Publications

III. Presentations

• S.C. Jacobson, "Fluidics at the Micro- and Nanoscale," Vanderbilt University, Nashville, Tennessee, November 2007.
• Yehia Mechref "Glycomics and Glycoproteomics in Cancer Biomarker Discovery". Presented as an invited lecture at the Heartland Mass Spectrometry Workshop on Biological Applications, Inn at Grand Glaize in Osaga Beach, MO, October 25-26, 2007.
• Yehia Mechref, Milos V. Novotny and Jason Starkey. "Glycomic Profiling through Capillary Electrophoresis as a Tool for Monitoring Cancer Progression". Presented as an invited lecture at the CE in the Biotechnology and Pharmaceutical Industries, 9th Symposium on the Practical Applications for the Analysis of Proteins, Nucleotides and Small Molecules. Hyatt Regency, Miami, October 14-18, 2007.
• Yehia Mechref "MS-Based Multimethodological Approaches in Biomarker Discovery: Glycomics, Glycoproteomics and Lipidomics". Presented as a Keynote lecture at the Fourth Symposium on the Practical Applications of Mass Spectrometry in the Biotechnology and Pharmaceutical Industries, Montreal, Canada, 5-7 September, 2007.
• Milos V. Novotny. "Capillary Separations in the Omics Era". 234th ACS 2007 Symposium, Boston, MA, August 19-23, 2007.
• S.C. Jacobson, M.L. Kovarik, and K. Zhou, "Separations at the Micro- and Nanoscale," 234th ACS 2007 Symposium, Boston, MA, August 19-23, 2007.
• M.V. Novotny, Y. Mechref, S.C. Jacobson, H. Tang, C. Sweeney, M. Zhang. "Early Cancer Detection and Prognosis Through Glycomics." Presented as an invited lecture at the National Cancer Institute (NCI) meeting, Rockville, MD, August 13-15, 2007.
• M.V. Novotny, Y. Mechref, Z. Kyselova, P. Kang, M. Madera, I. Klouckova. "Glycomic and Glycoproteomic Measurements in Biomedical Research: The Roles of Separation Science and Mass Spectrometry." Presented as an invited lecture at the 13th International Symposium on Separation Sciences (ISSS), High Tatras, Strbske Pleso, Slovakia, June 27-29, 2007.
• M.V. Novotny, Y. Mechref, Z. Kyselova, M. Al Bataineh, P. Kang, J. Goetz, V. Stanek, and J.A. Starkey. "Glycomic Profiling in Biomedical Research and Clinical Analysis" Presented as an invited lecture at HPLC 2007, Ghent, Belgium June 17-21, 2007.
• Milos V. Novotny, Yehia Mechref, Pilsoo Kang, Iveta Klouckova, Zuzana Kyselova, Milan Madera, Ben Mann. "Glycomic and Glycoproteomic Measurements in Health and Disease" Presented as an invited lecture at the 2nd Annual Human Proteomics Symposium, Madison, WI, June 10-11, 2007.
• Milos V. Novotny, Helena A. Soini and Yehia Mechref. "Biochemical Individuality Reflected in Chromatographic Profiles". Presented as an invited lecture at The Dalian International Symposium and Exhibition on Chromatography (DISEC) 2007, Dalian, China June 4-7, 2007.
• Milos V. Novotny. "Glycomic and Glycoproteomic Measurements in Health and Disease". University of Defense, Hradec Kralove, Czech Republic, March 13, 2007.
• Manolo D. Plasencia; Samuel I. Merenbloom; Stormy L. Koeniger; Dragan Isailovic; Yehia Mechref; David E. Clemmer "Resolution Of N-Linked Glycans From Ovalbumin Using Ion Mobility - Mass Spectrometry (IMS-MS)" presented as a poster at the 55th ASMS conference on Mass spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• Sarah Trimpin; Manolo Plasencia; Dragan Isailovic; Samuel Merenbloom; Yehia Mechref; Milos Novotny; David Clemmer "Analysis of N-linked Glycans from Human Plasma by IMS-MS" presented as a poster at the 55th ASMS conference on Mass spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• William R. Alley, Jr; Yehia Mechref; Milos V. Novotny "Comparing Collision-induced Dissociation and Electron-transfer Dissociation for Determining Site of Glycosylation in Glycopeptides Separated by Chip-based Liquid Chromatography" presented as a poster at the 55th ASMS conference on Mass spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• William R. Alley, Yehia Mechref; Milos V. Novotny "Using Graphitized Carbon for Glycopeptide Separations Prior to Mass Spectral Detection" presented as a poster at the 55th ASMS conference on Mass spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• Yuening Zhang; Iveta Klouckova; Yehia Mechref; Milan Madera, Milos V. Novotny "Comparative Proteomic Analysis of Healthy Individuals and Breast Cancer Patient Sera by Two-dimensional Liquid Chromatography-Tandem Mass Spectrometry" presented as a poster at the 55th ASMS conference on Mass spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• Arugadoss Devakumar; Yahia Mechref; Pilsoo kang; Milos V Novotny; James P Reilly "Isomeric Differentiation of N-Glycan Structures by Laser-Induced Photofragmentation inside an Ion-Trap Mass Spectrometer" presented as a poster at the 55th ASMS conference on Mass spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• Lenka Hernychova; Lucie Balonova; Zuzana Bilkova; Iveta Klouckova; Lucie Markova; Ivona Pavkova; Yehia Mechref; Milos V. Novotny; Jiri Stulik "Different proteomic approaches to analysis of Francisella tularensis bacterial glycoproteins" presented as a poster at the 55th ASMS conference on Mass spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• John A. Goetz; Yehia Mechref; Milos V. Novotny "Glycomic Profiling of the NCI-60 Cancer Cell Panel" presented as a poster at the 55th ASMS conference on Mass spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• Pilsoo Kang; Yehia Mechref; Milos V. Novotny "High-throughput Glycan Analysis using Solid-phase Permethylation and MALDI/TOF-MS" presented as a poster at the 55th ASMS conference on Mass spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• Iveta Klouckova; Milan Madera; Benjamin Mann; Yehia Mechref; Milos V. Novotny "Profiling of Lectin-enriched Glycoproteins from Healthy Individuals and Stage III Breast Cancer Patients" presented as a poster at the 55th ASMS conference on Mass Spectrometry and Allied Topics, Indianapolis, IN, June 3 - Jun 7, 2007.
• Zuzana Kyselova; Yehia Mechref; Pilsoo Kang; John A. Goetz; Lacey E. Dobrolecki; George Sledge; Lauren Schnaper; Robert J. Hickey; Linda H. Malkas; Milos V. Novotny "Blood Serum Profiling of Complex Glycans; a Potential Diagnostic/Prognostic Tool for Breast Cancer" presented as a poster at the 55th ASMS conference on Mass Spectrometry and Allied Topics, Indianapolis, IN, June 3 - Jun 7, 2007.
• Mohammad M. Al Bataineh; Zuzana Kyselova; Yehia Mechref; Lacey E. Dobrolecki; Robert J. Hickey; Christopher J. Sweeney; Milos V. Novotny "Prostate Cancer Detection Achieved by Profiling Human Blood Serum Glycome" presented as a poster at the 55th ASMS conference on Mass Spectrometry and Allied Topics, Indianapolis, IN, June 3 - Jun 7, 2007.
• Milan Madera; Yehia Mechref; Benjamin Mann; Quanhu Sheng; Haixu Tang; Milos V. Novotny "ProtQuant Suite: A Software Tool for Protein Quantification in High-Throughput Proteomics", presented as a poster at the 55th ASMS conference on Mass Spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• Randy J. Arnold, Pedro Alves, Haixu Tang, Predrag Radivojac "Extracting more information from shotgun proteomics data sets by learning peptide detectability", to be presented as a poster at the 55th ASMS conference on Mass Spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• Predrag Radivojac, Pedro Alves, Randy Arnold, Kang Peng, Haixu Tang "Improving proteomics by increasing the accuracy of peptide fragmentation spectrum prediction", to be presented as a poster at the 55th ASMS conference on Mass Spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• Haixu Tang, Pedro Alves, Predrag Radivojac, Randy Arnold, "Capturing more information from every shotgun proteomics experiment by carefully considering non-tryptic peptides", to be presented as a poster at the 55th ASMS conference on Mass Spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• Pedro Alves, Haixu Tang, Predrag Radivojac, Randy J. Arnold "Assigning proteins with confidence – applying peptide detectability to the protein inference problem" to be presented as a poster at the 55th ASMS conference on Mass Spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• C. Yuan, Q. Sheng, H. Tang, R. Zeng, Y. Li, R. J. Solaro, "Quantitative Comparison of Myofilament Phospho-Proteomes of Neonatal and Adult Rat Hearts" to be presented as a poster at the 55th ASMS conference on Mass Spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• Y. Wu, Y. Mechref, I. Klouckova, M. V. Novotny and H. Tang, "A computational approach for the identification of site-specific protein glycosylations through ion-trap mass spectrometry" to be presented as a poster at the 55th ASMS conference on Mass Spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• Q. Sheng, Y. Mechref, M. V. Novotny, Y. Li, R. Zeng and H. Tang, "A Computational Approach to Glycan Isoform Characterization Using MALDI-TOF-TOF Mass Spectrometry" to be presented as a poster at the 55th ASMS conference on Mass Spectrometry and Allied Topics, Indianapolis, IN, June 3 – Jun 7, 2007.
• D.E. Clemmer,"Pulling Apart Complex Protein Mixtures in the Gas Phase" US HUPO Third Annual Conference, Seattle, Washington (March 6, 2007)
• Y. Mechref, Z. Kyselova, P. Kang, M. Madera, I. Klouckova, Milos V. Novotny. "MS-Based Multimethodological Approaches in Functional Glycomics". Presented as an invited lecture at Pittcon'07, McCormick Place, Chicago, IL, Feb 25, March 2, 2007.
• S.C. Jacobson, Z. Zhuang, and M.A. Lerch, "High Performance Microfluidic Separations," presented as an invited talk at the PittCon Conference and Expo 2007, Chicago, Illinois, February 2007.
• Z. Zhuang and S.C. Jacobson, "High Performance Microfluidic Separations," presented as a talk at the PittCon Conference and Expo 2007, Chicago, Illinois, February 2007.
• Y. Liu and S.C. Jacobson, "Monolith-based Capillary Electrochromatography on a Microfluidic Device," presented as a talk at the PittCon Conference and Expo 2007, Chicago, Illinois, February 2007.
• D.E. Clemmer "On the structures of large ions and clusters in the gas phase, and the use of this information for high-throughput proteome analysis" 7th Igler Symposium on Mass Spectrometry, Obergurgl, Austria; plenary lecture (February 26, 2007)
• S.C. Jacobson, Z. Zhuang, and M.A. Lerch, "Two-Dimensional Separations on Microfluidic Devices," presented as an invited talk at the 21st International Symposium on Microscale Bioseparations, MSB 2007, Vancouver, British Columbia, January 2007.
• M.A. Lerch and S.C. Jacobson, "Sample Handling Strategies in Planar Microfluidic Devices," presented as a poster at the 21st International Symposium on Microscale Bioseparations, MSB 2007, Vancouver, British Columbia, January 2007.
• Pedro Alves, Advancement in Protein Inference from Shotgun Proteomics Using Peptide Detectability, Pacific Symposium of Biocomputing, Hawaii, Jan, 2007.
• Milos V. Novotny, Yehia Mechref, Pilsoo Kang, Iveta Klouckova, Zuzana Kyselova, Milan Madera, , Jason A. Starkey "Conquering Disease Biomarkers: Glycomics or Glycoproteomics?" presented as an invited lecture at the 12th Latin-American Symposium (LACE’06), Guaruja, Brazil, 4-8 December 2006.
• S.C. Jacobson, "Micro-and Nanofluidic Devices for Chemical Analysis," presented as an invited seminar at Purdue University, West Lafayette, Indiana, November 2006.
• S.C. Jacobson, "Micro-and Nanofabricated Devices for Chemical Analysis," presented as an invited seminar at SUNY Stony Brook, Stony Brook, New York, September 2006.
• D.E. Clemmer, "IMS-MS Analysis of complex mixtures" Wyeth Mass Spectrometry forum, Pearl River, New York, keynote lecture (October 18, 2006)
• D.E. Clemmer,"The Structures and Dynamics of Gas-Phase Protein Ions: Applications for Whole Proteome Analysis" University of Colorado and JILA, Boulder, CO (October 13 2006)
• D.E. Clemmer,"Developing IMS-IMS-IMS-MS" Colorado State University, Ft. Collins, CO (October 11, 2006)
• D.E. Clemmer,"IMS-IMS-MS and IMS-IMS-IMS-MS" opening lecture Waters Corp. Users meeting Philadelphia PA (October 10, 2006)
• D.E. Clemmer,"Edison Lectures (2)" –lecture 1, Inventing new technologies based on the physics and chemistry at the interfaces of droplets; and, lecture 2, -high-throughput ion mobility spectrometry for proteomics Notre Dame, Notre Dame, IN (September 26-28, 2006)
• Yehia Mechref, Pilsoo Kang, Zuzana Kyselova, John A. Goetz, Milos V. Novotny "Solid-phase Permethylation and Isotope labeling of Glycans for Comparative Glycomic Profiling" presented as a poster at the 17th International Mass Spectrometry Conference (IMSC), Prague, Czech Republic, August 27-Sept 1 2006.
• Milan Madera, Yehia Mechref, Iveta Klouckova, Milos V. Novotny "Comprehensive Profiling of Human Serum Glycoproteins Employing Immunoaffinity Depletion, Lectin Affinity Chromatography, High-temperature RP-HPLC, and LC-MS/MS" presented as a poster at the 17th International Mass Spectrometry Conference (IMSC), Prague, Czech Republic, August 27-Sept 1 2006.
• Iveta Klouckova, Yehia Mechref, Milan Madera, Milos V. Novotny "Multidimensional Separations of Immunodepleted Human Serum Proteins to Enhance Mass-Spectrometric Identification of Proteins at Trace Levels" presented as a poster at the 17th International Mass Spectrometry Conference (IMSC), Prague, Czech Republic, August 27-Sept 1 2006.
• S.C. Jacobson, M.A. Lerch, and Z. Zhuang, "High Speed Microfluidic Separations," presented as an invited talk at the 30th International Symposium & Exhibit on High Performance Liquid Phase Separations and Related Techniques, San Francisco, California, June 2006.
• Haixu Tang, Computational Proteomics, Institute for Mathematical Science, National University of Singapore, Singapore, Augest, 2006.
• S.C. Jacobson, "Micro-and Nanofluidic Devices for Chemical Analysis," presented as an invited seminar at Purdue University, West Lafayette, Indiana, November 2006.
• S.C. Jacobson, "Micro-and Nanofabricated Devices for Chemical Analysis," presented as an invited seminar at SUNY Stony Brook, Stony Brook, New York, September 2006.
• Yin Wu, A computational approach for the identi cation of site-speci c protein glycosylations through ion-trap mass spectrometry, RECOMB Satellite meeting on Proteomics, San Diego, CA, Sept, 2006.
• Haixu Tang, Computational methods for the identi cation of glycans and glycoproteins. The workshop of Frontier in glycomics: bioinformatics and biomarker discovery, National Institutes of Health, Bethesda, Maryland, 2006.