Dataset Information

A tissue-based draft map of the murine MHC class I immunopeptidome

ABSTRACT: The array of peptides presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC class I immunopeptidome. Although the MHC class I immunopeptidome is ubiquitous in mammals and represents a critical component of the adaptive immune system, very little is known about its baseline composition across all tissues and organs in vivo. In this study, we applied mass spectrometry (MS) technologies to draft a tissue-based atlas of the MHC class I immunopeptidome in the C56BL/6 mouse model. Overall, 19 normal mouse tissues were extracted and a total number of ~30,000 high-confidence H2Db/Kb-associated peptides were identified and annotated in the atlas. The raw MS output files, the catalogue of H2Db/Kb-associated peptides, the tissue origin(s) of individual peptides and the H2Db/Kb-specific peptide spectral libraries, which consist of consensus spectra calculated from repeat measurements of the same peptide sequence, were shared via the SysteMHC Atlas project (dataset identifier SYSMHC00018). We expect that this unique dataset will be further expended in the future and will be re-used by the community to 1) investigate the tissue-specificity of the immunopeptidome, 2) perform highly reproducible spectral library-based analysis of immunopeptidomes from mice cohorts, and 3) rapidly identify disease-specific H2Db/Kb peptide antigens from various mouse models of autoimmune diseases and cancers.

INSTRUMENT(S): Orbitrap Fusion Lumos, TripleTOF 5600

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Testis, Heart, Spleen, Stomach, Brain, Lung, Liver, Bladder, Kidney, Thymus, Ovary, Uterus, Spinal Cord, Skin, Colon, Pancreas, Bone Marrow, Adrenal Gland, Small Intestine

SUBMITTER: Etienne Caron

LAB HEAD: Ruedi Aebersold

PROVIDER: PXD008733 | Pride | 2018-06-19

REPOSITORIES: Pride

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			Action	DRS
	SYSMHC00018_150625_HS_mousetissue_brain_B22_25cm90min3s_350-650mz_msms6.mzXML	Mzxml
	SYSMHC00018_150625_HS_mousetissue_brain_B22_25cm90min3s_350-650mz_msms6.raw	Raw
	SYSMHC00018_150625_HS_mousetissue_brain_Y3_25cm90min3s_350-650mz_msms5.mzXML	Mzxml
	SYSMHC00018_150625_HS_mousetissue_brain_Y3_25cm90min3s_350-650mz_msms5.raw	Raw
	SYSMHC00018_150625_HS_mousetissue_colon_B22_25cm90min3s_350-650mz_msms12.mzXML	Mzxml

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A tissue-based draft map of the murine MHC class I immunopeptidome.

Schuster Heiko H Shao Wenguang W Weiss Tobias T Pedrioli Patrick G A PGA Roth Patrick P Weller Michael M Campbell David S DS Deutsch Eric W EW Moritz Robert L RL Planz Oliver O Rammensee Hans-Georg HG Aebersold Ruedi R Caron Etienne E

Scientific data 20180807

The large array of peptides presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC class I immunopeptidome. Although the MHC class I immunopeptidome is ubiquitous in mammals and represents a critical component of the immune system, very little is known, in any species, about its composition across most tissues and organs in vivo. We applied mass spectrometry (MS) technologies to draft the first tissue-based atlas of the murine MHC class I ...[more]

PMID: 30084848

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Project description:Peptides displayed by MHC molecules on a cell’s surface, referred to as its immunopeptidome, play an important role in the adaptive the immune response. Antigen processing for MHC class I presentation is a ubiquitous pathway present in all nucleated cells which generate and present peptides of both self and non-self origin. Peptides with post-translational modifications (PTMs) are one of the classes of peptides presented by MHC class I molecules. However, due to the high background of self-peptides presented by the cells, the diversity of peptides with post-translational modifications is not well reported. In this study, we have carried out MHC Class I immunopeptidomics analysis on Jurkat and A375 cell lines to characterize the diversity of post-translational modifications among MHC class I peptides. Using high resolution mass spectrometry, we identified 25,761 MHC-bound peptides across both the cell lines using Bolt and Sequest search engines. High specificity of the enrichment method is demonstrated by identifying ~90% of the peptides with typical length distribution of 8-12 aa and enriched motifs within those peptides similar to the binding motifs of MHC alleles. Among the MHC-bound peptides, we identified phosphorylation as a major post-translational modification followed by deamidation. We observed site-specific localization of these post-translational modifications, at position P4 for phosphorylated peptides and position P3 for deamidated peptides. We identified a smaller number of peptides with acetylated and methylated lysine, possibly due to very low stoichiometric levels of these post-translational modifications compared to phosphorylation and deamidation. Using PEAKS de novo sequencing algorithm, we identified spliced peptides that account for ~5-7% of MHC-bound peptides across the two cell lines. These peptides share similar features with respect to normal MHC-bound peptides such as peptide length distribution and binding motifs. We validated the identification of several post-translationally modified peptides and spliced peptides using synthetic peptide sequences. In conclusion, our study demonstrates unbiased identification of these low stoichiometric PTMs and unusual spliced peptides using high resolution mass spectrometry.

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