π-SPECFormer: A Mass Spectrometry-based Foundation Model for Decoding the Dark Proteome
Tianze Ling, Tao Liu, Fan Xu…·Cheng Chang
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.