Xiaowen Liu Department of BioHealth Informatics Indiana University-Purdue University Indianapolis Biography Publications Institution JoVE Articles Xiaowen Liu Xiaowen Liu is an associate professor of bioinformatics in the Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis (IUPUI). He received his bachelor’s and master’s degrees in computer science from Shandong University, China and obtained his PhD degree in computer science from the City University of Hong Kong. Before joining IUPUI, he worked as a postdoctoral fellow at the University of Western Ontario, the University of Waterloo, and the University of California, San Diego, from 2008 to 2012. His research focuses on computational proteomics, especially top-down proteomics, which is capable of identifying various proteoforms in biological samples. His lab has developed powerful software tools for top-down mass spectrometry-based proteoform identification, characterization, and quantitation, which have been widely used in the proteomics community. Publications Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography-Capillary Zone Electrophoresis-Tandem Mass Spectrometry Analytical Chemistry. Sep, 2018 | Pubmed ID: 30085653 Deep Top-Down Proteomics Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry: Identification of 5700 Proteoforms from the Escherichia Coli Proteome Analytical Chemistry. May, 2018 | Pubmed ID: 29620868 Systematic Evaluation of Protein Sequence Filtering Algorithms for Proteoform Identification Using Top-Down Mass Spectrometry Proteomics. Feb, 2018 | Pubmed ID: 29327814 A Spectrum Graph-Based Protein Sequence Filtering Algorithm for Proteoform Identification by Top-Down Mass Spectrometry Proceedings. IEEE International Conference on Bioinformatics and Biomedicine. Nov, 2017 | Pubmed ID: 29503761 De Novo Sequencing of Peptides from High-Resolution Bottom-Up Tandem Mass Spectra Using Top-Down Intended Methods Proteomics. Dec, 2017 | Pubmed ID: 29110399 Single-Shot Top-Down Proteomics with Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry for Identification of Nearly 600 Escherichia Coli Proteoforms Analytical Chemistry. Nov, 2017 | Pubmed ID: 29064224 A Mass Graph-based Approach for the Identification of Modified Proteoforms Using Top-down Tandem Mass Spectra Bioinformatics (Oxford, England). 05, 2017 | Pubmed ID: 28453668 Top-down Analysis of Immunoglobulin G Isotypes 1 and 2 with Electron Transfer Dissociation on a High-field Orbitrap Mass Spectrometer Journal of Proteomics. 04, 2017 | Pubmed ID: 28242452 Filling a Protein Scaffold With a Reference IEEE Transactions on Nanobioscience. 03, 2017 | Pubmed ID: 28207401 TopPIC: a Software Tool for Top-down Mass Spectrometry-based Proteoform Identification and Characterization Bioinformatics (Oxford, England). 11, 2016 | Pubmed ID: 27423895 Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore Journal of Proteome Research. 08, 2016 | Pubmed ID: 27291504 Top-down Analysis of Protein Samples by De Novo Sequencing Techniques Bioinformatics (Oxford, England). 09, 2016 | Pubmed ID: 27187201 MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics Molecular & Cellular Proteomics : MCP. Feb, 2016 | Pubmed ID: 26598644 Identification of Glycopeptides with Multiple Hydroxylysine O-Glycosylation Sites by Tandem Mass Spectrometry Journal of Proteome Research. Dec, 2015 | Pubmed ID: 26565680 De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra Journal of Proteome Research. Nov, 2015 | Pubmed ID: 26412692 An Efficient Algorithm for the Blocked Pattern Matching Problem Bioinformatics (Oxford, England). Feb, 2015 | Pubmed ID: 25322837 A New Scoring Function for Top-down Spectral Deconvolution BMC Genomics. Dec, 2014 | Pubmed ID: 25523396 Top-down Proteomics Reveals Concerted Reductions in Myofilament and Z-disc Protein Phosphorylation After Acute Myocardial Infarction Molecular & Cellular Proteomics : MCP. Oct, 2014 | Pubmed ID: 24969035 De Novo Protein Sequencing by Combining Top-down and Bottom-up Tandem Mass Spectra Journal of Proteome Research. Jul, 2014 | Pubmed ID: 24874765 Spectral Probabilities of Top-down Tandem Mass Spectra BMC Genomics. Month, 2014 | Pubmed ID: 24564718 Identification of Ultramodified Proteins Using Top-down Tandem Mass Spectra Journal of Proteome Research. Dec, 2013 | Pubmed ID: 24188097 Top-down Proteomics Reveals a Unique Protein S-thiolation Switch in Salmonella Typhimurium in Response to Infection-like Conditions Proceedings of the National Academy of Sciences of the United States of America. Jun, 2013 | Pubmed ID: 23720318 Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry Elijah N. McCool*1, Rachele Lubeckyj*1, Xiaojing Shen1, Qiang Kou2, Xiaowen Liu2,3, Liangliang Sun1 1Department of Chemistry, Michigan State University, 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 3Center for Computational Biology and Bioinformatics, Indiana University School of Medicine JoVE 58644 Chemistry
Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry Elijah N. McCool*1, Rachele Lubeckyj*1, Xiaojing Shen1, Qiang Kou2, Xiaowen Liu2,3, Liangliang Sun1 1Department of Chemistry, Michigan State University, 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 3Center for Computational Biology and Bioinformatics, Indiana University School of Medicine JoVE 58644 Chemistry
