PXD016669

PXD016669 is an original dataset announced via ProteomeXchange.

Title	Beyond target-decoy competition: stable validation of peptide and protein identifications in mass spectrometry-based discovery proteomics
Description	Target-decoy competition (TDC) is the most popular method for false discovery rate (FDR) control in bottom-up discovery proteomics. Despite unquestionable statistical foundations, we unveil a so far unknown weakness of TDC: its intrinsic lack of stability vis-à-vis practical conditions of application. Although some consequences of this instability have already been empirically described, they may have been misinterpreted. This work pinpoints evidence that TDC will become less reliable along with improved accuracies of modern mass spectrometers. We therefore propose to replace TDC by a totally different method to control the FDR at spectrum, peptide and protein levels, while benefiting from the theoretical guarantees of Benjamini-Hochberg framework. This method being simpler to use, faster to compute and more stable than TDC, we argue that it is more adapted to the standardization and throughput constraints of nowadays proteomic platforms.
HostingRepository	PRIDE
AnnounceDate	2021-07-06
AnnouncementXML	Submission_2021-07-05_22:55:39.484.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD016669
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Yohann Couté
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-12-10 01:19:56	ID requested
⏵ 1	2021-07-05 22:55:40	announced

Cout, é Y, Bruley C, Burger T, Beyond Target-Decoy Competition: Stable Validation of Peptide and Protein Identifications in Mass Spectrometry-Based Discovery Proteomics. Anal Chem, 92(22):14898-14906(2020) [pubmed]

submitter keyword: bottom-up discovery proteomics, peptide-spectrum match, false discovery rate, target decoy competition, Benjamini-Hochberg procedure

Virginie Brun
contact affiliation	EDyP
contact email	virginie.brun@cea.fr
lab head
Yohann Couté
contact affiliation	EDyP
contact email	yohann.coute@cea.fr
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/2020/12/PXD016669

PRIDE project URI

• PRIDE
  1. PXD016669
     1. Label: PRIDE project
     2. Name: Beyond target-decoy competition: stable validation of peptide and protein identifications in mass spectrometry-based discovery proteomics