PXD055277

PXD055277 is an original dataset announced via ProteomeXchange.

Title	NovoBoard: a comprehensive framework for evaluating the false discovery rate and accuracy of de novo peptide sequencing
Description	De novo peptide sequencing is a fundamental research area in mass spectrometry (MS) based proteomics. However, those methods have often been evaluated using a couple of simple metrics that do not fully reflect their overall performance. Moreover, there has not been an established method to estimate the false discovery rate (FDR) and the significance of de novo peptide-spectrum matches (PSMs). Here we propose NovoBoard, a comprehensive framework to evaluate the performance of de novo peptide sequencing methods. The framework consists of diverse benchmark datasets (including tryptic, nontryptic, immunopeptidomics, and different species), and a standard set of accuracy metrics to evaluate the fragment ions, amino acids, and peptides of the de novo results. More importantly, a new approach is designed to evaluate de novo peptide sequencing methods on target-decoy spectra and to estimate their FDRs. Our results thoroughly reveal the strengths and weaknesses of different de novo peptide sequencing methods, and how their performances depend on specific applications and the types of data. Our FDR estimation also shows that some tools may perform better than the others in distinguishing between de novo PSMs and random matches, and can be used to assess the significance of de novo PSMs.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:56:55.240.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ngoc Hieu Tran
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-28 01:42:18	ID requested
1	2024-08-28 02:00:59	announced
⏵ 2	2024-10-22 06:56:55	announced	2024-10-22: Updated project metadata.

10.1101/2024.04.16.589668;

submitter keyword: false discovery rate,de novo peptide sequencing

Baozhen Shan
contact affiliation	Bioinformatics Solutions Inc.
contact email	bshan@bioinfor.com
lab head
Ngoc Hieu Tran
contact affiliation	Bioinformatics Solutions Inc.
contact email	htran@bioinfor.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/2024/08/PXD055277

PRIDE project URI

• PRIDE
  1. PXD055277
     1. Label: PRIDE project
     2. Name: NovoBoard: a comprehensive framework for evaluating the false discovery rate and accuracy of de novo peptide sequencing