Proteins identification using proteomics
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)
TISSUE(S): Blood Serum
SUBMITTER: 
Meng-Ting Yang
LAB HEAD: Meng-Ting Yang
PROVIDER: PXD017472 | Pride | 2021-01-04
REPOSITORIES: Pride
Similar Datasets
Project description:To date few DDK substrates other than the MCM helicase have been identified, and none are implicated in fork protection or restart. Here we searched for such factors, using SILAC and quantitative mass spectrometry to identify the DDK phosphoproteome during fork stalling.
2021-06-29 | PXD014399 | Pride
Project description:The differentiation of human CD4+ T cells into different subtypes of T helper cells and regulatory T cells is crucial for an appropriate immunological response. Among all subtypes Th1 cells are the most prominent specific cell type, representing about 50% of all lymphocytes. So far most global proteomic studies have used either only partially purified T helper cell subpopulations and/or have employed artificial protocols for inducing specific T helper cell subtypes and/or applied gel based approaches. These studies have shed light on molecular details of certain aspects of the proteome. Nevertheless a more global analysis of highly pure primary naïve and Th1 cells by LC-MS/MS is needed in order to contribute to the proteome based T cell subtype characterization. We were able to identify 1757 proteins in total, out of which 49 were significantly regulated. The utilization of highly purified Th1 cells for a global proteome assessment and the bioinformatical comparison to naïve cells reveals the relevance of changes in the metabolism and the ubiquitination pathways upon T cell differentiation.
2015-10-13 | PXD001066 | Pride
Project description:DNA damage causes genomic instability underlying many diseases, with traditional analytical approaches providing minimal insight into the spectrum of DNA lesions in vivo. Here we used untargeted chromatography-coupled tandem mass spectrometry-based adductomics (LC-MS/MS) to define the landscape of DNA modifications in rat and human tissues. A basis set of 114 putative DNA adducts was identified in heart, liver, brain, and kidney in 1-26-month-old rats and 111 in human heart and brain by “stepped MRM” LC-MS/MS. Subsequent targeted analysis of these species revealed species-, tissue-, age-, and sex-biases. Structural characterization of 10 selected adductomic signals as known DNA modifications validated the method and established confidence in the DNA origins of the signals. Along with strong tissue biases, we observed significant age-dependence for 36 adducts, including N2-CMdG, 5-HMdC, and 8-Oxo-dG in rats and 1,N6-εdA in human heart, as well as sex biases for 67 adducts in rat tissues. These results demonstrate the potential of adductomics for discovering the true spectrum of disease-driving DNA adducts. Our dataset of 114 putative adducts serves as a resource for characterizing dozens of new forms of DNA damage, defining mechanisms of their formation and repair, and developing biomarkers of aging and disease.
2023-09-12 | PXD045311 | Pride
Project description:Palmitic acid (C16:0) is the most abundant saturated fatty acid in animals serving as a substrate in lipid synthesis and β-oxidation, and in the modification of proteins called palmitoylation. The influence of dietary palmitic acid on protein palmitoylation in the context of metabolic processes remains largely unknown. In this study we performed high-throughput proteomic analyses of the liver membrane fraction in the mouse to examine the influence of a palm oil-rich diet on the level and S-palmitoylation of proteins. For this purpose, mice were fed for 4 or 12 weeks a diet containing 19.1% of palm oil in addition to 4% soybean oil (45% kcal from fat) while 4% soybean oil (10% kcal from fat) was the only fat source in the control diet. Liver functioning and pro-inflammatory responses of the liver and peritoneal macrophages as well as the input of protein S-palmitoylation to these aspects were assessed in parallel. We found that the diet rich in palm oil induced transient accumulation of C16:0 and C18:1 fatty acids in murine liver leading to changes of the level and S-palmitoylation of numerous proteins involved in liver metabolism and selected innate immune responses. The relatively mild negative impact of such diet on liver functioning can be attributed to a lower bioavailability of palm oil-derived C16:0 vs. that of C18:1 and the efficiency of mechanisms preventing liver injury, including dynamic protein S-palmitoylation.
2021-12-14 | PXD025935 | Pride
Project description:Serum is an ideal source of biomarkers because of easy accessibility, noninvasiveness, and rapid response to disease. Given that the different clinical manifestation between early phase and late phase of sepsis, the change of serum proteins profile during different phase of sepsis can give insight into predictor for early diagnosis of sepsis. In this study, differential serum proteins were screened in mice treated with lipopolysaccharide (LPS) for 2 h, 24 h and controls using free-labeling coupled with two-dimensional liquid chromatography and tandem mass spectrometry (2D LC-MS/MS) technique.
2020-05-26 | PXD014259 | Pride
Project description:Although it has recently been shown that A/J mice are highly susceptible to Staphylococcus aureus sepsis as compared to C57BL/6J, the specific genes responsible for this differential phenotype are unknown. Using chromosome substitution strains (CSS), we found that factors on chromosomes (chr) 8, 11, and 18 are responsible for susceptibility to S. aureus sepsis in A/J mice. F1 mice from C57BL/6J X CSS8 cross (C8A) and C57BL/6J X CSS18 (C18A) were also susceptible to S. aureus (median survival < 48 h), whereas F1 mice from C57BL/6J X CSS11 cross (C11A) were resistant (median survival > 120 h) to S. aureus. Bacterial loads in the kidney were consistent with F1 median survivals, with higher bacterial counts in susceptible mice. No sexlinked associations with susceptibility were noted in F1 intercrosses. Using whole genome transcription profiling, we identified a total of 192 genes on chromosomes 8, 11, and 18 which are differentially expressed between A/J and C57BL/6J in the setting of S. aureus infection. Of these, 28 genes had Gene Ontology annotations indicating a potential immune response function. These 28 genes are associated with susceptibility to S. aureus in A/J mice, and are potential determinants of susceptibility to S. aureus infection in humans. To identify genes for which differential expression between A/J and C57BL/6J mice could contribute to host susceptibility to S. aureus infection, we compared the gene expression profiles between uninfected A/J and C57BL/6J mice and between infected A/J and C57BL/6J mice at 2, 4, 6, and 12 hours after infection.
2010-08-01 | E-GEOD-19668 | biostudies-arrayexpress
Project description:It has been shown that inbred strains of mice exhibit variable susceptibility to S. aureus infection, but the specific genes responsible for this differential phenotype are unknown. Using ISHM to identify genomic regions associated with the phenotypes, we considered genes within those interval to be candidate genes and used the gene expression patterns of the genes contained in the region to determine whether the genes are differentially expressed between the 2 phenotypically different groups of mice. To identify genes differentially expressed between mice susceptible and resistant to S. aureus infection that could contribute to host susceptibility to S. aureus infection, we compared the gene expression profiles between 2 groups of mice where 3 were susceptible (A/J, BALBcBy/J, AKR/J) and resistant (C57BL/J, C3H/HeJ, NOD/ShiLtJ) to S. aureus. The susceptible group had high bacterial count values in the kidney while the resistant group had low values.
2011-12-31 | E-GEOD-23584 | biostudies-arrayexpress
Project description:We looked for parent of origin effects on genome-wide gene expression in a reciprocal cross between C57BL/6J x B6(C)-H2bm12/KhEgJ mice (the latter strain is a knockout of H2-ab1 on a C57BL/6J background). The aim is to find genes whose expression is altered in trans depending on whether the mother or father carried a knockout allele for H2-ab1. In this experiment differential expression of a gene is inferred from a difference in its overall expression levels. We sequenced RNA from 30 F1 mice from the H2-ab1 heterozygous cross. Both heterozygous and wild type F1 animals were sequenced in order to find both parental and parent of origin effects. We measured expression in the lungs (average 6.2 million reads per sample) and hippocampus (6.6 million reads).
2013-11-01 | E-MTAB-1998 | biostudies-arrayexpress
Project description:We have performed quantitative proteomic TandemMassTag to investigate proteomic changes after deletion of epigenetic eraser genes Hdac1 and Hdac2 in intestinal epithelial cells. Both HDAC1 and HDAC2 are epigenetic erasers that drive specific and redundant gene expression patterns, in part by removing acetyl groups on histones. Deletion of these Hdac in intestinal epithelial cell (IEC) in vivo alters intestinal homeostasis, dependent on the Hdac deleted and the level of expression of both. To determine the specific IEC function of HDAC1 and HDAC2, we have performed transcriptomic and quantitative proteomic approaches on IEC deficient in Hdac1 and Hdac2. We have defined changes in both mRNA and protein expression patterns affecting IEC differentiation. We have identified IEC Hdac1- and Hdac2-dependent common as well as specific pathways and biological processes. These findings uncover unrecognized similarities and differences between Hdac1 and Hdac2 in IEC.
2021-09-09 | PXD022558 | Pride
Project description:In the present study, we employed a proteomics approach to identify parasite-derived proteins in the serum EVs from E. multilocularis-infected mice and assessed their diagnostic values. The study paves the way for the use of EVs to identify of diagnostic candidates and potentiates the applications of TER ATPase and TPx-1 in the early diagnosis and prognostic evaluation of echinococcosis.
2022-09-11 | PXD036031 | Pride