PXD067277

PXD067277 is an original dataset announced via ProteomeXchange.

Title	Enhancing Peptide Identification in Metaproteomics through Curriculum Learning in Deep Learning
Description	Metaproteomics offers a powerful window into the active functions of microbial communities, but accurately identifying peptides remains challenging due to the size and incompleteness of protein databases derived from metagenomes. These databases often contain vastly more sequences than those from single organisms, creating a computational bottleneck in peptide-spectrum match (PSM) filtering. Here we present WinnowNet, a deep learning–based method for PSM filtering, available in two versions: one using transformers and the other convolutional neural networks. Both variants are designed to handle the unordered nature of PSM data and are trained using a curriculum learning strategy that moves from simple to complex examples. WinnowNet consistently achieves more true identifications at equivalent false discovery rates compared to leading tools, including Percolator, MS$^2$Rescore, and DeepFilter, and outperforms filters integrated into popular analysis pipelines. It also uncovers more gut microbiome biomarkers related to diet and health, highlighting its potential to support advances in personalized medicine
HostingRepository	PRIDE
AnnounceDate	2025-10-20
AnnouncementXML	Submission_2025-10-19_16:21:18.573.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shichao Feng
SpeciesList	scientific name: marine metagenome; NCBI TaxID: NEWT:408172; scientific name: soil metagenome; NCBI TaxID: NEWT:410658; scientific name: human gut metagenome; NCBI TaxID: NEWT:408170;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2025-08-12 12:34:46	ID requested
⏵ 1	2025-10-19 16:21:19	announced

10.1038/s41467-025-63977-z;

Feng S, Zhang B, Wang H, Xiong Y, Tian A, Yuan X, Pan C, Guo X, Enhancing peptide identification in metaproteomics through curriculum learning in deep learning. Nat Commun, 16(1):8934(2025) [pubmed]

submitter keyword: LC-MS/MS, marine, human gut, soil

Xuan Guo
contact affiliation	Department of Computer Science and Engineering, University of North Texas
contact email	xuan.guo@unt.edu
lab head
Shichao Feng
contact affiliation	University of North Texas
contact email	fengfeng@my.unt.edu
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/2025/10/PXD067277

PRIDE project URI

• PRIDE
  1. PXD067277
     1. Label: PRIDE project
     2. Name: Enhancing Peptide Identification in Metaproteomics through Curriculum Learning in Deep Learning