PXD023581-1

PXD023581 is an original dataset announced via ProteomeXchange.

Title	Characterization of I-Ab MHCII immunopeptidome eluted from control and obese (Ob/Ob) mice using a combination of data-dependent (DDA) and data-independent acquisition (DIA) nanoLC mass spectrometry
Description	In 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.
HostingRepository	PRIDE
AnnounceDate	2021-03-21
AnnouncementXML	Submission_2021-03-21_14:59:06.513.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD023581
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Cristina Clement
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	dihydroxylated residue; deaminated residue; monohydroxylated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-14 01:49:04	ID requested
⏵ 1	2021-03-21 14:59:07	announced

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]

submitter keyword: mouse dendritic cells

I-Ab MHC-II immunopeptidome

DDA and DIA nanoLCMS

Laura Santambrogio and Lawrence J.Stern
contact affiliation	Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA; Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.
contact email	las4011@med.cornell.edu
lab head
Cristina Clement
contact affiliation	Weill Cornell Medicine
contact email	ccc4002@med.cornell.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD023581
     1. Label: PRIDE project
     2. Name: Characterization of I-Ab MHCII immunopeptidome eluted from control and obese (Ob/Ob) mice using a combination of data-dependent (DDA) and data-independent acquisition (DIA) nanoLC mass spectrometry