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PXD018783

PXD018783 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleCharacterization of I-Ab MHCII immunopeptidome eluted from control and obese (Ob/Ob) mice (2)
DescriptionIn Dendritic cells (DC), the MHC II eluted immunopeptidome reflects the antigenic composition of the microenvironment. Proteins are transported and processed into peptides in endosomal MHC II compartments through autophagy or phagocytosis; extracellular peptides can also directly bind MHC II proteins at the cell surface. Altogether, these mechanisms allow DC to sample both the intra and extracellular environment. With an increase in mass spectrometry sensitivity and accuracy, we can now finally tackle important questions on the nature and plasticity of the MHC-II immunopeptidome in health and disease. Presented epitopes, neoepitopes, and PTM-modified epitopes can be quantitatively and qualitatively analyzed to provide a comprehensive picture of DC role in immunosurveillance. To determine whether the redox metabolic conditions induce an altered spectrum of presented peptides, we eluted immunoaffinity-purified I-Ab from conventional dendritic cells isolated from control B6 or obese Ob/Ob mice, and analyzed MHC-II-associated peptides by LC/MS/MS using combined data-dependent (DDA) and data-independent acquisition (DIA) approaches. We analyzed the DIA data by employing a reference spectral library consisting of all peptides identified by database matching in the pool of spectra from combined DDA dataset, thus allowing a direct label-free quantitation of relative abundances between the two sample categories. The quantitative analysis of the I-Ab-eluted immunopeptidomes pinpoint important differences in peptide presentation and epitope selection in obese mice.
HostingRepositoryPRIDE
AnnounceDate2021-03-22
AnnouncementXMLSubmission_2021-03-21_23:04:31.411.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD018783
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterCristina Clement
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-04-24 01:32:00ID requested
12021-03-21 23:04:32announced
Publication List
Clement CC, Nanaware PP, Yamazaki T, Negroni MP, Ramesh K, Morozova K, Thangaswamy S, Graves A, Kim HJ, Li TW, Vigano' M, Soni RK, Gadina M, Tse HY, Galluzzi L, Roche PA, Denzin LK, Stern LJ, Santambrogio L, Pleiotropic consequences of metabolic stress for the major histocompatibility complex class II molecule antigen processing and presentation machinery. Immunity, 54(4):721-736.e10(2021) [pubmed]
Keyword List
submitter keyword: mouse I-Ab MHCII peptidome
LC/MS/MS DDA on QE mass spectrometer
Contact List
Laura Santambrogio MD PhD; contact: Cristina C Clement PhD
contact affiliationRadiation Oncology Department; Weill Cornell Medicine, NY, 10065
contact emailccc4002@med.cornell.edu
lab head
Cristina Clement
contact affiliationWeill Cornell Medicine
contact emailccc4002@med.cornell.edu
dataset submitter
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Dataset FTP location
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