PXD031709

PXD031709 is an original dataset announced via ProteomeXchange.

Title	Database search engines and target database features impinge upon the identification of post-translationally cis-spliced peptides in HLA class I immunopeptidomes
Description	Unconventional epitopes presented by HLA class I complexes are emerging targets for T cell targeted immunotherapies. Their identification by mass spectrometry required development of novel methods to cope with the large number of theoretical candidates. Methods to identify post-translationally spliced peptides led to a broad range of outcomes. We here investigated the impact of three common database search engines – i.e. Mascot, Mascot+Percolator and PEAKS DB – as final identification step, as well as the features of target database on the ability to correctly identify non-spliced and cis-spliced peptides. We used ground truth datasets measured by mass spectrometry to benchmark methods’ performance and extended the analysis to HLA class I immunopeptidomes. PEAKS DB showed better precision and recall of cis-spliced peptides and larger number of identified peptides in HLA class I immunopeptidomes than the other search engine strategies. The better performance of PEAKS DB appears to result from better discrimination between target and decoy hits and hence a more robust FDR estimation, and seems independent to peptide and spectrum features here investigated. Head of the research group Molecular Immunology at King’s College London and the Francis Crick Institute, London (UK). Email: michele.mishto@kcl.ac.uk,
HostingRepository	PRIDE
AnnounceDate	2022-04-06
AnnouncementXML	Submission_2022-04-06_04:10:24.340.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michele Mishto
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-02-16 03:18:14	ID requested
⏵ 1	2022-04-06 04:10:24	announced

Dataset with its publication pending

submitter keyword: Mass Spectrometry, HLA-I, Immunopeptidome, K562 cell line, peptide splicing, cis-spliced peptides

Juliane Liepe
contact affiliation	Head of research group Quantitative and Systems Biology; Max Planck Institute for Multidisciplinary Sciences; Goettingen (D); Germany (lab head).
contact email	jliepe@mpibpc.mpg.de
lab head
Michele Mishto
contact affiliation	King's College London
contact email	michele.mishto@kcl.ac.uk
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/2022/04/PXD031709

PRIDE project URI

• PRIDE
  1. PXD031709
     1. Label: PRIDE project
     2. Name: Database search engines and target database features impinge upon the identification of post-translationally cis-spliced peptides in HLA class I immunopeptidomes