Abdul Rehman Basharat, Yong Zang, Liangliang Sun, and Xiaowen Liu. TopFD: a proteoform feature detection tool for top-down proteomics. Analytical Chemistry, 95: 8189-8196, 2023. Pubmed.
Qiang Kou, Likun Xun, and Xiaowen Liu. TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization. Bioinformatics, 32:3495-3497, 2016. Pubmed.
Qiang Kou, Si Wu, Nikola Tolić, Ljiljana Paša-Tolić, Yunlong Liu, and Xiaowen Liu. A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra. Bioinformatics, 33:1309-16, 2017. Pubmed.
Abdul Rehman Basharat, Xia Ning, and Xiaowen Liu. EnvCNN: A convolutional neural network model for evaluating isotopic envelopes in top-down mass-spectral deconvolution. Analytical Chemistry 92:7778–7785,2020. Pubmed.
Qiang Kou, Zhe Wang, Rachele A. Lubeckyj, Si Wu, Liangliang Sun, and Xiaowen Liu. A Markov chain Monte Carlo method for estimating the statistical significance of proteoform identifications by top-down mass spectrometry. Journal of Proteome Research 18:878-889, 2019. Pubmed.
Qiang Kou, Si Wu and Xiaowen Liu. Systematic Evaluation of Protein Sequence Filtering Algorithms for Proteoform Identification Using Top-Down Mass Spectrometry. Proteomics, 18:1700306, 2018. Pubmed.
Qiang Kou, Binhai Zhu, Charles Ansong, Si Wu, Nikola Tolić, Ljiljana Paša-Tolić and Xiaowen Liu. Characterization of proteoforms with unknown post-translational modifications using the MIScore. Journal of Proteome Research, 15:2422-32, 2016. Pubmed.
Qiang Kou, Si Wu and Xiaowen Liu. A new scoring function for top-down spectral deconvolution. BMC Genomics, 15:1140, 2014. Pubmed.
Xiaowen Liu, Matthew W. Segar, Shuai Cheng Li and Sangtae Kim. Spectral probabilities of top-down tandem mass spectra. BMC Genomics, 15 Suppl 1:S9, 2014. Pubmed.
Xiaowen Liu, Shawna Hengel, Si Wu, Nikola Tolic, Ljiljana Pasa-Tolic, and Pavel A. Pevzner. Identification of ultramodified proteins using top-down tandem mass spectra. Journal of Proteome Research, 12: 5830-5838, 2013. Pubmed
Xiaowen Liu, Alessandro Mammana and Vineet Bafna. Speeding up tandem mass spectral identification using indexes. Bioinformatics, 28:1692-1697, 2012. Pubmed.
Xiaowen Liu, Yakov Sirotkin, Yufeng Shen, Gordon Anderson, Yihsuan S Tsai, Ying S Ting, David R Goodlett, Richard D Smith, Vineet Bafna and Pavel A Pevzner. Protein identification using top-down spectra. Molecular & Cellular Proteomics, M111.008524, 2012. Pubmed.
Xiaowen Liu, Yuval Inbar, Pieter C Dorrestein, Colin Wynne, Nathan Edwards, Puneet Souda, Julian P Whitelegge, Vineet Bafna and Pavel A Pevzner. Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach. Molecular & Cellular Proteomics, 9:2772-82, 2010. Pubmed.