<<< Full experiment listing


PXD027165 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleOptimized liquid and gas phase fractionations increase HLA-peptidome coverage for primary cell and tissue samples
DescriptionMass spectrometry is the most effective method to directly identify peptides presented on HLA molecules. However, current standard approaches often require billions of cells for input material to achieve high coverage of the immunopeptidome and are therefore not compatible with the often limiting amounts of tissue available from clinical tumor samples. Here, we evaluated microscaled basic reversed-phase fractionation to separate HLA peptide samples off-line followed by ion mobility coupled to LC-MS/MS for analysis. The combination of these two separation methods enabled identification of 20% to 50% more peptides compared to samples analyzed without either prior fractionation or use of ion mobility. We demonstrate coverage of HLA immunopeptidomes with up to 8,107 distinct peptides starting with as few as 50 million cells or 150 milligrams of wet weight tumor tissue. This increased sensitivity can improve HLA binding prediction algorithms and enable detection of clinically relevant epitopes such as neoantigens
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterHasmik Keshishian
SpeciesList scientific name: Homo sapiens; NCBI TaxID: 9606;
InstrumentTSQ Quantis
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-07-07 08:14:29ID requested
12021-08-30 09:44:30announced
Publication List
Klaeger S, Apffel A, Clauser KR, Sarkizova S, Oliveira G, Rachimi S, Le PM, Tarren A, Chea V, Abelin JG, Braun DA, Ott PA, Keshishian H, Hacohen N, Keskin DB, Wu CJ, Carr SA, Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples. Mol Cell Proteomics, 20():100133(2021) [pubmed]
Keyword List
submitter keyword: HLA, targeted MS
Contact List
Steve Carr
contact affiliationBroad Institute
contact emailscarr@broadinstitute.org
lab head
Hasmik Keshishian
contact affiliationBroad Institute
contact emailhasmik@broadinstitute.org
dataset submitter
Full Dataset Link List
Panorama Public dataset URI