Wen‐Feng Zeng

FastaLake constructs compact metaproteomic databases from sequence resources to improve peptide identification without requiring matched metagenomic sequencing.

AlphaPeptTools provides a scverse-native Python package for analyzing MS-based proteomics data, enabling scalable analysis and integration with other modalities.

Carafe generates high-quality in silico spectral libraries for DIA proteomics by training deep learning models directly on DIA data, improving fragment ion intensity prediction and peptide detection.

AlphaQuant improves proteoform regulation detection in bottom-up proteomics by using tree-based quantification and deep learning, revealing new patterns in mouse tissues.

AlphaDIA enables end-to-end transfer learning for feature-free proteomics, improving identification and quantification of post-translational modifications.

AlphaPept is an open-source framework for efficient processing of large MS-based proteomics datasets, achieving significant speed improvements using Python and machine learning.

The paper develops a sensitive method to analyze HLA peptides in plasma, revealing stable and tissue-representative immunopeptidomes with potential for biomarker discovery.

This paper introduces a multiplex-DIA workflow that enhances single-cell proteome depth using dimethyl labeling and a reference channel, achieving reliable quantification of nearly 4,000 proteins per cell.

AlphaPeptDeep predicts peptide properties using deep learning, offering a modular framework that matches or exceeds existing tools for retention time, ion mobility, and fragment intensity prediction.

AlphaViz validates proteomics results by visualizing raw data and comparing with automated analysis outputs.

The paper determines the structural context of PTMs across the human proteome and identifies regulatory sites by analyzing their distribution in folded and disordered regions.

pDeep3 improves spectrum prediction accuracy using few-shot learning with minimal computational resources across different mass spectrometry instruments.

pGlyco3 is a glycan-first search engine for analyzing glycopeptides and modified saccharide units, offering faster performance without sacrificing accuracy.