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PXD027048

PXD027048 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleOptimized liquid and gas phase fractionation increases HLA-peptidome coverage for primary cell and tissue samples
DescriptionKlaeger 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.
HostingRepositoryMassIVE
AnnounceDate2021-08-05
AnnouncementXMLSubmission_2021-08-05_07:46:44.353.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterKarl Clauser
SpeciesList scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationListunknown modification; unknown modification; unknown modification; unknown modification
InstrumentOrbitrap Exploris 480
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-07-01 18:55:19ID requested
12021-08-05 07:46:44announced
Publication List
no publication
Keyword List
submitter keyword: HLA class I, Immunopeptidomics, FAIMS, Ion mobility
Contact List
Steven A. Carr
contact affiliationBroad Institute of MIT and Harvard
contact emailscarr@broadinstitute.org
lab head
Karl Clauser
contact affiliationBroad Institute of MIT and Harvard
contact emailclauser@broadinstitute.org
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location
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