Papers › Introducing π-HelixNovo for practical large-scale de novo peptide sequencing

Introducing π-HelixNovo for practical large-scale de novo peptide sequencing

27 Aug 2023bioRxiv 2023 8archive 2025-07-28

Tingpeng Yang, Tianze Ling, Boyan Sun, Zhendong Liang, Fan Xu, Xiansong Huang, Linhai Xie, Yonghong He, Leyuan Li, Fuchu He, Yu Wang, Cheng Chang

De novo peptide sequencing is a promising approach for novel peptide discovery. We use a novel concept of complementary spectra to enhance ion information and propose a de novo sequencing model π-HelixNovo based on Transformer architecture. π-HelixNovo outperforms other state-of-the-art models and enhances the taxonomic resolution of gut metaproteome, taking a significant step forward in de novo sequencing.

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de novo peptide sequencing

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Absolute Position EncodingsAdamAttentionBPEDense ConnectionsDropoutLabel SmoothingLayer NormalizationLinear LayerMulti-Head AttentionPosition-Wise Feed-Forward LayerResidual ConnectionSoftmaxTransformer

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