PXD022950

PXD022950 is an original dataset announced via ProteomeXchange.

Title	Improved sensitivity of immunopeptidomics by leveraging available large-scale pan-HLA spectral libraries and data-independent acquisition
Description	Mass spectrometry is the state-of-the-art methodology for capturing the breadth and depth of the immunopeptidome across HLA allotypes and cell types. The majority of studies in the immunopeptidomics field are discovery-driven and data-dependent tandem mass spectrometry acquisition is commonly used, as it generates high quality references of peptide fingerprints. However, DDA suffers from the stochastic selection of abundant ions that leads to lower sensitivity and reproducibility. In contrast, in data-independent acquisition, the fragmentation and acquisition of all fragment ions from a predefined list of precursor isolation windows yields a comprehensive map for a given sample. Because often the amount of HLA peptides eluted from biological samples, is typically not sufficient for acquiring both meaningful DDA data necessary for generating comprehensive spectral libraries and DIA MS measurements, the implementation of DIA in the immunopeptidomics translational research domain has remained limited. We implemented a DIA immunopeptidomics workflow and assessed its sensitivity and accuracy by matching DIA data against libraries with growing complexity - from sample-specific libraries to libraries combining from two to forty different immunopeptidomics samples. Matching DIA immunopeptidomics data against complex pan-HLA spectral library resulted in a two-fold increase in peptide identification compared with sample-specific library and in a three-fold increase compared with DDA measurements, yet with no detrimental effect on the specificity. We concluded that a comprehensive pan-HLA library for DIA approach is highly advantageous for the clinical Immunopeptidomics where low amount of biological sample is available for immunopeptidomics.
HostingRepository	PRIDE
AnnounceDate	2021-04-13
AnnouncementXML	Submission_2021-04-13_09:45:36.310.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michal Bassani-Sternberg
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-07 02:34:39	ID requested
⏵ 1	2021-04-13 09:45:37	announced

Pak H, Michaux J, Huber F, Chong C, Stevenson BJ, M, ü, ller M, Coukos G, Bassani-Sternberg M, Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction. Mol Cell Proteomics, 20():100080(2021) [pubmed]

ProteomeXchange project tag: Human Immuno-Peptidome Project (HUPO-HIPP) (B/D-HPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

submitter keyword: DIA, immunopeptidomics, pan-HLA

Michal Bassani-Sternberg
contact affiliation	Department of oncology UNIL CHUV Ludwig Institute for Cancer Research Lausanne Centre de recherche Agora Rue du Bugnon 25A CH-1011 Lausanne Switzerland
contact email	michal.bassani@chuv.ch
lab head
Michal Bassani-Sternberg
contact affiliation	UNIL/CHUV
contact email	michal.bassani@chuv.ch
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/2021/04/PXD022950

PRIDE project URI

• PRIDE
  1. PXD022950
     1. Label: PRIDE project
     2. Name: Improved sensitivity of immunopeptidomics by leveraging available large-scale pan-HLA spectral libraries and data-independent acquisition