Sujun Li

FIDDLE: a deep learning method for chemical formulas prediction from tandem mass spectra

FIDDLE is a deep learning method that predicts chemical formulas from tandem mass spectra, achieving high accuracy and speed compared to existing methods.

3DMolMS: Prediction of Tandem Mass Spectra from Three Dimensional Molecular Conformations

3DMolMS predicts tandem mass spectra from 3D molecular conformations, achieving high cosine similarity with experimental spectra and enabling generalized predictions across instruments.

Using high abundance proteins as guides for fast and effective peptide/protein identification from metaproteomic data

The paper introduces HAPiID, a two-step method for faster and more effective peptide/protein identification in human gut metaproteomic data by using high abundance proteins as guides.

msCRUSH: fast tandem mass spectra clustering using locality sensitive hashing

msCRUSH clusters tandem mass spectra using LSH, achieving faster speed and better sensitivity than existing tools, improving peptide identification.

Computational proteogenomic identification and functional interpretation of translated fusions and micro structural variations in cancer

The paper introduces a computational framework integrating genomic, transcriptomic, and proteomic data to identify and interpret translated fusions and micro structural variations in cancer, finding many novel peptides and private aberrations in breast cancer.