Publications

II. Research articles

A. In Print

• H.W. Ressom, R.S Varghese, L. Goldman, Y. An, C.A Loffredo, M. Abdel-Hamid, Z. Kyselova, Y. Mechref, M. Novotny, S.K. Drake, R. Goldman "Analysis of MALDI-TOF Mass Spectrometry Data for Discovery of Peptide and Glycan Biomarkers of Hepatocellular Carcinoma" J. Proteome Res., 7 (2008) 603-610. Abstract
• P. Kang, Y. Mechref, Z. Kyselova, J. A. Goetz, M. V. Novotny Comparative Glycomic Mapping (C-GlycoMAP) through Quantitative Permethylation and Stable-isotope Labeling" Anal. Chem., 79 (2007) 6064-6073. Abstract
• Z. Kyselova, Y. Mechref, M. M. Al Bataineh, L. E. Dobrolecki, R. J. Hickey, J. Vinson, C. J. Sweeney, M. V. Novotny "Alterations in the Serum Glycome due to Metastatic Prostate Cancer" J. Proteome Res., 6 (2007) 1822-1832. Abstract
• W. R. Alley, Jr., Y. Mechref, I. Klouckova, M. V. Novotny "Collision-induced Dissociation Analysis of Peptides by Matrix-assisted Laser Desorption/Ionization Mass Spectrometry, Following Chemical Derivatization with a Sulfonated Reagent" J. Proteome Res., 6 (2007)124-132. Abstract
• M. Madera; Y. Mechref; I. Klouckova; M. V. Novotny " High-sensitivity profiling of glycoproteins from human blood serum through multiple-lectin affinity chromatography and liquid chromatography/tandem mass spectrometry" J. Chromatogr. B, 845 (2007) 121-137. Abstract
• Lass, Agnieszka; McConnell, Elizabeth; Nowis, Dominika; Mechref, Yehia; Kang, Pilsoo; Novotny, Milos V.; Wojcik, Cezary. "A novel function of VCP (valosin-containing protein; p97) in the control of N-glycosylation of proteins in the endoplasmic reticulum," Arch. Biochem. Biophys., 462 (2007) 62-73. Abstract
• M. Madera; Y. Mechref; I. Klouckova; M. V. Novotny, "Semiautomated High-Sensitivity Profiling of Human Blood Serum Glycoproteins through Lectin Preconcentration and Multidimensional Chromatography/Tandem Mass Spectrometry" J. Proteome Res. 5 (2006) 2348-2363. Abstract
• Yehia Mechref, Pilsoo Kang and Milos V. Novotny "Differentiating Sialylated Glycan Structural Isomers through MALDI/TOF/TOF Tandem Mass Spectrometry", Rapid Commun. Mass Spectrom., 20 (2006) 1381-1389. Abstract
• Z. Zhuang, J. A. Starkey, Y. Mechref, M. V. Novotny, and S. C. Jacobson "Rapid and Efficient Electrophoretic Analysis of N-Glycans on Microfluidic Devices" Anal. Chem., 79 (2007) 7170-7175. Abstract
• M.A. Lerch and S.C. Jacobson, "Electrokinetic Fluid Control in Two-Dimensional Planar Microfluidic Devices," Anal. Chem., 79 (2007) 7485-7491. Abstract
• M.A. Lerch and S.C. Jacobson, "Flow Control in Microfluidic Devices with a Planar Separation Format" Micro Total Analysis Systems 2006, Tokyo, Japan, November 2006, pp. 933-935.
• Xun, Z.; Sowell, R. A.; Kaufman, T. C.; Clemmer, D. E. "Protein Expression in a Drosophila Model of Parkinson’s Disease" J. Proteome Res., 6 (2007) 348-357. Abstract
• Merenbloom, S. I.; Bohrer, B. C.; Koeniger, S. L.; Clemmer, D. E. "Assessing the Peak Capacity of IMS-IMS Separations of Tryptic peptide ions in 300K He", Anal. Chem., 79 (2007) 515-522. Abstract
• Koeniger, S. L.; Clemmer, D. E. "Resolution and Structural Transitions of Elongated States of Ubiquitin," J. Am. Soc. Mass Spectrom., 18 (2007) 322-331. Abstract
• Valentine, S. J.; Plasencia, M. D.; Liu, X.; Krishnan, M.; Naylor, S.; Udseth, H. R.; Smith, R. D.; Clemmer, D. E. "Toward Plasma Proteome Profiling with Ion Mobility-Mass Spectrometry," J. Proteome Res. 5 (2006) 2977-2984. Abstract
• Merenbloom, S. I.; Koeniger, S. L.; Valentine, S. J.; Plasencia, M. D.; Clemmer, D. E. "IMS-IMS and IMS-IMS-IMS/MS for Separating Peptide and Protein Fragment Ions Manuscript" Anal. Chem., 78 (2006) 2802-2809. Abstract
• Koeniger, S. L.; Merenbloom, S. I.; Clemmer, D. E. "Evidence for Many Resolvable Structures within Conformation Types of Electrosprayed Ubiquitin Ions", J. Phys. Chem B, 110 (2006) 7017-7021. Abstract
• Koeniger, S. L.; Merenbloom, S. I.; Valentine, S. J.; Jarrold, M. F.; Udseth, H.; Smith, R.; Clemmer, D. E. "An IMS-IMS Analogue of MS-MS," Anal. Chem. , 78 (2006) 4161-4174. Abstract
• Koeniger, S. L.; Merenbloom, S. I.; Sevugarajan, S.; Clemmer, D. E. "Transfer of Structural Elements from Compact to Extended States in Unsolvated Ubiquitin," J. Am. Chem. Soc. 128 (2006) 11713-11719. Abstract
• Hilderbrand, A. E.; Myung, S.; Clemmer, D. E. "Crown Ethers as Shift Reagents for Ion Mobility Spectrometry" Anal. Chem., 78 (2006) 6792-6800. Abstract
• Valentine, S. J.; Sevugarajan, S.; Kurulugama, R. T.; Koeniger, S. L.; Merenbloom, S. I.; Bohrer, B. C.; Clemmer, D. E. "Split-Field Drift Tube/Mass Spectrometry and Isotopic Labeling Techniques for Determination of Single Amino Acid Polymorphisms" J. Proteome Res., 5 (2006) 1879-1887. Abstract
• A. Devakumar, Y. Mechref, P. Kang, M. V. Novotny and J. P. Reilly "Laser-induced photofragmentation of neutral and acidic glycans inside an ion-trap mass spectrometer" Rapid Commun. Mass Spectrom, 21 (2007) 1452-1460. Abstract
• Alves, P.; Arnold, R. J.; Clemmer, D. E.; Li, Y.; Reilly, J. P.; Sheng, Q.; Tang, H.; Xun, Z.; Zeng, R.; Radivojac, P. "Fast and accurate identification of semi-tryptic peptides in shotgun proteomics" Bioinform., 24 (2008) 102-109. Abstract
• P. Alves, R. J. Arnold, M. V. Novotny, P. Radivojac, H. Tang "Advancement in protein inference from shotgun proteomics using peptide detectability", Pacific Symposium of Biocomputing, 12 (2007) 409-420. Abstract
• Y. Wu, Y. Mechref, I. Klouckova, M. V. Novotny, H. Tang "A Computational Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry" LNBI, 4532 (2007) 97-108. Abstract
• H. Tang, R. J. Arnold, P. Alves, Z. Xun, D. E. Clemmer, M. V. Novotny, J. P. Reilly and P. Radivojac A computational approach toward label-free protein quantification using predicted peptide detectability, Bioinformatics, 22 (2006) e481-e488. Abstract
• Z. Kyselova, Y. Mechref, P. Kang, J. A. Goetz, L. E. Dobrolecki, G. Sledge, L. Schnaper, R. J. Hickey, L. H. Malkas, M. V. Novotny, “Breast Cancer Diagnosis/Prognosis through Quantitative Measurements of Serum Glycan Profiles” Clin. Chem., 54 (2008) 1166-1175.
• O. Gustafsson, K.B. Mogensen, P.D. Ohlsson, Y. Liu, S.C. Jacobson, and J.P. Kutter, “Electrochromatography Chip with Integrated Waveguides for UV Absorbance Detection,” J. Micromech. Microengin., 18 (2008) 055021.
• A. Devakumar, Y. Mechref, P. Kang, M. V. Novotny and J. P. Reilly, "Identification of Isomeric N-Glycan Structures by Mass Spectrometry with Laser-Induced Photofragmentation" J. Am. Soc. Mass. Spectrom., 19 (2008) 1027-1040.
• P. Kang, Y. Mechref, M. V. Novotny "High-throughput Solid-phase Spin-column Permethylation for MALDI-TOF-MS Analysis" Rapid Commun. Mass Spectrom., 22(5) (2008) 721-734.
• H. W. Ressom, R. S. Varghese, L. Goldman, Y. An, C. A. Loffredo, M. Abdel-Hamid, Z. Kyselova, Y. Mechref, M. Novotny, S. K. Drake, R. Goldman, "Analysis of MALDI-TOF Mass Spectrometry Data for Discovery of Peptide and Glycan Biomarkers of Hepatocellular Carcinoma" J. Proteome Res., 7 (2008) 603-610.
• D. Isailovic, R. T. Kurulugama, M. D. Plasencia, S. T. Stokes, Z. Kyselova, R. Goldman, Y. Mechref, M. V. Novotny, D. E. Clemmer "Profiling of Human Serum Glycans Associated with Liver Cancer and Cirrhosis by IMS-MS" J. Proteome Res., 7(3) (2008) 1109-1117.
• S. I. Merenbloom, S. L. Koeniger, B. C. Bohrer, S. J. Valentine, D. E. Clemmer, "Improving the Efficiency of IMS-IMS by a Combing Technique" Anal. Chem. 80 (2008) 1918-1927.
• P. Alves, R. J. Arnold, D. E. Clemmer, Y. Li, J. P. Reilly, Q. Sheng, H. Tang, Z. Xun, R. Zeng, P. Radivojac “Fast and Accurate Identification of Semi-tryptic Peptides in Shotgun Proteomics”, Bioinformatics, 24(2008) 102-109.
• M. A.Lerch, M. D.Hoffman, S. C.Jacobson "Influence of channel position on sample confinement in two-dimensional planar microfluidic devices." Lab on a Chip, 8 (2008) 316-322.
• Y. F. Li, R. J. Arnold, Y. Li, P. Radivojac, Q. Sheng and H. Tang, "A Bayesian approach to protein inference problem in shotgun proteomics" Proceedings of the 12th Annual International Conference on Computational Molecular Biology (RECOMB08), LNBI 4955 (2008) 167-180.
• Ressom HW, Varghese RS, Goldman L, Loffredo CA, Abdel-Hamid M, Kyselova Z, Mechref Y, Novotny M, Goldman R. Analysis of MALDI-TOF mass spectrometry data for detection of glycan biomarkers. Pacific Symposium on Biocomputing 13 (2008) 216-227.
• Devakumar, Arugadoss; O'Dell, David K.; Walker, J. Michael; Reilly, James P. "Structural Analysis of Leukotriene C4 Isomers Using Collisional Activation and 157 nm Photodissociation." J. Am. Soc. Mass. Spectrom., 19 (2008) 14-26.
• P. Kang, Y. Mechref, Z. Kyselova, J. A. Goetz, M. V. Novotny, Comparative Glycomic Mapping (C-GlycoMAP) through Quantitative Permethylation and Stable-isotope Labeling“ Anal. Chem., 79 (2007) 6064-6073.
• Z. Kyselova, Y. Mechref, M. M. Al Bataineh, L. E. Dobrolecki, R. J. Hickey, J. Vinson, C. J. Sweeney, M. V. Novotny, “Alterations in the Serum Glycome due to Metastatic Prostate Cancer” J. Proteome Res., 6 (2007) 1822-1832.
• W. R. Alley, Jr., Y. Mechref, I. Klouckova, M. V. Novotny, "Collision-induced Dissociation Analysis of Peptides by Matrix-assisted Laser Desorption/Ionization Mass Spectrometry, Following Chemical Derivatization with a Sulfonated Reagent” J. Proteome Res., 6 (2007)124-132.
• M. Madera; Y. Mechref; I. Klouckova; M. V. Novotny, " High-sensitivity profiling of glycoproteins from human blood serum through multiple-lectin affinity chromatography and liquid chromatography/tandem mass spectrometry" J. Chromatogr. B, 845 (2007) 121-137.
• Lass, Agnieszka; McConnell, Elizabeth; Nowis, Dominika; Mechref, Yehia; Kang, Pilsoo; Novotny, Milos V.; Wojcik, Cezary. "A novel function of VCP (valosin-containing protein; p97) in the control of N-glycosylation of proteins in the endoplasmic reticulum," Arch. Biochem. Biophys., 462 (2007) 62-73.
• Z. Zhuang, J. A. Starkey, Y. Mechref, M. V. Novotny, and S. C. Jacobson, “Electrophoretic Analysis of N-Glycans on Microfluidic Devices” Anal. Chem., 79 (2007) 7170-7175.
• M.A. Lerch and S.C. Jacobson, “Electrokinetic Fluid Control in Two-Dimensional Planar Microfluidic Devices,” Anal. Chem., 79 (2007) 7485-7491.
• Merenbloom, S. I.; Bohrer, B. C.; Koeniger, S. L.; Clemmer, D. E. "Assessing the Peak Capacity of IMS-IMS Separations of Tryptic peptide ions in 300K He", Anal. Chem., 79 (2007) 515-522.
• Koeniger, S. L.; Clemmer, D. E. "Resolution and Structural Transitions of Elongated States of Ubiquitin," J. Am. Soc. Mass Spectrom., 18 (2007) 322-331.
• A. Devakumar, Y. Mechref, P. Kang, M. V. Novotny and J. P. Reilly, “Laser-induced photofragmentation of neutral and acidic glycans inside an ion-trap mass spectrometer” Rapid Commun. Mass Spectrom, 21 (2007) 1452-1460.
• P. Alves, R. J. Arnold, M. V. Novotny, P. Radivojac, H. Tang, "Advancement in protein inference from shotgun proteomics using peptide detectability", Pacific Symposium of Biocomputing, 12 (2007) 409-420.
• Y. Wu, Y. Mechref, I. Klouckova, M. V. Novotny, H. Tang, "A Computational Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry" LNBI, 4532 (2007) 97-108.
• Running, William E.; Ravipaty, Shobha; Karty, Jonathan A.; Reilly, James P. "A Top-Down/Bottom-Up Study of the Ribosomal Proteins of Caulobacter crescentus" J J. Proteome Res. 6 (2007) 337-347.
• M.A. Lerch and S.C. Jacobson, “Flow Control in Microfluidic Devices with a Planar Separation Format” Micro Total Analysis Systems 2006, Tokyo, Japan, November 2006, pp. 933-935.
• M. Madera; Y. Mechref; I. Klouckova; M. V. Novotny, "Semiautomated High-Sensitivity Profiling of Human Blood Serum Glycoproteins through Lectin Preconcentration and Multidimensional Chromatography/Tandem Mass Spectrometry" J. Proteome Res. 5 (2006) 2348-2363.
• Yehia Mechref, Pilsoo Kang and Milos V. Novotny, “Differentiating Sialylated Glycan Structural Isomers through MALDI/TOF/TOF Tandem Mass Spectrometry”, Rapid Commun. Mass Spectrom., 20 (2006) 1381-1389.
• Valentine, S. J.; Plasencia, M. D.; Liu, X.; Krishnan, M.; Naylor, S.; Udseth, H. R.; Smith, R. D.; Clemmer, D. E. "Toward Plasma Proteome Profiling with Ion Mobility-Mass Spectrometry," J. Proteome Res. 5 (2006) 2977-2984.
• Merenbloom, S. I.; Koeniger, S. L.; Valentine, S. J.; Plasencia, M. D.; Clemmer, D. E. “IMS-IMS and IMS-IMS-IMS/MS for Separating Peptide and Protein Fragment Ions” Anal. Chem., 78 (2006) 2802-2809.
• Koeniger, S. L.; Merenbloom, S. I.; Clemmer, D. E. “Evidence for Many Resolvable Structures within Conformation Types of Electrosprayed Ubiquitin Ions”, J. Phys. Chem B, 110 (2006) 7017-7021.
• Koeniger, S. L.; Merenbloom, S. I.; Valentine, S. J.; Jarrold, M. F.; Udseth, H.; Smith, R.; Clemmer, D. E. "An IMS-IMS Analogue of MS-MS," Anal. Chem. , 78 (2006) 4161-4174.
• Koeniger, S. L.; Merenbloom, S. I.; Sevugarajan, S.; Clemmer, D. E. "Transfer of Structural Elements from Compact to Extended States in Unsolvated Ubiquitin," J. Am. Chem. Soc. 128 (2006) 11713-11719.
• Valentine, S. J.; Sevugarajan, S.; Kurulugama, R. T.; Koeniger, S. L.; Merenbloom, S. I.; Bohrer, B. C.; Clemmer, D. E. "Split-Field Drift Tube/Mass Spectrometry and Isotopic Labeling Techniques for Determination of Single Amino Acid Polymorphisms" J. Proteome Res., 5 (2006) 1879-1887.
• H. Tang, R. J. Arnold, P. Alves, Z. Xun, D. E. Clemmer, M. V. Novotny, J. P. Reilly and P. Radivojac A computational approach toward label-free protein quantification using predicted peptide detectability, Bioinformatics, 22 (2006) e481-e488.

B. In Press

• P. Kang, Y. Mechref, M. V. Novotny " High-throughput Solid-phase Spin-column Permethylation for MALDI-TOF-MS Analysis" Rapid Commun. Mass Spectrom., in press.
• Z. Kyselova, Y. Mechref, P. Kang, J. A. Goetz, L. E. Dobrolecki, G. Sledge, L. Schnaper, R. J. Hickey, L. H. Malkas, M. V. Novotny "Breast Cancer Diagnosis/Prognosis through Quantitative Measurements of Serum Glycan Profiles" Clin. Chem., (2007) in press.
• H.W. Ressom, R.S Varghese, L. Goldman, Y. An, C.A Loffredo, M. Abdel-Hamid, Z. Kyselova, Y. Mechref, M. Novotny, S.K. Drake, R. Goldman " Analysis of MALDI-TOF Mass Spectrometry Data for Discovery of Peptide and Glycan Biomarkers of Hepatocellular Carcinoma" J. Proteome Res., in press.
• B. Mann, M. Madera, Y. Mechref, Q. Sheng, H. Tang, M. V. Novotny "Application Of ProtQuant Suite Software Tool For Label-Free Proteomic Quantification In Biological Mixtures" J. Am. Soc. Mass. Spectrom., in press.
• J.A. Goetz, Y. Mechref, P. Kang, M-H. Jeng, M.V. Novotny " Glycomic Profiling of Invasive and Non-invasive Breast Cancer Cells" Glycoconjugate J., in press.
• M.A. Lerch and S.C. Jacobson, "Electrokinetic Fluid Control in Planar Microfluidic Devices," Anal. Chem., (2007), in press.
• D. Isailovic, R. T. Kurulugama, M. D. Plasencia, S. T. Stokes, Z. Kyselova, R. Goldman, Y. Mechref, M. V. Novotny, D. E. Clemmer " Profiling of Human Serum Glycans Associated with Liver Cancer and Cirrhosis by IMS-MS" J. Proteome Res., in press.
• Merenbloom, S. I.; Koeniger, S. L.; Bohrer, B. C.; Valentine, S. J.; Clemmer, D. E. "Improving the Efficiency of IMS-IMS by a Combing Technique" J. Proteome Res., in press.
• A. Devakumar, Y. Mechref, P. Kang, M.V. Novotny and J.P. Reilly " Identification of Isomeric N-Glycan Structures by Mass Spectrometry with Laser-Induced Photofragmentation" J. Am. Soc. Mass. Spectrom., in press.
• Yong Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang "A Bayesian approach to protein inference problem in shotgun proteomics" J. Computational Biol., in press.
• J. A. Goetz, Y. Mechref, P. Kang, M-H. Jeng, M. V. Novotny, " Glycomic Profiling of Invasive and Non-invasive Breast Cancer Cells" Glycoconjugate J., (2008),in press.
• M. Madera, B. Mann, Y. Mechref and M. V. Novotny "Efficacy of Glycoprotein Enrichment by Microscale Lectin Affinity Chromatography" J. Sep. Sci., (2008), in press.
• Yong Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang. “A Bayesian approach to protein inference problem in shotgun proteomics” J. Computational Biol., (2008), in press.
• R.T. Kurulugama, S. J. Valentine, R. A. Sowell, D. E. Clemmer “Development of a High-throughput IMS-IMS-MS Approach for Analyzing Mixtures of Biomolecules” J. Proteome Res. , (2008), in press.
• C. Yuan, Q. Sheng, H. Tang, Y. Li, R. Zeng, and R. J. Solaro "Quantitative Comparison of Sarcomeric Phospho-Proteomes of Neonatal and Adult Rat Hearts." Am J Physiol Heart Circ Physiol., (2008), in press.
• W. R. Alley, Jr., M. V. Novotny, Y. Mechref, "Collision-induced Dissociation and Electron transfer Dissociation in the Characterization of Glycopeptides" Rapid Commun. Mass Spectrom., revision-requested.

C. Submitted

• W.R. Alley, Jr., M.V. Novotny, Y. Mechref " Graphitized Carbon as a Stationary Phase for Chip-based Separations of Tryptic Glycopeptides prior to Tandem Mass Spectral Analysis" Rapid Commun. Mass Spectrom., submitted.
• W.R. Alley, Jr., M.V. Novotny, Y. Mechref "Collision-induced Dissociation and Electron transfer Dissociation in the Characterization of Glycopeptides" Rapid Commun. Mass Spectrom., submitted.
• R. Goldman, H.W. Ressom, R.S. Varghese, L. Goldman, G. Bascug, C.A. Loffredo, M. Abdel-Hamid, I. Gouda, S. Ezzat, Z. Kyselova, Y. Mechref, and M. V. Novotny "Detection of Hepatocellular Carcinoma using Glycomic Analysis" Clin. Cancer Res., submitted.
• Z. Zhuang and S.C. Jacobson, "Serial-to-Parallel Interfaces on Microfluidic Devices," Anal. Chem., (2007) submitted.
• O. Gustafsson, K.B. Mogensen, P.D. Ohlsson, Y. Liu, S.C. Jacobson, and J.P. Kutter, "Electrochromatography Chip with Integrated Waveguides for UV Absorbance Detection," submitted.
• Z. Zhuang and S.C. Jacobson, "Serial to Parallel Interfaces on Microfluidic Devices," submitted.
• S.B. Sudhoff, Z. Zhuang, A. Alexander, and S.C. Jacobson, "Fast-Slewing High Voltage Power Supply for Microfluidics," submitted.
• Y. Wu, Y. Mechref, I. Klouckova, M. V. Novotny and H. Tang, A Computational Approach to the Identification of Site-specific Protein N-Glycosylations through Liquid Chromatography/Mass Spectrometry. Proteomics, submitted.