PXD034017

PXD034017 is an original dataset announced via ProteomeXchange.

Title	Extending the Mass Spectrometry-Detectable Landscape of the Immunopeptidome by use of Restricted access Material
Description	Mass spectrometry-based immunopeptidomics enables the comprehensive identification of major histocompatibility complex (MHC) peptides from cell culture as well as from tissue or tumor samples and is increasingly applied for the identification of tumor-specific and viral T-cell epitopes. Although mass spectrometry is generally accounted as an unbiased method for MHC peptide identification, the physicochemical properties of MHC peptides can greatly influence their detectability. For instance, highly hydrophobic peptides get easily lost already during sample preparation when C18 solid phase extraction (SPE) is used for separating MHC peptides from proteins. To overcome this limitation, we established an optimized protocol for this sample preparation step applying restricted access material (RAM). Compared to C18-SPE, RAM-SPE improves the overall MHC peptide recovery and extends the landscape of mass spectrometry-detectable MHC peptides towards more hydrophobic peptides.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:53:39.496.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Melissa Bernhardt
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-20 10:47:12	ID requested
1	2022-11-07 07:15:22	announced
⏵ 2	2023-11-14 07:53:40	announced	2023-11-14: Updated project metadata.

Bernhardt M, Cruz-Garcia Y, Rech A, Meierjohann S, Erhard F, Schilling B, Schlosser A, Extending the Mass Spectrometry-Detectable Landscape of MHC Peptides by Use of Restricted Access Material. Anal Chem, 94(41):14214-14222(2022) [pubmed]

submitter keyword: Immunopeptidomics, Solid phase extraction, Restricted Access Material

Andreas Schlosser
contact affiliation	Mass spectrometry
contact email	andreas.schlosser@uni-wuerzburg.de
lab head
Melissa Bernhardt
contact affiliation	mass spectrometry
contact email	melissa.bernhardt@uni-wuerzburg.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/2022/11/PXD034017

PRIDE project URI

• PRIDE
  1. PXD034017
     1. Label: PRIDE project
     2. Name: Extending the Mass Spectrometry-Detectable Landscape of the Immunopeptidome by use of Restricted access Material