Shiaw-Lin (Billy) Wu
Phone: (617) 373-2857
Research Associate Professor
Over 14 years in drug industry, 3 years in mass spectrometry company, and 7 years in research institute to developing various analytical approaches for protein characterization, proteomic analysis, and biomarker discovery. Extensive experiences with therapeutic protein drugs from research, IND, NDA, to final commercial stages. Hands on experiences in various analytical instruments, including the use of narrow-bore LC with FTMS mass spectrometers for protein analysis at trace level, and the miniaturization of sample preparation methodologies such as immunoprecipitation and protein PTM characterization from minute amounts of tissues.
Thesis: "Conformational Behavior and Retention Theory of Proteins in High Performance Hydrophobic Interaction and Electrostatic Interaction Chromatography: On-line Spectroscopic and Chromatographic Characterization".
M.S. in Biochemistry (1978 - 1980)
National Taiwan University, Taipei, Taiwan (Advisor: K.T. Wang)
Thesis: "Oligopeptide Synthesis and Amino Acids Analysis from Taiwan Cobra Snake Venom".
B.S. in Chemistry (1974 - 1978)
Soochow University, Taipei, Taiwan. Thesis: "Hemocyanin Purification from Snare".
- Development of new LC-MS approaches (including ETD), Extended Range Proteomic Analysis, for characterizing and quantitating protein biomarkers in cancer cells or plasma, specifically for structure analysis of post-translational modification such as phosphorylation, glycostructures, and disulfide linkages in EGFR and Her2 from different cell lines and disease stages.
- Auto-antibody characterization from autoimmune diseases and IgG Fc glycosylation and Fab variable sequencing from HIV patients.
- Biomarker discovery in cervical cancer (in pre-cancer stage such as in high-grade lesions) using laser capture microdissection for cell capture (~10,000 cells), and using LC-MS with label-free quantitation strategy for proteomic analysis.
- Development of LC-MS platform for the detailed characterization and comparison of biosimilar and innovator drugs, and development of LC-MS approach for the study of pharmacokinetics and metabolism of protein (antibody) drugs.
- Integration of various analytical tools (efficient sample preparation of IP pull down and enzyme digestion with ultra-narrow LC separation and various mass spectrometric analysis) to the lowest detection level as possible.
ThermoFISHER, San Jose, CA, 2001 - p2003, Senior Scientist
- Developed Ion-Trap with FTMS Mass Spectrometry technology in proteomics related applications.
- Designed sample handling strategies and experiments to study the proteomics of cellular and tissue samples from laser capture microdissection to mass spectrometry.
- Analysis of protein's structures, phosphorylation modifications, and glycosylation from solution and gel spots by multi-dimensional LC with MS/MS. Designed and performed representative experiments for various customer samples.
ALZA, INC., mountain View, CA, 1999 - 2000, Senior Scientist and Consultant
- Designed strategies and experiments to comply with FDA question regarding a drug delivery formulation and its stability indication method; method development and validation under cGMP; characterization of a small molecule and related substances encapsulated in a liposome formulation by LC-MS.
Scios, Inc., Mountain View, CA, 1996 - 1999, Group Leader and Staff Scientist in Recovery Science / Protein Chemistry (1999)
- Designed a purification scheme to screen yeast and bacterial expression systems, and supported functional genomics group. Techniques used included Gaulin homogenizer, Amersham Akta HPLC, Bioprocess Skid, and Biocad systems with expanded-bed SP resin, HIC, Con-A, metal chelating, and reversed-phase HPLC chromatography. Recovered and refolded the desired protein (VEGF121) from E.coli inclusion bodies using factorial design approach.
Staff Scientist in Formulation and Pharmaceutical Manufacture Development (1997-1999)
- Developed a stable freeze-dried protein product in sucrose formulation.
- Developed a unique antibody-based assay (using BIAcore biosensor instrument) to on-line measure the slow release of FGF (in nano-gram level) from different gel-based (control-released) formulations.
- Deduced the relation between the meltback phenomenon of FGF and the glass transition temperature of sucrose formulation. Delineated a degradation pathway of meltback and crystalline sucrose in FGF formulation by DSC, X-ray diffraction, and LC-MS.
- Performed the final finished product and packaging compatibility. Defined the manufacturing process parameters. Responsible for the section of NDA filing.
- Identified the critical lyophilization conditions for mannitol formulation. Identified the cause of disulfide and non-disulfide aggregates. Delineated the mechanism of aggregation from the formation of the free thiolate ion (HS-).
Genentech, Inc., South San Francisco, CA, 1987 - 1996, Staff Scientist in Analytical Chemistry
- Characterization and trouble shooting of commercial and pipeline's products
- hGH and rt-PA protein-Identified the cause (oxidation) of low clot lysis activity problem in CHO cell expressed system. Prepared the protein chemistry and analytical assay data for FDA submission (NDA amendment for process yield improvement). Verified the pharmacokintic difference related to the modification of carbohydrate structure (using CE, CE-MS, Ion Chromatography, and LC with triple quadrupole and MALDI MS). Separation of structure variants by a new analytical HIC method.
- Anticoagulant drugs (small peptide molecules)-Confirmed the formation of cis-trans variants by N.M.R., the D.-L amino acid variants by chiral additives reversed-phase HPLC, and cysteine related sulfur variants (e.g., lanthionine) by various enzymatic mappings with LC-MS, MS/MS, and amino acid analysis.
- Lung surfactant protein-Developed a sample handling technique to analyze the strong hydrophobic protein in a complicated lipid matrix. Determined the size of non-covalent aggregation by SEC coupled on-line with Low Angle Laser Light Scattering detector. Analyzed the protein-related variants using LC-MS and Edman sequencing.
- Development of new analytical methods (1987-1991)
- Discovered detergent-based hydrophobic interaction chromatography (HIC) as a new general method for membrane protein analysis and purification.
- Studied protein aggregation, protein-receptor, and protein-antibody (IgE and anti-IgE) binding phenomenon in solution using Low Angle Laser Light Scattering on-line coupling with HPLC.
- Developed CE-MS approach to separate charge heterogeneity (e.g. carbohydrate, deamidation, and cleavage) and enzymatic digestion mixtures.
- Investigated unpaired cysteine in proteins through the study of oxidation, reduction, alkylation, and enzymatic digestion conditions.
Wu, Shiaw-Lin., Hancock, William S., Karger, Barry L. "Comprehensive Characterization of Complex Proteins at Trace Level". U.S. Patent No. 2008/0280317 A1, -Nov. 13, 2008.
1. S.-L. Wu*, K.H. Park, H. Jiang, K.J. Lee, H.S. Kim, W. S. Hancock, and J.S. Yoo*." Detection of Common Motif for Glycosylation and Deamidation by Ultra High Resolution Mass Spectrometry: from Biotech and Biosimilar Drugs to General Stability Issue". 2010, submission.
2. S.-L. Wu*, H. Jiang, W. S. Hancock, and B. L. Karger*. "Identification of the Unpaired Cysteine Status and Complete Mapping the 17 Disulfides of Recombinant Tissue Plasminogen Activator Using LC-MS with ETD/CID". Anal. Chem. 2010, 82, 5296-5303.
3. H. Jiang, S.-L. Wu*, B. L. Karger, and W. S. Hancock*. "Characterization of the Glycosylation Occupancy and the Active Site in the Follow-on Protein Therapeutic: TNK-Tissue Plasminogen Activator". Anal. Chem. 2010, 82, 6154-6162.
4. Lu, X. Zheng, T. McIntosh, H. Davis, J. F. Nemeth, C. Pendley, Murugesan, S. -L. Wu*, and W. S. Hancock. "The development of different analysis platforms with LC-MS for pharmacokinetic studies of protein drugs". Anal. Chem. 2009, 81, 8715-23.
5. X. Zheng, S.-L.Wu, M. Hincapie, and W.S. Hancock. "Study of the human plasma proteome of rheumatoid arthritis". J Chromatogr A. 2009, 1216, 3538-45.
6. S.-L. Wu, H. Jiang, Q. Lu, S. Dai, W. S. Hancock, and B. L. Karger. "Mass Spectrometric Determination of Disulfide Linkages in Recombinant Therapeutic Proteins Using On-line LC-MS with Electron Transfer Dissociation (ETD)". Anal. Chem. 2009, 81, 112-122.
7. H. Jiang, S.-L. Wu*, B.L. Karger, and W.S. Hancock. "Mass Spectrometric Analysis of Innovator, Counterfeit, and Follow-On Recombinant Human Growth Hormone". Biotechnology Progress. 2009, 25, 207-218.
8. Y. Jia, S.-L. Wu, J.S. Isenberg, S. Dai, J.M. Sipes, L. Field, B. Zeng, R. W. Bandle, L.A. Ridnour, D. A. Wink, R. Ramchandran, B. L. Karger, and D. D. Roberts, "Thiolutin inhibits endothelial cell adhesion by perturbing Hsp27 interactions with components of the actin and intermediate filament cytoskeleton". Cell Stress Chaperones. 2009 Jul 5 [Epub ahead of print].
9. S. Dai+, Y. Jia+, S.-L. Wu+, J.S. Isenberg, L. A. Ridnour, R. W. Bandle, D. A. Wink, D. D. Roberts, and B. L. Karger. "Comprehensive Characterization of Heat Shock Protein 27 Phosphorylation in Human Endothelial Cells Stimulated by the Microbial Dithiole Thiolutin". J Proteome Res. 2008, 7, 4384-4395.
10. C. Lu, N. Murugesan, J. A. Macdonald, S. -L. Wu*, J. Pachter, and W. S. Hancock. "Analysis of Mouse Brain Microvascular Endothelium Using Immuno-Laser Capture Microdissection coupled to a hybrid LTQ-FT MS proteomics platform". Electrophoresis. 2008, 29(12):2689-95.
11. Q. Luo, T. Rejtar, S.-L. Wu , B.L. Karger. "Hydrophilic interaction 10mum I.D. porous layer open tubular columns for ultratrace glycan analysis by liquid chromatography-mass spectrometry". J Chromatogr. 2009, 216, 1223-31.
12. Q. Luo , Y. Gu, S.-L. Wu, T. Rejtar, B.L. Karger. "Two Dimensional SCX/PLOT/MS for Ultratrace Proteomic Analysis Using a 10 _m i.d. Poly(styrene-divinylbenzene) Porous Layer Open Tubular Column with an On-Line Triphasic Trapping Columna)". Electrophoresis. 2008, 29(8):1604-11.
13. S. -L. Wu, A. Huhmer, Z.-Q. Hao, and B.L. Karger. "On-Line LC-MS Approach Combining Collision-Induced Dissociation (CID), Electron-Transfer Dissociation (ETD), and CID of an Isolated Charge-Reduced Species for the Trace-Level Characterization of Proteins with Post-Translational Modifications", J Proteome Res. 2007 Nov;6(11):4230-44.
14. Y. Gu+, S.-L. Wu+, D. Hanlon, J. Meyer, J. Linder, W.S. Hancock, B.L. Karger. "Proteomic Analysis of High-Grade Dysplastic Cervical Cells Obtained From ThinPrep® Slides Using Laser Capture Microdissection and Mass Spectrometry", J Proteome Res. 2007, 6(11):4256-68.
15. Q. Luo , Y. Yue, G.A,Valaskovic, Y. Gu, S.-L. Wu, B.L. Karger. "On-line 1D and 2D porous layer open tubular/LC-ESI-MS using 10-microm-i.d. poly(styrene-divinylbenzene) columns for ultrasensitive proteomic analysis". Anal Chem. 2007, 79, 6174-81.
16. G. Yue, Q. Luo, J. Zhang , S.-L. Wu, and B. L. Karger. "Ultratrace LC/MS Proteomic Analysis Using 10 μm i.d. Porous Layer Open Tubular (PLOT) Polystyrene-Divinylbenzene Capillary Columns". Anal. Chem. 2007, 79, 938-46.
17. J. Zhang+, S.-L.Wu+, JK. Kim, B.L. Karger. "Ultratrace liquid chromatography/mass spectrometry analysis of large peptides with post-translational modifications using narrow-bore poly(styrene-divinylbenzene) monolithic columns and extended range proteomic analysis". J Chromatogr A. 2007, 1154, 295-307.
18. V.P. Andreev, L. Li, L. Cao, Y. Gu, T. Rejtar, S.-L. Wu, B.L. Karger. "A New Algorithm Using Cross-Assignment for Label-Free Quantitation with LC-LTQ-FT MS". J Proteome Res. 2007, 6, 2186-94.
19. S. -L. Wu, JK. Kim, R.W. Bandle, L. Liotta, E. Petricoin, and B.L. Karger "Dynamic profiling of the post-translational modifications and interaction partners of epidermal growth factor receptor signaling after stimulation by EGF using extended range proteomic analysis (ERPA)". Mol. Cell Proteomics, 2006, 5, 1610-1627.
20. X.Y. Zheng, S.-L. Wu and W.S. Hancock "Glycation of Interferon-beta-1b and Human Serum Albumin in a Lyophilized Glucose Formulation - Part III: Application of Proteomic Analysis to Manufacturing of Biological Drugs". Int. J. of Pharmaceutics 2006, 322, 136-145.
21. Y.H. Wang, S.-L. Wu, and W.S. Hancock "Monitoring of glycoprotein products in cell culture lysates using lectin affinity chromatography and capillary HPLC coupled to electrospray linear ion trap-Fourier transform mass spectrometry (LTQ/FTMS)". Biotechnol Prog. 2006 May-Jun;22(3):873-80.
22. Y.H. Wang, S.-L. Wu, and W.S. Hancock "Approaches to the Study of N-linked Glycoproteins in Human Plasma Using Lectin Affinity Chromatography and Nano-HPLC Coupled to Electrospray Linear Ion Trap - Fourier Transform Sepctrometry (LTQ-FTMS)", Glycobiology 2006 Jun;16(6):514-23.
23. S. -L. Wu, J.K. Kim, W.S. Hancock, and B.L. Karger "Extended Range Proteomic Analysis (ERPA): A New and Sensitive LC-MS Platform for High Sequence Coverage of Complex Proteins with Extensive Posttranslational Modifications - Comprehensive Analysis of Beta-Casein and Epidermal Growth Factor Receptor (EGFR)", J. of Proteome Research 2005, 4, 1155-1170.
24. Y.H. Wang, S.-L. Wu, W. S. Hancock, R. Trala, M. Kessler, A.H. Taylor, and J. C. Aon "Proteomic Profiling of Escherichia coli Proteins under High Cell Density Fed-batch Cultivation with Overexpression of Phosphogluconolactonase" Biotechnol Prog. 2005 Sep-Oct;21(5):1401-11.
25. C.-C. Chao, S.-L. Wu and W. -M. Ching "Using LC-MS with De novo Software to Fully Characterize the Multiple Methylations of Lysine Residues in a Recombinant Fragment of Outer Membrane Protein from a virulent Rickettsia prowazekii" Biochimica et Biophysica Acta. 2004, 1702, 145-152.
26. S.-L. Wu, I. Jardine, W.S. Hancock, and B.L. Karger "A new and sensitive on-line liquid chromatography / mass spectrometric approach for top-down protein analysis: the comprehensive analysis of human growth hormone in an E. coli lysate using a hybrid linear ion trap Fourier transform ion cyclotron resonance mass spectrometer", Rapid Commun. Mass Spectrom. 2004; 18: 2201-2207.
27. S.-L Wu, W.S. Hancock, G. G. Goodrich, S. T. Kunitake: "A Proteomic Approach to the Detection of Tumor Marker Proteins in a Breast Cancer Cell line (SKBR-3)", Proteomics 2003, (3) 374, issue 6 (June).
28. S.-L Wu, G. Choudhary, M.Ramstrom, J. Bergquist, and W. S. Hancock: "Evaluation of Shotgun Sequencing for Proteomic Analysis of Human Plasma Using HPLC Coupled with Either Ion Trap or Fourier Transform Mass Spectrometry", .J. of Proteome Research 2003; 2(4); 383-393.
29. G. Choudhary, S.-L. Wu, P. Shieh, W. S. Hancock: "Multiple Enzymatic Digestion for Enhanced Sequence Coverage of Proteins in Complex Proteomic Mixtures using Capillary LC with Ion Trap MS/MS", J. of Proteome Research 2003; 2(1); 59-67.
30. W.S. Hancock, S.-L. Wu, R. Stanley, and E. Gombocz: "Publishing large proteome datasets: scientific policy meets emerging technologies", Trends Biotechnol. 2002 Dec., 20 (12 Suppl):S39-44.
31. D. Chelius, S-L Wu, P. Bondarenko: "Identification of N-linked oligosaccharides of rat insulin-like growth factor binding protein-4" Growth Hormone & IGF Research 2002, 12.
32. S.-L. Wu, P. Bondarenko, T. Shaler, P. Shieh, and W.S. Hancock: "Structure Analysis of Glycosylated Peptides in Complex Mixtures with Ion Trap MSn", Application Report, #300, Thermo Electron, 2002.
33. S.-L Wu, H. Amato, R. Biringer, G. Choudhary, P. Shieh, and W. S. Hancock: "Targeted Proteomics of Low Level Proteins in Human Plasma by LC/MSn: Using Human Growth Hormone as a Model System", J. of Proteome Research. 2002, 1, 459-465.
34. W.S. Hancock, S.-L. Wu, and P. Shieh: "The challenges of developing a sound proteomics strategy", Proteomics 2002, 2, 352-359.
35. W.S. Hancock, G. Choudhary, S.-L. Wu, and P. Shieh: "A high-throughput solution for proteomics", American Laboratory 2002, 34, 13-15.
36. S.-L. Wu, D.-M. Leung, L. Tretyakov, J. Hu, A. Guzzetta, and Y. J. Wang : "The formation and mechanism of multimerization in a freeze-dried peptide" Int. J. of Pharmaceutics, 2000, 200, 1-16.
37. A. Apffel, H. Ying, W. S. Hancock, D. McManigill, J. Frenz, S.-L. Wu: "Effect of electric field on liquid chromatographic separation of peptide digests. Combining capillary separation techniques", J Chromatogr A. 1999 Feb 5;832(1-2):149-63.
38. S.-L. Wu: ‘The Use of Sequential HPLC and CZE to Separate the Glycosylated Peptides from Recombinant Tissue Plasminogen Activator to a Detailed Level of Microheterogeneity", Anal. Biochem. 1997, 253, 85-97.
39. S.-L. Wu, Y.J. Wang, J. Hu, and D.-M. Leung : "The Detection of the Organic Extractables in a Biotech Product by Liquid Chromatography on-line with Electrospray Mass Spectrometry", J. of Pharmaceutical Science and Technology, 1997, 51, 229-237.
40. G. Teshima and S.-L. Wu: "Capillary Electrophoresis Analysis of Recombinant Proteins", Methods Enzymol. 1996, 271, 264.
41. S.-L. Wu and Barry Karger: "Hydrophobic Interaction Chromatography of Proteins", Methods Enzymol., 1996, 270, 27.
42. M.S. Malony, S.-L. Wu, L. K. Keyt, and R. J. Harris: "The unexpected presence of hydroxylysine in non-collagen protein", Techniques in Protein Chemistry VI, J.W. Crabb, Ed., Academic Press, Inc., San Diego, pp.91-98, 1995.
43. M. Herold and S.-L. Wu: "Automated Peptide Fraction Collection in CE", LC-GC. 1994, 12, 531.
44. I.S. Krull, M.E. Szulc, and S.-L. Wu : "Principles of biopolymer detection in HPLC", LC-GC.,11 (1993) 350.
45. L. Chen, J. Mazzeo, I.S. Krull, and S.-L. Wu : "Determination of peptide 520 in human plasma using post-column photolysis with electrochemical detection in liquid chromatography", J. Pharm. & Biom. Anal. 1993, 11, 999.
46. S.-L. Wu: "Rapid HPLC and Capillary Electrophoresis: A Perspective of Protein Analysis from Analytical Biotechnology", LC-GC. 1992, 10, 430.
47. P. Oroszlan, S. Wicar, G. Teshima, S.-L. Wu, W.S. Hancock, B.L. Karger: "Conformational Effects in the Reversed-Phase Chromatographic Behavior of Recombinant Human Growth Hormone (rhGH) and N-Methionine Recombinant Human Growth Hormone (Met-hGH)", Anal. Chem. 1992, 64, 1623.
48. S.-L. Wu and B.L. Karger: "On-line Conformational Monitoring of Proteins in HPLC". CRC. HPLC of Peptides and Proteins: Separation, Analysis, and Conformation, R.S. Hodges, Eds. CRC Press, pp. 613-620, 1991.
49. S.-L. Wu, G. Teshima, J. Cacia, and W.S. Hancock: "The use of High Performance Capillary Electrophoresis to Monitor Charge Heterogeneity in Recombinant DNA-Derived Proteins", J. Chromatogr. 1990, 515, 115.
50. S.-L. Wu, B. Pavlu, Par Gellerfors, and W.S. Hancock: "Recombinant Human Growth Hormone in high Performance Hydrophobic Interaction Chromatography", J. Chromatogr. 1990, 500, 595.
51. H.J. Sievert, S. -L. Wu, R.C. Chloupek and W.S. Hancock: "Automated Evaluation of Tryptic Digest from Recombinant Human Growth Hormone using UV Spectra and Numeric peak Information", J. Chromatogr. 1990, 499, 221.
52. R. Shansky, S. -L. Wu, A. Figueroa, and B.L. Karger: "Hydrophobic Interaction Chromatography of Biopolymers" in HPLC-Biological Macromolecules: Methods and Applications, K.M. Gooding, F.E. Regnier, Eds., Marcel Dekker, Inc. New York, vol. 51,chap. 5, 1990.
53. J. Frenz, S. -L. Wu, and W.S. Hancock: "Characterization of Human Growth Hormone by Capillary Electrophoresis", J. Chromatogr. 1989, 480, 379.
54. W.S. Hancock, E. Canova-Davis, R.C. Chloupek, S. -L. Wu, I.P. Baldonado, J.E. Battersby, M.W. Spellman, L.J. Basa and J.A. Chakel, Banbury Report 29: "Characterization of Degradation Production of rhGH, Cold Spring Harbor Laboratory, 0-87969-229-4, "Therapeutic Peptides and Proteins": Assessing the New Technologies, Cold Spring Harbor, NY, 1988, p. 95.
55. S.-L. Wu, A. Figueroa, and B.L. Karger: "Studies on Protein Conformational Effects in Hydrophobic Interaction Chromatography: Retention Characterization and the Role of Mobile Phase Additives and Stationary Phase Hydrophobicity". J. Chromatogr. 1986, 371, 3.
56. S.-L. Wu, K. Benedeck, and B.L. Karger: "Thermal Behavior of Proteins in High Performance Hydrophobic Interaction Chromatography: On-line Spectroscopic and Chromatographic Characterization" J. Chromatogr. 1986, 359, 3.