PXD044451

PXD044451 is an original dataset announced via ProteomeXchange.

Title	iBench Ground Truth Validation Tool 2.0
Description	iBench is an open-source tool that provides enhanced validation of Mass Spectrometry identification methods. In this updated version, iBench 2.0 takes high confidence peptide identifications from previously measured MS data and embeds the sequences in an in silico-only proteome as spliced or non-spliced peptides. The MS data can then be reanalyzed with the modified proteome, thereby representing a (pseudo) ground truth dataset, to enable benchmarking of an identification method. In particular, precision-recall curves are generated, comparing the fraction of PSMs identified which are correct and the fraction of all PSMs assigned by a method. Reference to this dataset: Soh WT, Roetschke HP, Cormican JA, Teo BF, Chiam NC, Raabe M, Pflanz R, Henneberg F, Becker S, Chari A, Liu H, Urlaub H, Liepe J, Mishto M. Degradation of proteins by human 20S proteasomes sheds light on the interplay between peptide hydrolysis and peptide splicing. Nat. Comm., accepted.
HostingRepository	PRIDE
AnnounceDate	2023-12-21
AnnouncementXML	Submission_2023-12-21_04:22:04.989.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	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-08 08:04:48	ID requested
⏵ 1	2023-12-21 04:22:05	announced

Dataset with its publication pending

submitter keyword: Mass Spectrometry, 20S proteasomes, Benchmarking, MHC-I presentation, PCPS

Juliane Liepe
contact affiliation	Juliane Liepe, Head of research group Quantitative and Systems Biology; Max Planck Institute for Multidisciplinary Sciences; Goettingen (D); Germany (lab head). Email: jliepe@mpinat.mpg.de Michele Mishto, 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
contact email	jliepe@mpinat.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/2023/12/PXD044451

PRIDE project URI

• PRIDE
  1. PXD044451
     1. Label: PRIDE project
     2. Name: iBench Ground Truth Validation Tool 2.0