PXD011628

PXD011628 is an original dataset announced via ProteomeXchange.

Title	MHCquant: Automated and reproducible data analysis for immunopeptidomics
Description	Personalized multi-peptide vaccines are currently being discussed intensively for tumor immunotherapy. In order to find epitopes - short, immunogenic peptides - suitable to elicit an immune response, human leukocyte antigen-presented peptides from cancer tissue samples are purified using immunoaffinity purification and analyzed by high performance liquid chromatography coupled to mass spectrometry. Here we report on a novel computational pipeline to identify peptides from large-scale immunopeptidomics raw data sets. In the conducted experiments we benchmarked our workflow to other existing mass spectrometry analysis software and achieved higher sensitivity. A dataset of 38 HLA immunopeptidomics raw files of peripheral blood mononuclear cells (PBMCs) from 10 healthy volunteers and 4 JY cell lines was used to assess the performance of the pipeline at each processing step. In addition, 66 isotope labeled known HLA-presented peptides were spiked into the JY cell extracts decreasing in concentration by log10 steps from 100 fmol to 0.1 fmol.
HostingRepository	PRIDE
AnnounceDate	2019-10-14
AnnouncementXML	Submission_2019-10-14_01:16:59.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Leon Bichmann
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-08 04:54:30	ID requested
⏵ 1	2019-10-14 01:17:01	announced

Bassani-Sternberg M, Br, ä, unlein E, Klar R, Engleitner T, Sinitcyn P, Audehm S, Straub M, Weber J, Slotta-Huspenina J, Specht K, Martignoni ME, Werner A, Hein R, H Busch D, Peschel C, Rad R, Cox J, Mann M, Krackhardt AM, Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry. Nat Commun, 7():13404(2016) [pubmed]

Bichmann L, Nelde A, Ghosh M, Heumos L, Mohr C, Peltzer A, Kuchenbecker L, Sachsenberg T, Walz JS, Stevanovi, ć S, Rammensee HG, Kohlbacher O, MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics. J Proteome Res, 18(11):3876-3884(2019) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: Human, MHC, Benchmark

Professor Oliver Kohlbacher
contact affiliation	Dept. of Computer Science, University of Tübingen Germany, Center for Bioinformatics, University of Tübingen, Germany, Quantitative Biology Center, University of Tübingen, Germany, Max Planck Institute for Developmental Biology, Germany,
contact email	oliver.kohlbacher@uni-tuebingen.de
lab head
Leon Bichmann
contact affiliation	University of Tübingen
contact email	Leon.Bichmann@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/2019/10/PXD011628

PRIDE project URI

• PRIDE
  1. PXD011628
     1. Label: PRIDE project
     2. Name: MHCquant: Automated and reproducible data analysis for immunopeptidomics