PXD056519-1

PXD056519 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Evaluation of the False Discovery Rate in Library-free Search by DIA-NN Using in vitro Human Proteome
Description	In recent years, deep learning-based in silico spectral libraries have gained increasing attention. Several data-independent acquisition (DIA) software tools have integrated this feature, known as library-free search, making DIA analysis more accessible. However, controlling the false discovery rate (FDR) is challenging due to the vast amount of peptide information in in silico libraries. In this study, we introduce a stringent method to evaluate FDR control in DIA software. Recombinant proteins were synthesized from full-length human cDNA libraries, measured using liquid chromatography-mass spectrometry (LC-MS/MS), and analyzed with DIA software. The results were compared to known protein sequences to calculate FDR. We compared the identification performance of DIA-NN versions 1.8.1 and 1.9.2. Our results show that version 1.9.2 identified more peptides than version 1.8.1, though no significant difference was observed at the protein level. DIA-NN 1.9.2 uses a more conservative identification approach, significantly improving FDR control. Across 12 samples analyzed, the average FDR at the peptide level was 0.58% for version 1.8.1 and 0.43% for version 1.9.2, and at the protein level, 2.74% and 1.77%, respectively. Our dataset provides valuable insights for comparing FDR control across DIA software and aiding bioinformaticians in enhancing their tools.
HostingRepository	jPOST
AnnounceDate	2025-07-23
AnnouncementXML	Submission_2025-07-22_08:00:20.380.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sumio Ohtsuki
SpeciesList	scientific name: cellular organisms; NCBI TaxID: 131567;
ModificationList	S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; O-phospho-L-serine; O-phospho-L-threonine
Instrument	TripleTOF 5600

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-05 03:35:19	ID requested
⏵ 1	2025-07-22 08:00:21	announced

Publication List

Gu K, Kenko M, Ogawa K, Goshima N, Masuda T, Ito S, Ohtsuki S, Human Proteome. J Proteome Res, 24(8):3874-3883(2025) [pubmed]

Gu K, Kenko M, Ogawa K, Goshima N, Masuda T, Ito S, Ohtsuki S, Human Proteome. J Proteome Res, 24(8):3874-3883(2025) [pubmed]

Keyword List

submitter keyword: proteomics, data-independent acquisition (DIA), False Discovery Rate (FDR), DIA-NN, contamination, in vitro human proteome

submitter keyword: proteomics, data-independent acquisition (DIA), False Discovery Rate (FDR), DIA-NN, contamination, in vitro human proteome

Contact List

Sumio Ohtsuki, Kumamoto University
lab head
Sumio Ohtsuki
contact affiliation	Kumamoto University
dataset submitter

Full Dataset Link List

jPOST dataset URI
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jPOST dataset URI

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.jpostdb.org/JPST003404/