80 Publications (Page 2 of 4)
2018
A graph-based approach for proteoform identification and quantification using top-down homogeneous multiplexed tandem mass spectra
Zhu, Kaiyuan and Liu, Xiaowen
BMC bioinformatics, vol. 19, (no. Suppl 9), pp. 280, 2018-Aug-13. | Journal Article
 
Deep Top-Down Proteomics Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry: Identification of 5700 Proteoforms from the Escherichia coli Proteome
McCool, Elijah N⋅Lubeckyj, Rachele A⋅Shen, Xiaojing⋅Chen, Daoyang⋅Kou, Qiang⋅Liu, Xiaowen and Sun, Liangliang
Analytical Chemistry, vol. 90, (no. 9), pp. 5533, 20180501. | Journal Article
 
Evaluation of top-down mass spectral identification with homologous protein sequences
Li, Ziwei⋅Li, Ziwei⋅He, Bo⋅He, Bo⋅Kou, Qiang⋅Kou, Qiang⋅Wang, Zhe⋅Wang, Zhe⋅Wu, Si⋅Wu, Si⋅Liu, Yunlong⋅Liu, Yunlong⋅Feng, Weixing⋅Feng, Weixing⋅Liu, Xiaowen and Liu, Xiaowen
BMC bioinformatics, vol. 19, (no. Suppl 17), pp. 494, 2018-Dec-28. | Journal Article
 
Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry
McCool, Elijah N⋅Lubeckyj, Rachele⋅Shen, Xiaojing⋅Kou, Qiang⋅Liu, Xiaowen and Sun, Liangliang
Journal of Visualized Experiments, (no. 140), 10-2018. | Journal Article
 
Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography–Capillary Zone Electrophoresis–Tandem Mass Spectrometry
Shen, Xiaojing⋅Kou, Qiang⋅Guo, Ruiqiong⋅Yang, Zhichang⋅Chen, Daoyang⋅Liu, Xiaowen⋅Hong, Heedeok and Sun, Liangliang
Analytical Chemistry, vol. 90, (no. 17), pp. 10099, 20180904. | Journal Article
 
Systematic Evaluation of Protein Sequence Filtering Algorithms for Proteoform Identification Using Top‐Down Mass Spectrometry
Kou, Qiang⋅Wu, Si and Liu, Xiaowen
PROTEOMICS, vol. 18, (no. 3-4), pp. n/a, February 2018. | Journal Article
2017
A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.
Kou, Qiang⋅Kou, Qiang⋅Wu, Si⋅Wu, Si⋅Tolic, Nikola⋅Tolic, Nikola⋅Paša-Tolic, Ljiljana⋅Paša-Tolic, Ljiljana⋅Liu, Yunlong⋅Liu, Yunlong⋅Liu, Xiaowen and Liu, Xiaowen
Bioinformatics (Oxford, England), vol. 33, (no. 9), pp. 1309-1316, May 1, 2017. | Journal Article
 
A spectrum graph-based protein sequence filtering algorithm for proteoform identification by top-down mass spectrometry
Yang, Runmin⋅Yang, Runmin⋅Zhu, Daming⋅Zhu, Daming⋅Kou, Qiang⋅Kou, Qiang⋅Bhat-Nakshatri, Poornima⋅Bhat-Nakshatri, Poornima⋅Nakshatri, Harikrishna⋅Nakshatri, Harikrishna⋅Wu, Si⋅Wu, Si⋅Liu, Xiaowen and Liu, Xiaowen
2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), vol. 2017, pp. 229, 2017-Nov.. | Journal Article
 
De Novo Sequencing of Peptides from High‐Resolution Bottom‐Up Tandem Mass Spectra using Top‐Down Intended Methods
Vyatkina, Kira⋅Dekker, Lennard J. M⋅Wu, Si⋅VanDuijn, Martijn M⋅Liu, Xiaowen⋅Tolić, Nikola⋅Luider, Theo M and Paša‐Tolić, Ljiljana
PROTEOMICS, vol. 17, (no. 23-24), pp. n/a, December 2017. | Journal Article
 
Filling a Protein Scaffold With a Reference.
Qingge, Letu⋅Liu, Xiaowen⋅Zhong, Farong and Zhu, Binhai
IEEE transactions on nanobioscience, vol. 16, (no. 2), pp. 123-130, March 2017. | Journal Article
 
Single-Shot Top-Down Proteomics with Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry for Identification of Nearly 600 Escherichia coli Proteoforms
Lubeckyj, Rachele A⋅McCool, Elijah N⋅Shen, Xiaojing⋅Kou, Qiang⋅Liu, Xiaowen and Sun, Liangliang
Analytical Chemistry, vol. 89, (no. 22), pp. 12067, 20171121. | Journal Article
 
Top-down analysis of immunoglobulin G isotypes 1 and 2 with electron transfer dissociation on a high-field orbitrap mass spectrometer.
Fornelli, Luca⋅Ayoub, Daniel⋅Aizikov, Konstantin⋅Liu, Xiaowen⋅Damoc, Eugen⋅Pevzner, Pavel A⋅Makarov, Alexander⋅Beck, Alain and Tsybin, Yury O
Journal of proteomics, February 24, 2017. | Journal Article
2016
A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.
Kou, Qiang⋅Kou, Qiang⋅Wu, Si⋅Wu, Si⋅Tolić, Nikola⋅Tolić, Nikola⋅Paša-Tolić, Ljiljana⋅Paša-Tolić, Ljiljana⋅Liu, Yunlong⋅Liu, Yunlong⋅Liu, Xiaowen and Liu, Xiaowen
Bioinformatics (Oxford, England), December 21, 2016. | Journal Article
 
Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore.
Kou, Qiang⋅Zhu, Binhai⋅Wu, Si⋅Ansong, Charles⋅Tolić, Nikola⋅Paša-Tolić, Ljiljana and Liu, Xiaowen
Journal of proteome research, vol. 15, (no. 8), pp. 2422-2432, August 5, 2016. | Journal Article
 
Filling a protein scaffold with a reference
Qingge, L.⋅Liu, X.⋅Zhong, F. and Zhu, B.
2016
 
MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics.
Cai, Wenxuan⋅Guner, Huseyin⋅Gregorich, Zachery R⋅Chen, Albert J⋅Ayaz-Guner, Serife⋅Peng, Ying⋅Valeja, Santosh G⋅Liu, Xiaowen and Ge, Ying
Molecular & cellular proteomics : MCP, vol. 15, (no. 2), pp. 703-714, February 2016. | Journal Article
 
Mass graphs and their applications in top-down proteomics
Kou, Q.⋅Wu, S.⋅Toli?, N.⋅Liu, Y.⋅Pa?a-Toli?, L. and Liu, X.
2016
 
Mass graphs and their applications in top-down proteomics
Kou, Q.⋅Wu, S.⋅Toli?, N.⋅Liu, Y.⋅Pa?a-Toli?, L. and Liu, X.
(pp. XII)
 
Proteomic Characterization Reveals That MMP-3 Correlates With Bronchiolitis Obliterans Syndrome Following Allogeneic Hematopoietic Cell and Lung Transplantation.
Liu, X.⋅Liu, X⋅Yue, Z.⋅Yue, Z⋅Yu, J.⋅Yu, J⋅Daguindau, E⋅Daguindau, E.⋅Kushekhar, K.⋅Kushekhar, K⋅Zhang, Q⋅Zhang, Q.⋅Ogata, Y⋅Ogata, Y.⋅Gafken, P.R.⋅Gafken, P R⋅Inamoto, Y⋅Inamoto, Y.⋅Gracon, A⋅Gracon, A.⋅Wilkes, D S⋅Wilkes, D.S.⋅Hansen, J A⋅Hansen, J.A.⋅Lee, S J⋅Lee, S.J.⋅Chen, J Y⋅Chen, J.Y.⋅Paczesny, S. and Paczesny, S
American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, vol. 16, (no. 8), pp. 2342-2351, August 2016. | Journal Article
 
SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra.
Kolmogorov, Mikhail⋅Liu, Xiaowen and Pevzner, Pavel A
Journal of proteome research, vol. 15, (no. 1), pp. 144-151, January 4, 2016. | Journal Article
 
Top-down analysis of protein samples by de novo sequencing techniques.
Vyatkina, Kira⋅Vyatkina, Kira⋅Wu, Si⋅Wu, Si⋅Dekker, Lennard J M⋅Dekker, Lennard J M⋅VanDuijn, Martijn M⋅VanDuijn, Martijn M⋅Liu, Xiaowen⋅Liu, Xiaowen⋅Tolić, Nikola⋅Tolić, Nikola⋅Luider, Theo M⋅Luider, Theo M⋅Paša-Tolić, Ljiljana⋅Paša-Tolić, Ljiljana⋅Pevzner, Pavel A and Pevzner, Pavel A
Bioinformatics (Oxford, England), vol. 32, (no. 18), pp. 2753-2759, September 15, 2016. | Journal Article
 
TopPIC: A software tool for top-down mass spectrometry-based proteoform identification and characterization.
Kou, Qiang⋅Xun, Likun and Liu, Xiaowen
Bioinformatics (Oxford, England), July 16, 2016. | Journal Article
2015
An efficient algorithm for the blocked pattern matching problem.
Deng, Fei⋅Wang, Lusheng and Liu, Xiaowen
Bioinformatics (Oxford, England), vol. 31, (no. 4), pp. 532-538, February 15, 2015. | Journal Article
 
De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra.
Vyatkina, Kira⋅Wu, Si⋅Dekker, Lennard J M⋅VanDuijn, Martijn M⋅Liu, Xiaowen⋅Tolić, Nikola⋅Dvorkin, Mikhail⋅Alexandrova, Sonya⋅Luider, Theo M⋅Paša-Tolić, Ljiljana and Pevzner, Pavel A
Journal of proteome research, vol. 14, (no. 11), pp. 4450-4462, November 6, 2015. | Journal Article
 
Identification of Glycopeptides with Multiple Hydroxylysine O-Glycosylation Sites by Tandem Mass Spectrometry.
Zhang, Yanlin⋅Zhang, Yanlin⋅Yu, Chuan-Yih⋅Yu, Chuan-Yih⋅Song, Ehwang⋅Song, Ehwang⋅Li, Shuai Cheng⋅Li, Shuai Cheng⋅Mechref, Yehia⋅Mechref, Yehia⋅Tang, Haixu⋅Tang, Haixu⋅Liu, Xiaowen and Liu, Xiaowen
Journal of proteome research, vol. 14, (no. 12), pp. 5099-5108, December 4, 2015. | Journal Article