| A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides ZL Chen, JM Meng, Y Cao, JL Yin, RQ Fang, SB Fan, C Liu, WF Zeng, ... Nature communications 10 (1), 3404, 2019 | 428 | 2019 |
| Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine H Chi, C Liu, H Yang, WF Zeng, L Wu, WJ Zhou, RM Wang, XN Niu, ... Nature biotechnology 36 (11), 1059-1061, 2018 | 357 | 2018 |
| pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification MQ Liu, WF Zeng, P Fang, WQ Cao, C Liu, GQ Yan, Y Zhang, C Peng, ... Nature communications 8 (1), 438, 2017 | 311 | 2017 |
| pDeep: predicting MS/MS spectra of peptides with deep learning XX Zhou, WF Zeng, H Chi, C Luo, C Liu, J Zhan, SM He, Z Zhang Analytical chemistry 89 (23), 12690-12697, 2017 | 241 | 2017 |
| Artificial intelligence for proteomics and biomarker discovery M Mann, C Kumar, WF Zeng, MT Strauss Cell systems 12 (8), 759-770, 2021 | 240 | 2021 |
| Deep learning in proteomics B Wen, WF Zeng, Y Liao, Z Shi, SR Savage, W Jiang, B Zhang Proteomics 20 (21-22), 1900335, 2020 | 159 | 2020 |
| Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3 WF Zeng, WQ Cao, MQ Liu, SM He, PY Yang Nature Methods 18 (12), 1515-1523, 2021 | 140 | 2021 |
| AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics WF Zeng, XX Zhou, S Willems, C Ammar, M Wahle, I Bludau, E Voytik, ... Nature Communications 13 (1), 7238, 2022 | 120 | 2022 |
| pGlyco: a pipeline for the identification of intact N-glycopeptides by using HCD-and CID-MS/MS and MS3 WF Zeng, MQ Liu, Y Zhang, JQ Wu, P Fang, C Peng, A Nie, G Yan, W Cao, ... Scientific reports 6 (1), 25102, 2016 | 110 | 2016 |
| pNovo+: de novo peptide sequencing using complementary HCD and ETD tandem mass spectra H Chi, H Chen, K He, L Wu, B Yang, RX Sun, J Liu, WF Zeng, CQ Song, ... Journal of proteome research 12 (2), 615-625, 2013 | 108 | 2013 |
| The structural context of posttranslational modifications at a proteome-wide scale I Bludau, S Willems, WF Zeng, MT Strauss, FM Hansen, MC Tanzer, ... PLoS biology 20 (5), e3001636, 2022 | 99 | 2022 |
| MS/MS spectrum prediction for modified peptides using pDeep2 trained by transfer learning WF Zeng, XX Zhou, WJ Zhou, H Chi, J Zhan, SM He Analytical chemistry 91 (15), 9724-9731, 2019 | 98 | 2019 |
| pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework H Yang, H Chi, WF Zeng, WJ Zhou, SM He Bioinformatics 35 (14), i183-i190, 2019 | 93 | 2019 |
| pQuant improves quantitation by keeping out interfering signals and evaluating the accuracy of calculated ratios C Liu, CQ Song, ZF Yuan, Y Fu, H Chi, LH Wang, SB Fan, K Zhang, ... Analytical chemistry 86 (11), 5286-5294, 2014 | 79 | 2014 |
| pTop 1.0: a high-accuracy and high-efficiency search engine for intact protein identification RX Sun, L Luo, L Wu, RM Wang, WF Zeng, H Chi, C Liu, SM He Analytical chemistry 88 (6), 3082-3090, 2016 | 75 | 2016 |
| Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel M Thielert, ECM Itang, C Ammar, FA Rosenberger, I Bludau, L Schweizer, ... Molecular Systems Biology 19 (9), e11503, 2023 | 59 | 2023 |
| A theoretical foundation of the target-decoy search strategy for false discovery rate control in proteomics K He, Y Fu, WF Zeng, L Luo, H Chi, C Liu, LY Qing, RX Sun, SM He arXiv preprint arXiv:1501.00537, 2015 | 49 | 2015 |
| AlphaPept: a modern and open framework for MS-based proteomics MT Strauss, I Bludau, WF Zeng, E Voytik, C Ammar, JP Schessner, ... Nature Communications 15 (1), 2168, 2024 | 46 | 2024 |
| Open-pNovo: de novo peptide sequencing with thousands of protein modifications H Yang, H Chi, WJ Zhou, WF Zeng, K He, C Liu, RX Sun, SM He Journal of proteome research 16 (2), 645-654, 2017 | 43 | 2017 |
| pDeep3: toward more accurate spectrum prediction with fast few-shot learning C Tarn, WF Zeng Analytical Chemistry 93 (14), 5815-5822, 2021 | 40 | 2021 |
Mingqi LiuUniverity of California / Fudan UniversityPatvirtintas el. paštas fudan.edu.cn