arrayexpress