pFind Studio: a computational solution for mass spectrometry-based proteomics

Molecular & cellular Proteomics. April 25, 2025.[abstract]

Global analysis of protein and small-molecule substrates of ubiquitin-like proteins (UBLs)

Guang-Can Shao, Zhen-Lin Chen, Shan Lu, Qing-Cui Wu, Yao Sheng, Jing Wang, Yan Ma, Jian-Hua Sui, Hao Chi, Xiang-Bing Qi, Si-Min He, Li-Lin Du, Meng-Qiu Dong.

J. Proteome Res. Dec 29, 2023.[abstract]

PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors

Ching Tarn, Yu-Zhuo Wu, Kai-Fei Wang.

International Journal of Mass Spectrometry. October 29, 2022.[abstract]

A universal database reduction method based on the sequence tag strategy to facilitate large-scale database search in proteomics

Kai-Fei Wang, Yu-Zhuo Wu, Hao Chi.

Methods in Molecular Biology. June 04, 2022.[abstract]

Accurate Proteoform Identification and Quantitation Using pTop 2.0

Rui-Xiang Sun, Rui-Min Wang, Lan Luo, Chao Liu, Hao Chi, Wen-Feng Zeng & Si-Min He.

Nature Chemical Biology. July 21, 2022.[abstract]

A modification-centric assessment tool for the performance of chemoproteomic probes

Ji-Xiang He, Zheng-Cong Fei, Ling Fu, Cai-Ping Tian, Fu-Chu He, Hao Chi & Jing Yang.

Journal of Proteomics. January 16, 2022.[abstract]

pValid 2: A deep learning based validation method for peptide identification in shotgun proteomics with increased discriminating power

Wen-Jing Zhou, Zhuo-Hong Wei, Si-Min He, Hao Chi.

Nature Methods. November 25, 2021.[abstract]

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

Wen-Feng Zeng, Wei-Qian Cao, Ming-Qi Liu, Si-Min He, Peng-Yuan Yang.

生物化学与生物物理进展. July 28, 2021.[abstract]

化学交联质谱技术的研究进展

陈镇霖, 曹勇, 贺思敏.

Biophysics Reports. June 30, 2021.[abstract]

How to use open-pFind in deep proteomics data analysis?— A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data

Shao Guangcan, Cao Yong, Chen Zhenlin, Liu Chao, Li Shangtong, Chi Hao, Dong Meng-Qiu.

Journal of Proteome Research. April 6, 2021.[abstract]

pDeepXL: MS/MS Spectrum Prediction for Cross-Linked Peptide Pairs by Deep Learning

Zhen-Lin Chen, Peng-Zhi Mao, Wen-Feng Zeng, Hao Chi, and Si-Min He.

Analytical Chemistry. April 2, 2021.[abstract]

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

Ching Tarn and Wen-Feng Zeng.

Proteomics. September 14, 2020.[abstract]

GameTag: A New Sequence Tag Generation Algorithm Based on Cooperative Game Theory

Zhengcong Fei, Kaifei Wang, Hao Chi.

Proteomics. September 16, 2020.[abstract]

Deep Learning in Proteomics

Bo Wen, Wen‐Feng Zeng, Yuxing Liao, Zhiao Shi, Sara R. Savage, Wen Jiang, Bing Zhang.

Nature Communications. July 30, 2019.[abstract]

A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

Zhen-Lin Chen, Jia-Ming Meng, Yong Cao, Ji-Li Yin, Run-Qian Fang, Sheng-Bo Fan, Chao Liu, Wen-Feng Zeng, Yue-He Ding, Dan Tan, Long Wu, Wen-Jing Zhou, Hao Chi, Rui-Xiang Sun, Meng-Qiu Dong, Si-Min He.

Proceedings of the 27th Annual International Conference on Intelligent System for Molecular Biology (ISMB 2019), also appears in Bioinformatics. 2019, 35(14):i183-i190. [abstract]

pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework

Hao Yang, Hao Chi, Wen-Feng Zeng, Wen-Jing Zhou, Si-Min He.

Journal of Proteome Research. June 24, 2019.[abstract]

pValid: Validation Beyond the Target-Decoy Approach for Peptide Identification in Shotgun Proteomics

Wen-Jing Zhou, Hao Yang, Wen-Feng Zeng, Kun Zhang, Hao Chi, Si-Min He.

Analytical Chemistry. June 25, 2019.[abstract]

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

Wen-Feng Zeng, Xie-Xuan Zhou, Wen-Jing Zhou, Hao Chi, Jian-feng Zhan, Si-Min He.

Journal of The American Society for Mass Spectrometry. May 30, 2019.[abstract]

Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition

Wenxue Li,Hao Chi,Barbora Salovska,Chongde Wu,Liangliang Sun,George Rosenberger,Yansheng Liu.

Molecular & cellular Proteomics. April 1, 2019.[abstract]

Precision de novo peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics

Hao Yang, Yanchang Li, Mingzhi Zhao, Feilin Wu, Xi Wang, Weidi Xiao, Yihao wang, Junling Zhang, Fuqiang Wang, Feng Xu, Wen-Feng Zeng, Christopher M. Overall, Si-Min He, Hao Chi and Ping Xu.

Nature Biotechnology. October 8, 2018.[abstract]

Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine

Hao Chi, Chao Liu, Hao Yang, Wen-Feng Zeng, Long Wu, Wen-Jing Zhou, Rui-Min Wang, Xiu-Nan Niu, Yue-He Ding, Yao Zhang, Zhao-Wei Wang, Zhen-Lin Chen, Rui-Xiang Sun, Tao Liu, Guang-Ming Tan, Meng-Qiu Dong, Ping Xu, Pei-Heng Zhang & Si-Min He.

Biophysics Reports. April 30, 2018.[abstract]

Mapping disulfide bonds from sub-micrograms of purified proteins or micrograms of complex protein mixtures

Shan Lu, Yong Cao, Sheng-Bo Fan, Zhen-Lin Chen, Run-Qian Fang, Si-Min He, Meng-Qiu Dong.

Journal of proteome research. November 13, 2017.[abstract]

pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization

Hao Yang, Hao Chi, Wen-Jing Zhou, Wen-Feng Zeng, Chao Liu, Rui-Min Wang, Zhao-Wei Wang, Xiu-Nan Niu, Zhen-Lin Chen, and Si-Min He.

Analytical Chemistry. November 10, 2017.[abstract]

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

Xie-Xuan Zhou, Wen-Feng Zeng, Hao Chi, Chun-Jie Luo, Chao Liu, Jian-Feng Zhan, Si-Min He, and Zhi-Fei Zhang.

Nature Communications. September 5, 2017.[abstract]

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

Ming-Qi Liu, Wen-Feng Zeng, Pan Fang, Wei-Qian Cao, Chao Liu, Guo-Quan Yan, Yang Zhang, Chao Peng, Jian-Qiang Wu, Xiao-Jin Zhang, Hui-Jun Tu, Hao Chi, Rui-Xiang Sun, Yong Cao, Meng-Qiu Dong, Bi-Yun Jiang, Jiang-Ming Huang, Hua-Li Shen, Catherine C. L. Wong, Si-Min He, Peng-Yuan Yang.

Molecular Plant. February 13, 2017.[abstract]

Immunopurification and Mass Spectrometry Identifies Protein Phosphatase 2A (PP2A) and BIN2/GSK3 as Regulators of AKS Transcription Factors in Arabidopsis

Shuo-Lei Bu,Chao Liu(co-first),Ning Liu,Ji-Long Zhao,Lian-Feng Ai,Hao Chi,Kathy L. Li,Chih-Wei Chien,Alma L. Burlingame,Sheng-Wei Zhang,Zhi-Yong Wang.

Journal of proteome research. December 26, 2016.[abstract]

Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications

Hao Yang, Hao Chi, Wen-Jing Zhou, Wen-Feng Zeng, Kun He, Chao Liu, Rui-Xiang Sun, Si-Min He.

Scientific Reports. May 3, 2016.[abstract]

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

Wen-Feng Zeng, Ming-Qi Liu, Yang Zhang, Jian-Qiang Wu, Pan Fang, Chao Peng, Aiying Nie, Guoquan Yan, Weiqian Cao, Chao Liu, Hao Chi, Rui-Xiang Sun, Catherine C. L. Wong, Si-Min He, Pengyuan Yang.

生物化学与生物物理进展. April 21, 2016.[abstract]

N-糖肽的规模化质谱解析方法进展

曾文锋,张扬,刘铭琪,吴建强,张晓今,杨皓,刘超,迟浩,张昆,孙瑞祥,杨芃原,贺思敏.

Analytical Chemistry. February 4, 2016.[abstract]

pTop 1.0: a High-accuracy and High-efficiency Search Engine for Intact Protein Identification

Rui-Xiang Sun, Lan Luo, Long Wu, Rui-Min Wang, Wen-Feng Zeng, Hao Chi, Chao Liu, Si-Min He.

Journal of Proteome Research. Nov 6, 2015.[abstract]

Pulsed Azidohomoalanine Labeling in Mammals (PALM) Detects Changes in Liver-Specific LKB1 Knockout Mice

Daniel B. McClatchy,Yuanhui Ma,Chao Liu,Benjamin D. Stein,Salvador Martínez-Bartolomé,Debbie Vasquez,Kristina Hellberg,Reuben J. Shaw,John R. Yates.

Journal of Proteomics. July 1, 2015.[abstract]

pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data

Hao Chi, Kun He, Bing Yang, Zhen Chen, Rui-Xiang Sun, Sheng-Bo Fan, Kun Zhang, Chao Liu, Zuo-Fei Yuan, Quan-Hui Wang, Si-Qi Liu, Meng-Qiu Dong, Si-Min He.

Current protocols in bioinformatics. Mar 9, 2015.[abstract]

Using pLink to Analyze Cross-Linked Peptides

Sheng-Bo Fan, Jia-Ming Meng, Shan Lu, Kun Zhang, Hao Yang, Hao Chi, Rui-Xiang Sun, Meng-Qiu Dong, Si-Min He.

Nature Methods. Feb. 9, 2015. [abstract]

Mapping native disulfide bonds at a proteome scale

Shan Lu, Sheng-Bo Fan, Bing Yang, Yu-Xin Li, Jia-Ming Meng, Long Wu, Pin Li, Kun Zhang, Mei-Jun Zhang, Yan Fu, Jin-Cai Luo, Rui-Xiang Sun, Si-Min He, Meng-Qiu Dong.

Bioinformatics. June. 14, 2015. [abstract]

A Note on the False Discovery Rate of Novel Peptides in Proteogenomics

Kun Zhang, Yan Fu, Wen-Feng Zeng, Kun He, Hao Chi, Chao Liu, Yan-Chang Li, Yuan Gao, Ping Xu, Si-Min He.

生物化学与生物物理进展. 2015, 42(2):101-104. [abstract]

“自顶向下（Top-down）”的蛋白质组学：蛋白质变体的规模化鉴定

孙瑞祥，罗兰，迟浩，刘超，贺思敏.

arXiv. Jan, 2015. [abstract]

A theoretical foundation of the target-decoy search strategy for false discovery rate control in proteomics

Kun He, Yan Fu, Wen-Feng Zeng, Lan Luo, Hao Chi, Chao Liu, Lai-Yun Qing, Rui-Xiang Sun, Si-Min He.

生物化学与生物物理进展. May 26, 2014. 41(11):1109-1125. [abstract]

蛋白质结构与相互作用研究新方法——交联质谱技术

樊盛博，吴妍洁，杨兵，迟浩，孟佳明，卢珊，张昆，邬龙，孙瑞祥，董梦秋，贺思敏.

Anal Chem. May 3, 2014. 86(11):5286-94. [abstract]

pQuant Improves Quantitation by Keeping out Interfering Signals and Evaluating the Accuracy of Calculated Ratios

Chao Liu, Chun-Qing Song, Zuo-Fei Yuan, Yan Fu, Hao Chi, Le-Heng Wang, Sheng-Bo Fan, Kun Zhang, Wen-Feng Zeng, Si-Min He, Meng-Qiu Dong, and Rui-Xiang Sun.

生物化学与生物物理进展. Jan 28, 2013. [abstract]

蛋白质基因组学：运用蛋白质组技术注释基因组

张昆，王乐珩，迟浩，卜德超，袁作飞，刘超，樊盛博，陈海丰，曾文锋，罗海涛，孙瑞祥，贺思敏，谢鹭，赵屹.

Journal of Proteome Research. Feb. 1, 2013. [abstract]

pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra

Hao Chi, Hai-Feng Chen, Kun He, Long Wu, Bing Yang, Rui-Xiang Sun, Jian-Yun Liu, Wen-Feng Zeng, Chun-Qing Song, Si-Min He, Meng-Qiu Dong.

2012

生物化学与生物物理进展. Aug 10, 2012. [abstract]

规模化蛋白质鉴定中母离子的准确检测技术研究

袁作飞，邬龙，刘超，迟浩，樊盛博，张昆，曾文锋，孙瑞祥，贺思敏.

Nature Methods. July 08, 2012. [abstract]

Identification of cross-linked peptides from complex samples

Bing Yang, Yan-Jie Wu, Ming Zhu, Sheng-Bo Fan, Jin-Zhong Lin, Kun Zhang, Shuang Li, Hao Chi, Yu-Xin Li, Hai-Feng Chen, Shu-Kun Luo, Yue-He Ding, Le-Heng Wang, Zhi-Qi Hao, Li-Yun Xiu, She Chen, Ke-Qiong Ye, Si-Min He and Meng-Qiu Dong.

Proceedings of the National Academy of Sciences. January 31, 2012. [abstract]

Nematode sperm maturation triggered by protease involves sperm-secreted serine protease inhibitor (Serpin)

Yanmei Zhao, Wei Sun, Pan Zhang, Hao Chi, Mei-Jun Zhang, Chun-Qing Song, Xuan Ma, Yunlong Shang, Bin Wang, Youqiao Hu, Zhiqi Hao, Andreas F.Huhmei, Fanxia Meng, Steven W.L'Hernault, Si-Min He, Meng-Qiu Dong and Long Miao.

Proteomics, Volume 12, Issue 2, pages 226–235, No. 2 January 2012. [abstract]

pParse: a method for accurate determination of monoisotopic peaks in high-resolution mass spectra

Zuo-Fei Yuan, Chao Liu, Hai-Peng Wang, Rui-Xiang Sun, Yan Fu, Jing-Fen Zhang, Le-Heng Wang, Hao Chi, You Li, Li-Yun Xiu, Wen-Ping Wang, Si-Min He.

2011

Molecular & Cellular Proteomics. 2011, 10(5). [abstract]

DeltAMT: A Statistical Algorithm for Fast Detection of Protein Modifications From LC-MS/MS Data

Yan Fu, Li-Yun Xiu, Wei Jia, Ding Ye, Rui-Xiang Sun, Xiao-Hong Qian, and Si-Min He.

2010

色谱. 2010, 28(6):529-534. [abstract]

肽段反相色谱保留时间预测算法及其在蛋白质鉴定中的应用

刘超，王海鹏，付岩，袁作飞，迟浩，王乐珩，孙瑞祥，贺思敏.

BMC Bioinformatics. 2010, 11:577. [abstract]

Speeding up tandem mass spectrometry-based database searching by longest common prefix

Chen Zhou, Hao Chi, Le-Heng Wang, You Li, Yan-Jie Wu, Yan Fu, Rui-Xiang Sun, Si-Min He.

Journal of Proteome Research. 2010, 9(12):6354–6367. [abstract]

Improved Peptide Identification for Proteomic Analysis Based on Comprehensive Characterization of Electron Transfer Dissociation Spectra

Rui-Xiang Sun, Meng-Qiu Dong, Chun-Qing Song, Hao Chi, Bing Yang, Li-Yun Xiu, Li Tao, Zhi-Yi Jing, Chao Liu, Le-Heng Wang, Yan Fu, and Si-Min He.

生物化学与生物物理进展. 2010, (1). [abstract]

基于电子捕获裂解/电子转运裂解串联质谱技术的蛋白质组学研究

孙瑞祥，董梦秋，迟浩，杨兵，秀丽蕴，王乐珩，付岩，贺思敏.

Rapid Communications in Mass Spectrometry. 2010, 24(12):1791-1798. [abstract]

An efficient parallelization of phosphorylated peptide and protein identification

Leheng Wang, Wenping Wang, Hao Chi, Yanjie Wu, You Li, Yan Fu, Chen Zhou, Ruixiang Sun, Haipeng Wang, Chao Liu, Zuofei Yuan, Liyun Xiu, Si-Min He.

Proceedings of the 18th Annual International Conference on Intelligent System for Molecular Biology (ISMB 2010), also appears in Bioinformatics. 2010, 26(12):i399-i406. [abstract]

Open MS/MS Spectral Library Search to Identify Unanticipated Post-Translational Modifications and Increase Spectral Identification Rate

Ding Ye, Yan Fu, Rui-Xiang Sun, Hai-Peng Wang, Zuo-Fei Yuan, Hao Chi and Si-Min He.

Journal of Proteome Research, 9 (5), 2713–2724, 2010. [abstract]

pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra

Hao Chi , Rui-Xiang Sun , Bing Yang , Chun-Qing Song , Leheng Wang , Chao Liu , Yan Fu , Zuo-Fei Yuan , Hai-Peng Wang , Si-Min He and Meng-Qiu Dong.

Rapid Communications in Mass Spectrometry, 24:807 - 814, 2010. [abstract]

Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing

You Li, Hao Chi, Le-Heng Wang, Hai-Peng Wang, Yan Fu, Zuo-Fei Yuan, Su-Jun Li, Yan-Sheng Liu, Rui-Xiang Sun, Rong Zeng, Si-Min He.

2009

Rapid Commun. Mass Spectrom. 2009; 23: 3448–3456. [abstract]

Isotope pattern vector based tandem mass spectral data calibration for improved peptide and protein identification

Jingfen Zhang, Dong Xu, Wen Gao, Guohui Lin and Simin He.

Molecular & Cellular Proteomics, 8:913-923, 2009. [abstract]

A Strategy for Precise and Large-Scale Identification of Core Fucosylated Glycoproteins

Wei Jia, Zhuang Lu, Yan Fu, Hai-Peng Wang, Le-Heng Wang, Hao Chi, Zuo-Fei Yuan, Zhao-Bin Zheng, Li-Na Song, Huan-Huan Han, Yi-Min Liang, Jing-Lan Wang, Yun Cai, Yu-Kui Zhang, Yu-Lin Deng, Wan-Tao Ying, Si-Min He, and Xiao-Hong Qian.

Accepted by APBC 2009, BMC Bioinformatics, 10(Suppl 1): S50, 2009. [abstract]

Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences

Yan Fu, Wei Jia, Zhuang Lu, Haipeng Wang, Zuofei Yuan, Hao Chi, You Li, Liyun Xiu, Wenping Wang, Chao Liu, Leheng Wang, Ruixiang Sun, Wen Gao, Xiaohong Qian, Si-Min He.

2008

Rapid Communications in Mass Spectrometry,22,1203-1212,2008. [abstract]

PeakSelect:preprocessing tandem mass spectra for better peptide identification

Jing-Fen Zhang, Si-Min He, Charles X.Ling, Xing-Jun Cao, Rong Zeng and Wen Gao.

2007 or earlier

Rapid Communications in Mass Spectrometry, 21,2985-2991,2007. [abstract]

pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry

Le-Heng Wang, De-Quan Li, Yan Fu, Hai-Peng Wang, Jing-Fen Zhang, Zuo-Fei Yuan,Rui-Xiang Sun, Rong Zeng, Si-Min He, Wen Gao.

Proceedings of the 12th Pacific Symposium on Biocomputing, 421-432, 2007. [abstract]

Mining tandem mass spectral data to develop a more accurate mass error model for peptide identification

Yan Fu, Wen Gao, Si-Min He, Rui-Xiang Sun, Hu Zhou, Rong Zeng.

中国科学 E辑 信息科学 36(2): 222-234, 2006. [abstract]

基于质谱技术的计算蛋白质组学研究

孙瑞祥，付岩，李德泉，张京芬，王晓彪，盛泉虎，曾嵘，陈益强，贺思敏，高文.

Proceedings of the Pacific Symposium on Biocomputing, 303-314, 2006. [abstract]

An SVM Scorer for More Sensitive and Reliable Peptide Identification via Tandem Mass Spectrometry

Hai-Peng Wang, Yan Fu, Rui-Xiang Sun, Si-Min He, Rong Zeng, Wen Gao.

Bioinformatics, 22(20), 2572-2573, 2006. [abstract]

IndexToolkit: An Open Source Toolbox to Index Protein Databases for High-throughput Proteomics

De-Quan Li, Wen Gao, Charles X. Ling, Xiaobiao Wang, Rui-Xiang Sun, and Si-Min He.

IEEE/ACM Transactions on Computational Biology and Bioinformatics,2(3), 217-230, 2005. [abstract]

Predicting Molecular Formulas of Fragment Ions with Isotope Patterns in Tandem Mass Spectra

Jing-Fen Zhang, Wen Gao, Jingjing Cai, Si-Min He, Rong Zeng, and Run-Sheng Chen.

Genomics, Proteomics & Bioinformatics, 3(4), 231-237, 2005. [abstract]

Preprocessing of tandem mass spectrometric data based on decision tree classification

Jing-Fen Zhang, Si-Min He, Jingjing Cai, Xing-Jun Cao, Rui-Xiang Sun, Yan Fu, Rong Zeng and Wen Gao.

Bioinformatics, 21(13), 3049-3050, 2005. [abstract]

pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry

De-Quan Li, Yan Fu, Rui-Xiang Sun, Charles X. Ling, Yonggang Wei, Hu Zhou, Rong Zeng, Qiang Yang, Si-Min He and Wen Gao.

Bioinformatics 20, 1948-1954, 2004. [abstract]

Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry

Yan Fu, Qiang Yang, Rui-Xiang Sun, De-Quan Li, Rong Zeng, Charles X. Ling, Wen Gao.

In Proceedings of the 8th Pacific Rim International Conference on Artificial Intelligence (PRICAI 2004), Auckland, New Zealand, August 9-13, 2004, LNAI 3157, 544–553. [abstract]

A Kernel-based Case Retrieval Algorithm with Application to Bioinformatics

Yan Fu, Qiang Yang, Charles X. Ling, Hai-Peng Wang, De-Quan Li, Rui-Xiang Sun, Hu Zhou, Rong Zeng, Yiqiang Chen, Si-Min He, Wen Gao.