PXD012437 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | MHC immunopeptidome of JY cells analysed by EThcD or HCD 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. Key features of the observed cysteinylation pattern were independent of the applied fragmentation methods HCD or EThcD. 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_09:17:27.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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2019-01-21 01:29:51 | ID requested | |
⏵ 1 | 2020-11-11 09:17:28 | announced | |
Publication List
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] |
Keyword List
curator keyword: Biological |
submitter keyword: MHC bound peptides, HLA ligandome, mild acid elution, cysteinylation, post-translational modification, EThcD, HCD |
Contact List
Albert J.R. Heck |
contact affiliation | 1.) Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands 2.) 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD012437
- Label: PRIDE project
- Name: MHC immunopeptidome of JY cells analysed by EThcD or HCD at Orbitrap Fusion after mild acid elution