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Author Details

Xiaowen Liu
Tulane Center for Biomedical Informatics and Genomics, Tulane University
2009
51
22
Leah V Schaffer (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36281278A benchmarking protocol for intact protein-level Tandem Mass Tag (TMT) labeling for quantitative top-down proteomics.MethodsX2022
35616364Evaluation of Machine Learning Models for Proteoform Retention and Migration Time Prediction in Top-Down Mass Spectrometry.J Proteome Res2022
35934336Optimization of protein-level tandem mass tag (TMT) labeling conditions in complex samples with top-down proteomics.Anal Chim Acta2022
33183009Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry.J Proteome Res2021
33780241TopMSV: A Web-Based Tool for Top-Down Mass Spectrometry Data Visualization.J Am Soc Mass Spectrom2021
33725447Quantitative Top-Down Proteomics in Complex Samples Using Protein-Level Tandem Mass Tag Labeling.J Am Soc Mass Spectrom2021
32356965EnvCNN: A Convolutional Neural Network Model for Evaluating Isotopic Envelopes in Top-Down Mass-Spectral Deconvolution.Anal Chem2020
35615582TopPIC Gateway: A Web Gateway for Top-Down Mass Spectrometry Data Interpretation.PEARC20 (2020)2020
32857493Development of an Online 2D Ultrahigh-Pressure Nano-LC System for High-pH and Low-pH Reversed Phase Separation in Top-Down Proteomics.Anal Chem2020
32786689MASH Explorer: A Universal Software Environment for Top-Down Proteomics.J Proteome Res2020
30638379A Markov Chain Monte Carlo Method for Estimating the Statistical Significance of Proteoform Identifications by Top-Down Mass Spectrometry.J Proteome Res2019
31755044Deep Intact Proteoform Characterization in Human Cell Lysate Using High-pH and Low-pH Reversed-Phase Liquid Chromatography.J Am Soc Mass Spectrom2019
31073891Capillary Zone Electrophoresis-Tandem Mass Spectrometry with Activated Ion Electron Transfer Dissociation for Large-scale Top-down Proteomics.J Am Soc Mass Spectrom2019
30972727Large-Scale Qualitative and Quantitative Top-Down Proteomics Using Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry with Nanograms of Proteome Samples.J Am Soc Mass Spectrom2019
30787393Top-down Mass Spectrometry Analysis of Human Serum Autoantibody Antigen-Binding Fragments.Sci Rep2019
31050378Identification and Quantification of Proteoforms by Mass Spectrometry.Proteomics2019
29327814Systematic Evaluation of Protein Sequence Filtering Algorithms for Proteoform Identification Using Top-Down Mass Spectrometry.Proteomics2018
30085653Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography-Capillary Zone Electrophoresis-Tandem Mass Spectrometry.Anal Chem2018
30367573A graph-based approach for proteoform identification and quantification using top-down homogeneous multiplexed tandem mass spectra.BMC Bioinformatics2018
30417888Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry.J Vis Exp2018
30591035Evaluation of top-down mass spectral identification with homologous protein sequences.BMC Bioinformatics2018
29620868Deep Top-Down Proteomics Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry: Identification of 5700 Proteoforms from the Escherichia coli Proteome.Anal Chem2018
29064224Single-Shot Top-Down Proteomics with Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry for Identification of Nearly 600 Escherichia coli Proteoforms.Anal Chem2017
28453668A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.Bioinformatics2017
28242452Top-down analysis of immunoglobulin G isotypes 1 and 2 with electron transfer dissociation on a high-field Orbitrap mass spectrometer.J Proteomics2017
28207401Filling a Protein Scaffold With a Reference.IEEE Trans Nanobioscience2017
29503761A Spectrum Graph-Based Protein Sequence Filtering Algorithm for Proteoform Identification by Top-Down Mass Spectrometry.Proceedings (IEEE Int Conf Bioinformatics Biomed)2017
29110399De Novo Sequencing of Peptides from High-Resolution Bottom-Up Tandem Mass Spectra using Top-Down Intended Methods.Proteomics2017
26887344Proteomic Characterization Reveals That MMP-3 Correlates With Bronchiolitis Obliterans Syndrome Following Allogeneic Hematopoietic Cell and Lung Transplantation.Am J Transplant2016
26629978SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra.J Proteome Res2016
26598644MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics.Mol Cell Proteomics2016
27423895TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization.Bioinformatics2016
27291504Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore.J Proteome Res2016
27187201Top-down analysis of protein samples by de novo sequencing techniques.Bioinformatics2016
26227315Erratum to: Improving protein order-disorder classification using charge-hydropathy plots.BMC Bioinformatics2015
26412692De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra.J Proteome Res2015
26565680Identification of Glycopeptides with Multiple Hydroxylysine O-Glycosylation Sites by Tandem Mass Spectrometry.J Proteome Res2015
24564718Spectral probabilities of top-down tandem mass spectra.BMC Genomics2014
25523396A new scoring function for top-down spectral deconvolution.BMC Genomics2014
25559583Improving protein order-disorder classification using charge-hydropathy plots.BMC Bioinformatics2014
24969035Top-down proteomics reveals concerted reductions in myofilament and Z-disc protein phosphorylation after acute myocardial infarction.Mol Cell Proteomics2014
24874765De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.J Proteome Res2014
24591407Quantitative analysis of human salivary gland-derived intact proteome using top-down mass spectrometry.Proteomics2014
23720318Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions.Proc Natl Acad Sci U S A2013
24188097Identification of ultramodified proteins using top-down tandem mass spectra.J Proteome Res2013
22027200Protein identification using top-down.Mol Cell Proteomics2012
23132949Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery.Proc Natl Acad Sci U S A2012
22543365Speeding up tandem mass spectral identification using indexes.Bioinformatics2012
20122213Better score function for peptide identification with ETD MS/MS spectra.BMC Bioinformatics2010
20855543Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach.Mol Cell Proteomics2010
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Collaborators

Si Wu
The Fourth Hospital of Hebei Medical University
Co-authored papers 21
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University of California
Co-authored papers 10
Liangliang Sun
Michigan State University
Co-authored papers 9
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Co-authored papers 9
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University of Oklahoma
Co-authored papers 7
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University of Wisconsin-Madison
Co-authored papers 4
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Pacific Northwest National Laboratory
Co-authored papers 3
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University of California San Diego
Co-authored papers 3
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University of Pennsylvania
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Regeneron Pharmaceuticals, Inc.
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Gordon A Anderson
Co-authored papers 1
Neil L Kelleher
Northwestern University
Co-authored papers 1
Ronald J Moore
Co-authored papers 1
Qing Zhang
Beijing Hospital of Traditional Chinese Medicine, Capital Medical University
Co-authored papers 1
Lissa C Anderson
Florida State University
Co-authored papers 1
Yuval Inbar
Co-authored papers 1
Paul M Thomas
Northwestern University
Co-authored papers 1
Ryan T Fellers
Northwestern University
Co-authored papers 1
Lloyd M Smith
University of Wisconsin-Madison College of Letters and Sciences
Co-authored papers 1
Leah V Schaffer (CM4AI)
University of California San Diego
Co-authored papers 1
Joshua N Adkins
Co-authored papers 1
Release 1.2