PepNet

algorithm · CNN

PepNet: algorithm · CNN. Temporal convolutional network

Temporal convolutional network

Kind	algorithm
Deep learning	yes
Acquisition	DDA
Family	CNN

Code

• https://github.com/lkytal/PepNet

Live stars, open issues and last-push figures are on the Code activity chart.

Benchmarks

• ProteoBench, on the nine-species benchmark, ProteoBench selection: peptide-level AUC 0.682; precision 0.399 at 100% coverage; amino-acid AUC 0.774 (version v0.0.1, submitted 2026-08-10).

Both are mass-based matches on the tool’s most recent run. What these numbers mean.

Papers describing it (2)

• PepNet: A Fully Convolutional Neural Network for De novo Peptide Sequencing (2022, Research Square, preprint)
• Accurate de novo peptide sequencing using fully convolutional neural networks (2023, Nature Communications, peer-reviewed)

Paper using it

An application or evaluation that ran this method. It is not counted among its authors below.

• Evaluation of the accuracy of false alarm frequency control methods for de novo spectrum (2025, Proceedings of the Southwest State University. Series: IT Management, Computer Science, Computer Engineering. Medical Equipment Engineering, peer-reviewed)

Authors (4)

Kaiyuan Liu, Yuzhen Ye, Haixu Tang, Sujun Li

Seen in the charts

• The architectures
• Code activity
• Models and the authors behind them

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