Xiaowen Liu

发表

Qualitative and quantitative top-down proteomics of human colorectal cancer cell lines identified 23000 proteoforms and revealed drastic proteoform-level differences between metastatic and non-metastatic cancer cells

A. Hummon, Elijah N. McCool, Tian Xu, 2021, bioRxiv.

Capillary Zone Electrophoresis-Tandem Mass Spectrometry with Activated Ion Electron Transfer Dissociation for Large-scale Top-down Proteomics

Abdul Rehman Basharat, J. Coon, Elijah N. McCool, 2019, Journal of The American Society for Mass Spectrometry.

Deconvolution and Database Search of Complex Tandem Mass Spectra of Intact Proteins

P. Pevzner, V. Bafna, P. Dorrestein, 2010, Molecular & Cellular Proteomics.

Identification of ultramodified proteins using top-down tandem mass spectra.

P. Pevzner, L. Paša-Tolić, Xiaowen Liu, 2013, Journal of proteome research.

Protein Identification Using Top-Down Spectra*

Ying S. Ting, Richard D. Smith, P. Pevzner, 2012, Molecular & Cellular Proteomics.

De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.

P. Pevzner, L. Paša-Tolić, T. Luider, 2014, Journal of proteome research.

Identification and Quantification of Proteoforms by Mass Spectrometry

Liangliang Sun, Zhijie Wu, Ying Ge, 2019, Proteomics.

A new scoring function for top-down spectral deconvolution

Qiang Kou, Si Wu, Xiaowen Liu, 2014, BMC Genomics.

Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore.

Nikola Tolić, Ljiljana Paša-Tolić, Binhai Zhu, 2016, Journal of proteome research.

Single-Shot Top-Down Proteomics with Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry for Identification of Nearly 600 Escherichia coli Proteoforms.

Liangliang Sun, Qiang Kou, Rachele A Lubeckyj, 2017, Analytical chemistry.

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.

L. Paša-Tolić, Yunlong Liu, Xiaowen Liu, 2017, Bioinformatics.

Spectral probabilities of top-down tandem mass spectra

Shuai Cheng Li, Xiaowen Liu, Sangtae Kim, 2014, BMC Genomics.

Filling a Protein Scaffold With a Reference

B. Zhu, Xiaowen Liu, Letu Qingge, 2016, IEEE Transactions on NanoBioscience.

Top-down Mass Spectrometry Analysis of Human Serum Autoantibody Antigen-Binding Fragments

J. James, Kenneth Smith, Xiaowen Liu, 2019, Scientific Reports.

EnvCNN: A Convolutional Neural Network Model for Evaluating Isotopic Envelopes in Top-Down Mass-spectral Deconvolution.

Abdul Rehman Basharat, Xia Ning, Xiaowen Liu, 2020, Analytical chemistry.

Development of an Online 2D Ultra-High-Pressure Nano-LC System for High-pH and Low-pH Reversed Phase Separation in Top-Down Proteomics.

Kenneth Smith, Xiaowen Liu, Si Wu, 2020, Analytical chemistry.

Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy

Bin Ma, Yonghua Han, Xiaowen Liu, 2009, Bioinform..

Proteoform Identification by Combining RNA-Seq and Top-down Mass Spectrometry

Wenrong Chen, Xiaowen Liu, 2020, bioRxiv.

Quantitative Top-Down Proteomics in Complex Samples Using Protein-Level Tandem Mass Tag Labeling.

Kenneth Smith, Xiaowen Liu, Si Wu, 2021, Journal of the American Society for Mass Spectrometry.

MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics*

Ying Peng, Xiaowen Liu, Ying Ge, 2015, Molecular & Cellular Proteomics.

Quantitative analysis of human salivary gland‐derived intact proteome using top‐down mass spectrometry

Joseph N. Brown, Ronald J. Moore, Richard D. Smith, 2014, Proteomics.

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry.

Elijah N. McCool, Xiaowen Liu, Liangliang Sun, 2018, Journal of visualized experiments : JoVE.

Optimization of protein-level tandem mass tag (TMT) labeling conditions in complex samples with top-down proteomics.

Xiaowen Liu, Si Wu, Dahang Yu, 2022, Analytica chimica acta.

A benchmarking protocol for intact protein-level Tandem Mass Tag (TMT) labeling for quantitative top-down proteomics

Xiaowen Liu, Dahang Yu, Kellye A. Cupp-Sutton, 2022, MethodsX.

TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization

Qiang Kou, Xiaowen Liu, Likun Xun, 2016, Bioinform..

Deep Intact Proteoform Characterization in Human Cell Lysate Using High-pH and Low-pH Reversed-Phase Liquid Chromatography

Si Wu, Xiaowen Liu, Xiaowen Liu, 2019, Journal of The American Society for Mass Spectrometry.

A graph-based approach for proteoform identification and quantification using top-down homogeneous multiplexed tandem mass spectra

Xiaowen Liu, Kaiyuan Zhu, Xiaowen Liu, 2018, BMC Bioinformatics.

Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions

Charles Ansong, Fred Heffron, Ernesto S Nakayasu, 2013, Proceedings of the National Academy of Sciences.

Erratum to: Improving protein order-disorder classification using charge-hydropathy plots

Li Shen, Fei Huang, Bin Xue, 2015, BMC Bioinformatics.

Improving protein order-disorder classification using charge-hydropathy plots

Fei Huang, A. Keith Dunker, Wei-Lun Hsu, 2014, BMC bioinformatics.

TopMSV: A Web-Based Tool for Top-Down Mass Spectrometry Data Visualization.

In Kwon Choi, Sreekanth R. Kankara, Xiaowen Liu, 2021, Journal of the American Society for Mass Spectrometry.

Deep Top-Down Proteomics Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry: Identification of 5700 Proteoforms from the Escherichia coli Proteome.

Liangliang Sun, Qiang Kou, Rachele A Lubeckyj, 2018, Analytical chemistry.

Top-down analysis of protein samples by de novo sequencing techniques

Xiaowen Liu, Pavel A. Pevzner, Kira Vyatkina, 2016, Bioinform..

De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra.

Nikola Tolić, Ljiljana Paša-Tolić, Pavel A Pevzner, 2015, Journal of proteome research.

Better score function for peptide identification with ETD MS/MS spectra

Bin Ma, Baozhen Shan, Xiaowen Liu, 2010, BMC Bioinformatics.

Identification of Ultramodified Proteins Using Top-Down Spectra

Si Wu, Pavel A. Pevzner, Nikola Tolic, 2013, RECOMB.

Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery

Chad W. Johnston, N. Magarvey, Xiaowen Liu, 2012, Proceedings of the National Academy of Sciences.

Evaluation of Machine Learning Models for Proteoform Retention and Migration Time Prediction in Top-Down Mass Spectrometry

Xia Ning, Elijah N. McCool, Wenrong Chen, 2021, bioRxiv.

A mass graph‐based approach for the identification of modified proteoforms using top‐down tandem mass spectra

Xiaowen Liu, Yunlong Liu, Nikola Tolic, 2016, Bioinform..

Identification of Glycopeptides with Multiple Hydroxylysine O-Glycosylation Sites by Tandem Mass Spectrometry.

Y. Mechref, Ehwang Song, Haixu Tang, 2015, Journal of proteome research.

Top-down Proteomics Reveals Concerted Reductions in Myofilament and Z-disc Protein Phosphorylation after Acute Myocardial Infarction*

Ying Ge, Huseyin Guner, Timothy A. Hacker, 2014, Molecular & Cellular Proteomics.

A Markov Chain Monte Carlo Method for Estimating the Statistical Significance of Proteoform Identifications by Top-Down Mass Spectrometry.

Qiang Kou, Zhe Wang, Xiaowen Liu, 2019, Journal of proteome research.

Systematic Evaluation of Protein Sequence Filtering Algorithms for Proteoform Identification Using Top‐Down Mass Spectrometry

Qiang Kou, Xiaowen Liu, Si Wu, 2018, Proteomics.

Top-down analysis of immunoglobulin G isotypes 1 and 2 with electron transfer dissociation on a high-field Orbitrap mass spectrometer.

Pavel A Pevzner, Alexander Makarov, Yury O Tsybin, 2017, Journal of proteomics.

SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra.

Pavel A Pevzner, Xiaowen Liu, Mikhail Kolmogorov, 2016, Journal of proteome research.

Improving protein order-disorder classification using charge-hydropathy plots

Christopher J. Oldfield, Fei Huang, P. Romero, 2014, BMC Bioinformatics.

Large-Scale Qualitative and Quantitative Top-Down Proteomics Using Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry with Nanograms of Proteome Samples

Abdul Rehman Basharat, Xiaowen Liu, Liangliang Sun, 2019, Journal of The American Society for Mass Spectrometry.

Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography-Capillary Zone Electrophoresis-Tandem Mass Spectrometry.

Liangliang Sun, Qiang Kou, Daoyang Chen, 2018, Analytical chemistry.

Sorting a Permutation by Best Short Swaps

Daming Zhu, Jiong Guo, Haodi Feng, 2021, Algorithmica.

De Novo Sequencing of Peptides from High‐Resolution Bottom‐Up Tandem Mass Spectra using Top‐Down Intended Methods

Nikola Tolić, Ljiljana Paša-Tolić, Xiaowen Liu, 2017, Proteomics.

An efficient algorithm for the blocked pattern matching problem

Lusheng Wang, Fei Deng, Xiaowen Liu, 2015, Bioinform..

Speeding up tandem mass spectral identification using indexes

Vineet Bafna, Xiaowen Liu, Alessandro Mammana, 2012, Bioinform..

MASH Explorer: A Universal Software Environment for Top-Down Proteomics.

Zhijie Wu, David S Roberts, Jake A Melby, 2020, Journal of proteome research.

Calling the amino acid sequence of a protein/peptide from the nanospectrum produced by a sub-nanometer diameter pore

G. Timp, Zhuxin Dong, Xiaowen Liu, 2021, bioRxiv.

Quantitative analysis of human salivary gland‐derived intact proteome using top‐down mass spectrometry

Joseph N. Brown, Ronald J. Moore, P. Pevzner, 2014, Proteomics.

MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics*

Ying Ge, Xiaowen Liu, Wenxuan Cai, 2015, Molecular & Cellular Proteomics.

Mass graphs and their applications in top-down proteomics

Nikola Tolić, Xiaowen Liu, Qiang Kou, 2015, bioRxiv.

Deep Top-Down Proteomics Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry: Identification of 5700 Proteoforms from the Escherichia coli Proteome.

Elijah N. McCool, Xiaowen Liu, Liangliang Sun, 2018, Analytical chemistry.

Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery

Chad W. Johnston, N. Magarvey, Xiaowen Liu, 2012, Proceedings of the National Academy of Sciences.

An efficient algorithm for the blocked pattern matching problem

Lusheng Wang, Xiaowen Liu, Fei Deng, 2015, Bioinform..

Correlation Analysis of Histopathology and Proteogenomics Data for Breast Cancer*

Kun Huang, Zhi Han, Jie Zhang, 2019, Molecular & Cellular Proteomics.