PXD012498

PXD012498 is an original dataset announced via ProteomeXchange.

Title	MHC immunopeptidome of JY cells analysed by EThcD at Orbitrap Fusion after mild acid elution
Description	To understand and treat immunology-related diseases, a comprehensive, unbiased characterization of major histocompatibility complex (MHC) peptide ligands is of key importance. Preceding the analysis by mass spectrometry, MHC peptide ligands are typically isolated by MHC immunoaffinity chromatography (MHC-IAC). Less often, mild acid elution (MAE) is used to extract MHC class I peptide ligands. MAE may provide a cheap alternative to MHC-IAC for suspension cells, but it is thought to be hampered by the high number of contaminating peptides not derived from the MHC. Here, we optimized the MAE protocol yielding MHC peptide ligand purities of more than 80%. We discovered distinct cysteinylation frequencies at individual positions of MHC peptide ligands and propose that MAE conserves the native cysteinylation pattern of MHC peptide ligands better than MHC-IAC. Our improved and carefully documented MAE workflow represents a high-quality, cost-effective alternative to MHC-IAC for suspension cells and should be applicable also in laboratories not specialized in MHC peptide ligand analyses.
HostingRepository	PRIDE
AnnounceDate	2020-11-11
AnnouncementXML	Submission_2020-11-11_09:17:11.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Theo Sturm
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	cysteinylation (disulfide with free L-cysteine); monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion ETD

Revision	Datetime	Status	ChangeLog Entry
0	2019-01-25 00:27:50	ID requested
⏵ 1	2020-11-11 09:17:12	announced

Sturm T, Sautter B, W, ö, rner TP, Stevanovi, ć S, Rammensee HG, Planz O, Heck AJR, Aebersold R, Mild Acid Elution and MHC Immunoaffinity Chromatography Reveal Similar Albeit Not Identical Profiles of the HLA Class I Immunopeptidome. J Proteome Res, 20(1):289-304(2021) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: MHC bound peptides, HLA ligandome, mild acid elution, cysteinylation, post-translational modification, EThcD

Albert J.R. Heck
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands Netherlands Proteomics Centre, Utrecht, The Netherlands
contact email	A.J.R.Heck@uu.nl
lab head
Theo Sturm
contact affiliation	Utrecht University, Biomolecular Mass Spectrometry and Proteomics, Padualaan 8, 3584 CH, Utrecht
contact email	theosturm@gmx.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD012498

PRIDE project URI

• PRIDE
  1. PXD012498
     1. Label: PRIDE project
     2. Name: MHC immunopeptidome of JY cells analysed by EThcD at Orbitrap Fusion after mild acid elution