Tingpeng Yang

π-SPECFormer: A Mass Spectrometry-based Foundation Model for Decoding the Dark Proteome

This paper introduces π-SPECFormer, a foundation model for mass spectrometry-based proteomics that decodes the dark proteome by pre-training on unannotated spectra and outperforms baselines in peptide sequencing and modification detection.

False discovery rate control enables trustworthy deep-learning-based de novo peptide sequencing

This paper introduces a method to control false discovery rates in deep-learning-based de novo peptide sequencing, improving reliability of peptide identifications.

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

The paper introduces π-HelixNovo, a Transformer-based model for de novo peptide sequencing that outperforms existing methods and improves taxonomic resolution in gut metaproteomes.