PXD016669 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2019-12-10 01:19:56 | ID requested | |
⏵ 1 | 2021-07-05 22:55:40 | announced | |
Publication List
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] |
Keyword List
submitter keyword: bottom-up discovery proteomics, peptide-spectrum match, false discovery rate, target decoy competition, Benjamini-Hochberg procedure |
Contact List
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 | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD016669
- Label: PRIDE project
- Name: Beyond target-decoy competition: stable validation of peptide and protein identifications in mass spectrometry-based discovery proteomics