Ontology highlight
ABSTRACT:
PROVIDER: PRJNA562970 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10072290_1.fastq.gz | Fastqsanger.gz | |||
| SRR10072290_2.fastq.gz | Fastqsanger.gz | |||
| SRR10072291_1.fastq.gz | Fastqsanger.gz | |||
| SRR10072291_2.fastq.gz | Fastqsanger.gz | |||
| SRR10072292_1.fastq.gz | Fastqsanger.gz |
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Project description:Antigen-antibody interactions play a key role in the immune response post vaccination and the mechanism of action of antibody-based biopharmaceuticals. 4CMenB is a multicomponent vaccine against Neisseria meningitidis serogroup B in which factor H binding protein (fHbp) is one of the key antigens. In this study, we use hydrogen/deuterium exchange mass spectrometry (HDX-MS) to identify epitopes in fHbp recognized by polyclonal antibodies (pAb) from two human donors (HDs) vaccinated with 4CMenB. Our HDX-MS data reveal several epitopes recognized by the complex mixture of human pAb. Furthermore, we show that the pAb from the two HDs recognize the same epitope regions. Epitope mapping of total pAb and purified fHbp-specific pAb from the same HD reveals that the two antibody samples recognize the same main epitopes, showing that HDX-MS based epitope mapping can, in this case at least, be performed directly using total IgG pAb samples that have not undergone Ab-selective purification. Two monoclonal antibodies (mAb) were previously produced from B-cell repertoire sequences from one of the HDs and used for epitope mapping of fHbp with HDX-MS. The epitopes identified for the pAb from the same HD in this study, overlap with the epitopes recognized by the two individual mAbs. Overall, HDX-MS epitope mapping appears highly suitable for simultaneous identification of epitopes recognized by pAb from human donors and to thus both guide vaccine development and study basic human immunity to pathogens, including viruses.
2024-05-22 | PXD047712 | Pride
Project description:Antigen-antibody interactions play a key role in the immune response post vaccination and the mechanism of action of antibody-based biopharmaceuticals. 4CMenB is a multicomponent vaccine against Neisseria meningitidis serogroup B in which factor H binding protein (fHbp) is one of the key antigens. In this study, we use hydrogen/deuterium exchange mass spectrometry (HDX-MS) to identify epitopes in fHbp recognized by polyclonal antibodies (pAb) from two human donors (HDs) vaccinated with 4CMenB. Our HDX-MS data reveal several epitopes recognized by the complex mixture of human pAb. Furthermore, we show that the pAb from the two HDs recognize the same epitope regions. Epitope mapping of total pAb and purified fHbp-specific pAb from the same HD reveals that the two antibody samples recognize the same main epitopes, showing that HDX-MS based epitope mapping can, in this case at least, be performed directly using total IgG pAb samples that have not undergone Ab-selective purification. Two monoclonal antibodies (mAb) were previously produced from B-cell repertoire sequences from one of the HDs and used for epitope mapping of fHbp with HDX-MS. The epitopes identified for the pAb from the same HD in this study, overlap with the epitopes recognized by the two individual mAbs. Overall, HDX-MS epitope mapping appears highly suitable for simultaneous identification of epitopes recognized by pAb from human donors and to thus both guide vaccine development and study basic human immunity to pathogens, including viruses.
2024-05-24 | PXD046572 | Pride
Project description:Rapid diagnostic tests are first line assays for diagnosing infectious diseases, such as malaria. To minimize false positive and false negative test results in population screening assays, high quality reagents and well characterized antigens and antibodies are needed. An important property of antigen - antibody binding is recognition specificity which best can be estimated by mapping an antibodys epitope. The MBP-pfMSP119 antigen was chosen as mutual target for population screening. Also, since an anti-pfMSP119 antibody is planned to function as positive control in screening assays, its binding characteristics to the antigen was investigated. Intact Transition Epitope Mapping - Targeted High-Energy Rupture of Extracted Epitopes (ITEM-THREE) was carried out to map the epitope of a monoclonal anti-pfMSP119 antibody, i.e. the recognized area on the MBP-pfMSP119 antigen surface. The MBP-pfMSP119 fusion protein was cloned and expressed in E.coli which then was enriched by affinity purification on amylose resin. The enriched and purified MBP-pfMSP119 fusion protein was structurally and functionally characterized before and after high pressure-assisted tryptic digestion or after GluC digestion of the reduced and alkylated fusion protein.
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Project description:These assays represent antibody-binding assays to analyze seroprevalence of antigens and epitopes at the individual level and also to perform fine epitope mapping characterizations. In this screening 392,299 peptides derived from reactive (antigenic) regions of Trypanosoma cruzi proteins were displayed in the form of short peptides (tiling array, overlapped) and assayed with individual serum samples (antibodies) from Chagas Disease patients across the Americas. Sectorized peptide arrays (QX12-plex slides, Roche Nimblegen) were incubated with serum samples (primary antibodies), washed, and then incubated with a fluorescently-labeled anti-human IgG commercial antibody (secondary antibodies). Raw readouts of fluoresence (signal), as well as normalized signal values are provided in this submission for all samples analyzed. All samples were analyzed in duplicate (r1 = replicate 1; r2 = replicate 2).
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2025-10-27 | PXD051156 | Pride
Project description:Elucidating the interactions that drive antigen recognition is central to understanding antibody-based protection and is vital for the rational design of immunogens. Often, structural knowledge of epitopes targeted by antibodies is derived from isolated studies of monoclonal antibodies, for which numerous structural techniques exist. In contrast, there are very few approaches capable of mapping the full scope of antigen surfaces targeted by polyclonal sera through the course of a natural antibody response. Here, we develop an approach using immobilized antigen coupled to hydrogen/deuterium exchange with mass spectrometry (HDX-MS) to probe epitope targeting in the context of the fully native serum environment. Using the well-characterized Staphylococcal enterotoxin B as a model system (SEB), we show that complex combinations of epitopes can be detected and subtle differences across different anti-sera can be discerned. This work reveals new insight into how neutralizing antibodies and antisera target SEB, and more importantly, establishes a novel method for directly mapping the epitope landscape of polyclonal sera.
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Project description:Epitope mapping of novel p73 isoform antibodies
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Project description:A number of seven proteins were selected during immunoscreening and further analyses. The proteins were in silico divided into overlapping 15-mer oligopeptides with an overlap of 11 residues. The microarrays were incubated with different antibodies to C. jejuni, Escherichia coli and Salmonella enterica. Each microarray was separated into three individual incubation chambers using ProPlate 3-Well modules. Within each incubation chamber, each peptide was spotted in triplicate with the controls spotted nine times each. The controls included human-IgG, rabbit-IgG, mouse-IgG and myelin basal protein (MBP). Each chamber was incubated independently using different polyclonal antibodies to C. jejuni, and for specificity testing, with an antibody to E. coli or S. enterica. Thus, samples 4_1, 4_2, 5_1 and 5_2 represent epitope mapping of three proteins with C. jejuni antibodies, while 6_1, 6_2, 7_1 and 7_2 represent the data after incubation with an E. coli antibody investigating unspecific interactions of the antibody to the potential linear epitopes from C. jejuni. Finally, for four different proteins from C. jejuni, the set two indicated by S2 was performed. Here, S2_6_1, S2_7_1, S2_7_2, S2_8_1 and S2_8_2 indicate epitope mapping after incubation with antibodies to C. jejuni, while the remaining samples were performed to test these latter 4 proteins for specificity by incubation with antibody to S. enterica.
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Project description:We acquied the RNA polymerase II binding profiles in ama-1 transgenic worms. The large subuint of POL II, AMA-1, was C-terminally tagged with GFP, the binding regions were determined using chromatin immunoprecipitation with anti-GFP and anti-polymerase II antibodies followed by illumina high-throughput sequencing (ChIP-seq). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf RNA polymerase II binding profiles at L4/young adult stage were acquied with anti-native protein antibody (8WG16) and anti-epitope (GFP) antibody
2009-04-11 | E-GEOD-15535 | biostudies-arrayexpress