PXD052267

PXD052267 is an original dataset announced via ProteomeXchange.

Title	Label-free quantitative data dependent (DDA) and independent (DIA) analysis of the I-Ab-MHCII peptidomes eluted from cervical and mesenteric dendritic cells (DCs) of B6 mice.
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. To understand the contribution of the lymph proteome to the MHC-II immunopeptidome we eluted I-Ab complexes from DCs harvested from the deep cervical or mesenteric nodes and investigated whether the I-Ab presented peptidome reflects the anatomical distribution of the proteomes carried by the lymph collected from the same anatomical districts. Heatmap representation and cluster analysis indicated differences among the two immunopeptidome. Similarly, regression analysis showed a much higher regression coefficient among MHC II immunopeptidomes eluted from the same anatomical district (r=0.699) as compared to the one eluted from the two different anatomical districts (deep cervical, average r = 0.877 and mesenteric, average r = 0.937). Overall, all analyzed peptides displayed the expected I-Ab binding motives, binding affinity and expected range of peptide length. A combination of data dependent (DDA) and data independent (DIA) analysis indicated that around 36% of the eluted peptides were shared by both the cervical and mesenteric lymph nodes. The rest of the eluted peptides were distinct to each lymph node reflecting the qualitatively different proteome associated with each of the two anatomical districts: peptides unique to the cervical lymph nodes displayed many proteins known to be enriched in brain tissue, whereas those unique to mesenteric lymph nodes were enriched in mesenteric organ proteins. As such, the quantitative analysis of the I-Ab-eluted immunopeptidomes pinpoint important differences in peptide presentation and epitope selection in distinct anatomical districts.
HostingRepository	MassIVE
AnnounceDate	2024-05-14
AnnouncementXML	Submission_2024-05-14_21:56:53.769.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Cristina C Clement
SpeciesList	scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090;
ModificationList	Oxidation; Deamidated
Instrument	Orbitrap Fusion; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-14 21:16:25	ID requested
⏵ 1	2024-05-14 21:56:54	announced

no publication

submitter keyword: mouse MHCII I-Ab immunopeptidome, LC/MS/MS DDA and DIA

Laura Santambrogio
contact affiliation	Weill Cornell Medicine College
contact email	las4011@med.cornell.edu
lab head
Cristina Clement
contact affiliation	Weill Cornell Medicine College
contact email	ccc4002@med.cornell.edu
lab head
Cristina C Clement
contact affiliation	Weill Cornell Medicine
contact email	ccc4002@med.cornell.edu
dataset submitter

MassIVE dataset URI

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