PXD027048

PXD027048 is an original dataset announced via ProteomeXchange.

Title	Optimized liquid and gas phase fractionation increases HLA-peptidome coverage for primary cell and tissue samples
Description	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. 2021. Mass spectrometry is the most effective method to directly identify peptides presented on HLA molecules. However, current standard approaches often use 500 million or more cells as input to achieve high coverage of the immunopeptidome and therefore these methods are not compatible with the often limited 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 alone. We demonstrate coverage of HLA immunopeptidomes with up to 8,107 distinct peptides starting with as few as 100 million cells. The increased sensitivity obtained using our methods can provide data useful to improve HLA binding prediction algorithms as well as to enable detection of clinically relevant epitopes such as neoantigens.
HostingRepository	MassIVE
AnnounceDate	2021-08-05
AnnouncementXML	Submission_2021-08-05_07:46:44.353.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Karl Clauser
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	unknown modification; unknown modification; unknown modification; unknown modification
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-01 18:55:19	ID requested
⏵ 1	2021-08-05 07:46:44	announced

no publication

submitter keyword: HLA class I, Immunopeptidomics, FAIMS, Ion mobility

Steven A. Carr
contact affiliation	Broad Institute of MIT and Harvard
contact email	scarr@broadinstitute.org
lab head
Karl Clauser
contact affiliation	Broad Institute of MIT and Harvard
contact email	clauser@broadinstitute.org
dataset submitter

MassIVE dataset URI

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