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

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

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 for more accurate mass error model for peptide identification.

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

2006

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.