pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification

Mingqi Liu, Wen‐Feng Zeng, Fang Pan, +18

Nature Communications

pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning

Xie‐Xuan Zhou, Wen‐Feng Zeng, Hao Chi, +5

Analytical Chemistry

Molecular BiologyCandidate PeptidesBioanalysisSimilar PeptidesTandem Mass Spectrometry +17

Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3

Wen‐Feng Zeng, Weiqian Cao, Mingqi Liu, +2

Nature Methods

AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics

Wen‐Feng Zeng, Xie‐Xuan Zhou, Sander Willems, +6

Nature Communications

pGlyco: a pipeline for the identification of intact N-glycopeptides by using HCD- and CID-MS/MS and MS3

Wen‐Feng Zeng, Mingqi Liu, Yang Zhang, +12

Scientific Reports

GlycoproteomicsProtein GlycosylationBiochemistryIntact GlycopeptidesNatural Sciences +13

MS/MS Spectrum Prediction for Modified Peptides Using pDeep2 Trained by Transfer Learning

Wen‐Feng Zeng, Xie‐Xuan Zhou, Wenjing Zhou, +3

Analytical Chemistry

Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel

Marvin Thielert, Ericka C M Itang, Constantin Ammar, +14

Molecular Systems Biology

pDeep3: Toward More Accurate Spectrum Prediction with Fast Few-Shot Learning

Ching Tarn, Wen‐Feng Zeng

Analytical Chemistry

Few-shot LearningFast Few-shot LearningSpectrum PredictionEngineeringMachine Learning +18

AlphaPept: a modern and open framework for MS-based proteomics

Maximilian T. Strauss, Isabell Bludau, Wen‐Feng Zeng, +8

Nature Communications

EngineeringMolecular BiologyBioinformatics DatabaseProteomic TechnologyData Science +17

pGlycoQuant with a deep residual network for quantitative glycoproteomics at intact glycopeptide level

Siyuan Kong, Pengyun Gong, Wen‐Feng Zeng, +12

Nature Communications

Intact Glycopeptide LevelGlycobiologyMolecular BiologyQuantitative GlycoproteomicsCarbohydrate-protein Interaction +16