PXD023202-2

PXD023202 is an original dataset announced via ProteomeXchange.

Title	The choice of search engine for interpretation of immunopeptidomics datasets affects the sequencing depth and the extent of detected HLA allele-specific peptide repertoires
Description	Standardisation of Immunopeptidomics experiments across laboratories is a pressing issue within the field, and currently a variety of different methods for sample preparation and data analysis tools are applied. Here, we compared different software packages commonly used to interrogate immunopeptidomics datasets, in order to understand to which extent differences in performance can be observed. We found that a de novo-assisted database search reports substantially more peptide sequences (~30-70%) compared to three database search engines at a global FDR of <1%. This effect was reproducible across four immunopeptidomic datasets. We validated the results using data generated with a synthetic library of 2000 HLA-associated peptides from four HLA alleles, half of which were previously observed by LC-MS, and half were predicted only. Our investigation reveals that search engines create a bias in peptide sequence length distribution and peptide amino acid composition. Therefore, the choice of peptide identification method highly influences the proportion of peptide sequences identified for each HLA allele, and resulting data should be interpreted with caution.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:56:47.662.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Robert Parker
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-17 11:06:28	ID requested
1	2024-08-27 14:25:14	announced
⏵ 2	2024-10-22 06:56:48	announced	2024-10-22: Updated project metadata.

Parker R, Tailor A, Peng X, Nicastri A, Zerweck J, Reimer U, Wenschuh H, Schnatbaum K, Ternette N, The Choice of Search Engine Affects Sequencing Depth and HLA Class I Allele-Specific Peptide Repertoires. Mol Cell Proteomics, 20():100124(2021) [pubmed]

10.1016/j.mcpro.2021.100124;

submitter keyword: Immunopeptidomics, Search Engine

Nicola Ternette
contact affiliation	Nuffield Department of Medicine, Centre for Cellar and Medical Physiology, University of Oxford, OX3 7BN
contact email	nicola.ternette@ndm.ox.ac.uk
lab head
Robert Parker
contact affiliation	Jenner Institute
contact email	robert.rparker@gmail.com
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/2024/08/PXD023202

PRIDE project URI

• PRIDE
  1. PXD023202
     1. Label: PRIDE project
     2. Name: The choice of search engine for interpretation of immunopeptidomics datasets affects the sequencing depth and the extent of detected HLA allele-specific peptide repertoires