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PXD017407 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMultiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition
DescriptionMajor histocompatibility complex (MHC) class I peptides play a critical role in immune cell recognition and can trigger an antitumor immune response in cancer. Surface MHC levels can be modulated by anticancer agents, altering immunity. However, understanding the peptide repertoire response to treatment remains challenging and is limited by quantitative mass spectrometry-based strategies lacking robust normalization controls. We describe a novel approach that leverages recombinant heavy isotope-coded peptide MHCs (hipMHCs) and multiplex isotope tagging to quantify peptide repertoire alterations using low sample input. HipMHCs improve quantitative accuracy of peptide repertoire changes by normalizing for variation across analyses and enable absolute quantification using internal calibrants to determine copies per cell of MHC antigens, which can inform targeted and combination immunotherapy design. Applying this platform to profile the immunopeptidome response to CDK4/6 inhibition and Interferon gamma, known modulators of antigen presentation, uncovered treatment-specific alterations, connecting the intracellular response to extracellular immune presentation.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterLauren Stopfer
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListTMT6plex-126 reporter+balance reagent acylated residue; amidated residue; monohydroxylated residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-02-05 07:27:45ID requested
12020-06-04 03:21:04announced
Publication List
Stopfer LE, Mesfin JM, Joughin BA, Lauffenburger DA, White FM, Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition. Nat Commun, 11(1):2760(2020) [pubmed]
Keyword List
submitter keyword: LC-M
Contact List
Forest White
contact affiliationMassachusetts Institute of Technology
contact emailfwhite@mit.edu
lab head
Lauren Stopfer
contact affiliationMIT
contact emaillstopfer@mit.edu
dataset submitter
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