Dr. Liu Fan, Ph.D
Research areas: Biomolecular Mass Spectrometry and Proteomics Group.
Mar. 2013-present, Post-doctoral Fellow
Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands. Fellowship Advisor: Dr. Albert Heck
Aug. 2007-Jan 2013, Ph.D. Student in Biochemistry
Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
Thesis Advisor: Dr. Michael B. Goshe
Dec. 2010 - Sep. 2011, NIH Pre-doctoral Visiting Fellow
Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, Maryland, USA
Fellowship Advisor: Dr. William E. Paul
Sep. 2003 - Sep. 2007, B.S. in Biology
School of Life Sciences, Fudan University, Shanghai, China
AWARDS AND FELLOWSHIPS
May. 2013, A. R. Main - Becton Dickinson Award given in recognition of outstanding graduate achievement in research in Biochemistry at North Carolina State University.
Dec. 2010 – Sep. 2011, NIH Pre-doctoral Visiting Fellowship
- Yang Y.*, Liu F.*, Heck A.J., Combining high-resolution native mass spectrometry with middle-down proteomics for the structural analysis of complex glycoproteins and its usage in defining biosimilarity. Submitted to Nature Biotech.(*.Co-first authors)
- Liu F., Heck A.J., Interrogating the architecture of protein assemblies and protein interaction networks by cross-linking mass spectrometry. Accepted in Current Opinion in Structural Biology.
- Liu F., Rijkers D.T.S., Post H., Heck A.J., Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry. Nature Methods.2015, doi:10.1038/nmeth.3603.
- Glas M., van den Berg van Saparoea H.B., McLaughlin S.H., Roseboom W., Liu F., Koningstein G.M., Fish A., den Blaauwen T., Heck A.J., de Jong L., Bitter W., de Esch I.J., Luirink J.. The Soluble Periplasmic Domains of Escherichia coli Cell Division Proteins FtsQ/FtsB/FtsL Form a Trimeric Complex with Submicromolar Affinity. J Biol Chem. 2015, doi: 10.1074/jbc.M115.654756.
- Argo AS, Shi C, Liu F, Goshe MB. Performing Protein Crosslinking using Gas-phase Cleavable Chemical Crosslinkers and Liquid Chromatography-Tandem Mass Spectrometry. Methods. 2015, doi: 10.1016/j.ymeth.2015.06.011.
- Brunner AM, Lössl P, Liu F, Huguet R, Mullen C, Yamashita M, Zabrouskov V, Makarov A, Altelaar AF, Heck AJ. Benchmarking multiple fragmentation methods on an Orbitrap Fusion for top-down phospho-proteoform characterization. Anal Chem. 2015 Apr 8, doi: 10.1021/acs.analchem.5b00162.
- Liu F., Breukelen B., Heck A.J., Facilitating protein disulfide mapping by a combination of pepsin digestion, Electron Transfer higher energy Dissociation (EThcD) and a dedicated search algorithm SlinkS. Mol Cell Proteomics. 2014 Oct;13(10):2776-86, doi:10.1074/mcp.O114.039057.
- Olson A.L.*, Liu F.*, Tucker A.T., Goshe M.B., Cavanagh J. Chemical crosslinking and LC/MS analysis to determine protein domain orientation: Application to AbrB. Biochem Biophys Res Commun. 2013 Feb 8;431(2):253-7, doi: 10.1016/j.bbrc.2012.12.124.
- Liu F., Wu C., Sweedler J.V., Goshe M.B. An enhanced protein crosslink identification strategy using CID-cleavable chemical crosslinkers and LC/MSn analysis. Proteomics. 2012 Feb;12(3):401-5, doi: 10.1002/pmic.201100352.
- Liu F., Goshe M.B. (2010). Combinatorial electrostatic collision-induced dissociative chemical cross-linking reagents for probing protein surface topology. Anal. Chem. 2010 Jul 15;82(14):6215-23, doi: 10.1021/ac101030w.
- Liu F., 5th International Thermo Scientific Proteome Discoverer Users' Meeting and 1st Compound Discoverer Users' Meeting in Bremen, Germany, December, 2015.
- Liu F., Towards the Full Post-translational Modification Profile of Proteins: Combining Native and Bottom-up Mass Spectrometry, presented in ASMS, St. Louis, MO, May 2015.
- Liu F., The advance of disulfide-bridged and cross-linked peptide identification using EThcD, presented in Netherlands Proteome Center Progress Meeting, Utrecht, The Netherlands, Jan 2015.
- Liu F., The Development and Application of Novel Crosslinking Mass Spectrometry Approaches to Study Protein Structure and Interactions, presented at Molecular and Structural Biochemistry North Carolina State University, Raleigh, NC, Jan 2013.
- Liu F., Chemical Cross-linking and Mass Spectrometry, presented at NIH Proteomics Interest Group (ProtIG Fellows Seminar), Bethesda, MD, Sep 2011.
- Liu F., Probing the Electrostatic Surface Topology of Proteins Using Combinatorial Collision-Induced dissociative Chemical Cross-linking Reagents and Mass Spectrometry Analysis, presented at the Triangle Area Mass Spectrometry Discussion Group, Durham, NC, Jan 2010.
- Liu F., Breukelen B., Heck A.J., Combining acidic pepsin digestion, EThcD and a dedicated search engine SLinkS, presented in EMBO|FEBS Lecture Courses on Nuclear Proteomics, Kos Island, Greece, May 2014.
- Liu F., Breukelen B., Heck A.J., Combining acidic pepsin digestion, EThcD and a dedicated search engine SLinkS, presented in Netherlands Proteome Center Progress Meeting, Utrecht, The Netherlands, Jan 2014.
- Liu F., Blackburn K., Clouse S.D., Goshe M.B., “Interaction Studies of BRI1 and BAK1 using Chemical Crosslinking and Mass Spectrometry”, presented at the 2012 Arabidopsis Phosphorylation workshop, Key Stone, CO, Sep 2012.
- Liu F., Chen T., Blackburn K., Wollenzien P., Goshe M.B., “Developing a High-Throughput LC/MS/MS Platform to Comprehensively Characterize Protein-Protein Interactions and Networks”, presented at the 60th ASMS Conference on Mass Spectrometry and Allied Topics, Vancouver, BC, Canada, May 2012.
- Liu F., Blackburn K., Clouse S.D., Goshe M.B., “Using CID-Cleavable Chemical Cross-linkers and LC/MSn to Understand Plant Kinase Interactions”, presented at the 2011 Arabidopsis Phosphorylation workshop, Tahoe City, CA, Sep 2011.
- Liu F., Wu C., Sweedler J.V., Goshe M.B., “An Enhanced Protein Crosslink Identification Strategy using CID-Cleavable Chemical Crosslinkers and LC/MSn Analysis”, presented at the 59th ASMS Conference on Mass Spectrometry and Allied Topics, Denver, CO, May 2011.
- Liu F., Brown D.T., Goshe M.B., “Probing Topology Changes of Sindbis Virus Structural Proteins Using Novel CID-Cleavable Chemical Crosslinking Reagents and Mass Spectrometry Analysis”, presented at the 58th ASMS Conference on Mass Spectrometry and Allied Topics, Salt Lake City, UT, May 2010.
- Liu F., Goshe M.B., “Probing the Electrostatic Surface Topology of Proteins Using Combinatorial Collision-Induced Dissociative Chemical Crosslinking Reagents and Mass Spectrometry Analysis”, presented at the 57th ASMS Conference on Mass Spectrometry and Allied Topics, Philadelphia, PA, May 2009.
- 2007–2009, Teaching Assistant, Analytical chemistry, North Carolina State University, Raleigh, North Carolina, USA
- 2007–2009, Teaching Assistant, Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
- Sep. 2014, Biomolecular Mass Spectrometry Course, Utrecht, The Netherlands
- Extensive knowledge of the Thermo Orbitrap family (LTQ Orbitrap XL/Velos/Elite/Fusion/Fusion Lumos), and thermo EASY-nLC system including troubleshooting and maintenance
- Working knowledge of Thermo LTQ-FT, Waters Q-TOF premier, Waters nanoACQUITY UPLC and Agilent capillary HPLC
- Working knowledge of native MS on Waters LCT Premier, Waters QTof II, and Thermo Oribitrap EMR instruments
- Extensive knowledge of quantitative proteomic approaches (e.g., label free, stable isotope labeling by amino acids in cell culture (SILAC), dimethyl labeling and tandem mass tag (TMT) labeling)
- Extensive knowledge of phospho-peptide enrichment (e.g., TiO2, IMAC and Ti4+-IMAC)
- Extensive knowledge of cross-linking MS approaches, including cross-linking sample preparation, cross-link enrichment and fractionation (affinity purification using biotin tagging and online/offline SCX)
- Extensively experienced in primary CD4 T cell differentiation and culture (native, Th1, Th2, Th17 and iTreg), animal handling and dissection, molecular cloning, protein purification and characterization, shRNA lentiviral transduction and chromatin immunoprecipitation experiment
- Skilled at FACS and confocal microscopy
- Skilled at peptide synthesis
- Extensively experienced on MS data analysis software including Proteome Discover, Maxquant, Perseus, Protein Deconvolution, ProSightPC, MassLynx, Byonic
- Extensive programming skill of R
- Basic programming skill of Matlab and perl
- American Society for Mass Spectrometry
- The Netherlands Society for Biochemistry and Molecular Biology (NVBMB)
Email address: F.firstname.lastname@example.org