Publications

Published Papers

2008

Ouvry-Patat, S.A., Torres, M.P., Quek, H., Gelfand, C.A., Schroeder, G.K., Han, J., Elliott, M., Dryhurst, D., Ausio, J., Wolfenden R., Borchers, C.H., Free-Flow Electrophoresis for Top-Down Proteomics by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Proteomics, Accepted for Publication (2008)

Rosenzweig, D., Smith, D., Myler, P. J., Olafson, R.W., Zilberstein, D. Post-translational modification of cellular proteins during Leishmania donovani differentiation Proteomics, Accepted for Publication (2008)

Jun Han, Ryan M. Danell, Jayanti R. Patel, Dmitry R. Gumerov, Cameron O. Scarlett,
J. Paul Speir, Carol E. Parker, Ivan Rusyn, Steven Zeisel and Christoph H. Borchers. Towards High Throughput Metabolomics using Ultrahigh Field Fourier Transform Ion
Cyclotron Resonance Mass Spectrometry Metabolomics, Accepted for Publication

Parker, C.E., Warren, M.R., Mocanu, V., Greer, S.F., Borchers, C.H., Mass spectrometric determination of protein ubiquitination Methods Mol Biol, 2008 446:109-30

Funk VA, Olafson RW, Raap M, Smith D, Aitken L, Haddow JD, Wang D, Dawson-Coates JA, Burke RD, Miller KM. Identification, characterization and deduced amino acid sequence of the dominant protease from Kudoa paniformis and K. thyrsites: A unique cytoplasmic cysteine protease. Comp Biochem Physiol B Biochem Mol Biol. 2008 Mar;149(3):477-89.

Rosenzweig D, Smith D, Opperdoes F, Stern S, Olafson RW, Zilberstein D.

Retooling Leishmania metabolism: from sand fly gut to human macrophage.

FASEB Journal. 2008 Feb;22(2):590-602.

2007

Wagner, R.E., Mugnaini, S., Sniezko, R., Hardie, D., Poulis, B., Nepi, M., Pacini, E., von Aderkas, P., Proteomic evaluation of gymnosperm pollination drop proteins indicates highly conserved and complex biological functions Sex Plant Reprod 20:181-189 (2007)

Jian Jiang; Carol E Parker; James R Fuller; Thomas H Kawula; Christoph H Borchers , Wainwright CE, Wainwright BJ. An Immunoaffinity Tandem Mass Spectrometry (iMALDI) assay for Detection of Francisella tularensis. Analytica Chimica Acta, 2007 Dec 12;605(1):70-9. Epub 2007 Oct 23. PMID: 18022413

Jiang, J., Parker C.E., Hoadley, K.A., Perou, C.M., Borchers C.H., Development of an Immuno Tandem Mass Spectrometry² (iMASS²) Assay for EGFR Diagnosis,Proteomics Clin. Appl. 1, 1651–1659, (2007)

McMorran BJ, Ouvry Patat SA, Carlin JB, Grimwood K, Jones A, Armstrong DS, Galati JC, Cooper PJ, Byrnes CA, Francis PW, Robertson CF, Hume DA, Borchers CH , Wainwright CE, Wainwright BJ. Novel neutrophil-derived proteins in bronchoalveolar lavage fluid indicate an exaggerated inflammatory response in pediatric cystic fibrosis patients. Journal of Clinical Chemistry 2007 Oct;53(10):1782-91. Epub 2007 Aug 16. PMID: 17702859

Richard A. Dean, Christopher M. Overall, Derek Smith.Proteomic Identification of Cellular Protease Substrates Using Isobaric Tags for Relative and Absolute Quantification.
Current Protocols in Protein Science 21.18.1-21.18.12, August 2007

Reid, J.D., Parker, C.E. Borchers, C.H.,Protein arrays for biomarker discovery Current Opinion in Molecular Therapeutics, 9(3):216-21.(2007)

Torres, M.P., Borchers, C.H., Phosphorylation of the APC Inhibitory Subunit Mnd2 is Necessary for Efficient Progression Through Meiosis JBC, 15;282(24):17351-62 (2007)

Boysen G., Scarlett C.O., Temple B., Combs T.P., Brooks, N.L., Borchers C.H., Swenberg J.A., Identification of covalent modifications in P450 2E1 by 1,2-epoxy-3-butene in vitro. Chem. Biol. Interact., 166(1-3): 170-5 (2007)

Hao, N., Behar, M., Parnell, S.C., Torres, M.P., Borchers, C.H. Elston, T.C., Dohlman, H.G., Experimental and computational analysis of feedback inhibition of the Sho1 osmotic stress-response pathway Current Biology, 17(8): 659-67 (2007)

Thelin, W.R., Chen, Y., Gentzsch, M., Kreda, S., Sallee, J., Scarlett, C., Borchers, C.H. Jacobson, K., Jackson Stutts, M., Milgram, S.L. A direct interaction with filamins modulates the stability and plasma membrane expression of CFTR. Journal of Clinical Investigation, 117(2): 364-374 (2007)

Dial, J.M., Petrotchenko, E.V., Borchers, C.H. Inhibition of APCCdh1 activity by Cdh1/Acm1/Bmh1 ternary complex formation. JBC, 282(8): 5237-48 (2007)

Bhati, R., Goekmen-Polar, Y., Sledge G.W. Jr., Nakshatri, H., Ketelsen, D., Fan, C., Borchers, C.H. Dial, M.J., Patterson, C., Klauber-DeMoore, N. 2-Methoxyestradiol Inhibits the Anaphase Promoting Complex and Protein Translation in Human Breast Cancer Cells. Cancer Research, 67(2): 702-708 (2007)

2006

Jiang, J., Parker, C.E., Robinette, D., Borchers, C.H. A Clinical Diagnostics Platform – Protein Detection Using an Immunoaffinity-based Peptide Chip BIOforum Europe, 10/2006: 18-20 (2006)

Inoue, K., Borchers, C.H. Negishi, M., Cohesin protein SMC1 represses the nuclear receptor CAR-mediated synergistic activation of a human P450 gene by xenobiotics. Biochemical Journal, 398(1): 125-133 (2006)

Petrotchenko, E.V., Pasek, D., Elms, P., Dokholyan, N.V., Meissner, G., Borchers C.H., Combining fluorescence detection and mass spectrometric analysis for comprehensive and quantitative analysis of redox-sensitive cysteines in native membrane proteins. Analytical Chemistry, 78(23): 7959-7966 (2006)

Laith, Q.A-M., Fikkert, V., Dayam, R., Burke, T.R., Borchers, C.H. Neamti, N. Discovery of a novel small molecule HIV-1 integrase inhibitor binding-site through photoaffinity labeling and mass spectrometry. PNAS, 103(26): 10080-10085 (2006)

Robinette, D., Neamati, N., Tomer, K.B., Borchers, C.H. Photoaffinity Labeling Combined with Mass Spectrometric Approaches as a Tool for Structural Proteomics. Expert Review in Proteomics, 3(4): 399-408 (2006)

Borchers, C.H. Thapar, R., Petrotchenko, E.V., Torres M.P., Speir, S.P., Easterling M., Dominski, Z., Marzluff, W.F., Combined Top-down and Bottom-up Proteomics Identifies a Phosphorylation Site in Stem-Loop Binding Proteins That Contributes to High-affinity RNA Binding. PNAS, 103(9): 3094-3099 (2006)

Tsukada, Y-I.; Fang, J.; Erdjument-Bromage, H.; Warren, M.E.; Borchers, C.H. Tempst, P.; Zhang, Y., Histone demethylation by a family of JmjC domain-containing proteins. Nature, 439(7078): 811-816 (2006)

2005

Dai, Q., Qian, S-B., Li H-H., McDonough, H., Borchers, C., Huang, D., Takayama, S., Younger J.M., Cyr, D.M., Patterson, C., Regulation of the cytoplasmic quality control protein degradation pathway by BAG2. J. Biol. Chem., 280(46): 38673-81 (2005)

Torres, P.T., Thapar, R., Marzluff, W.F., Borchers, C.H. Phosphatase-Directed Phosphorylation-Site Determination: A synthesis of Methods for the Detection and Identification of Phosphopeptides. Journal of Proteome Research, 4(5): 992-7 (2005)

Parnell, S.C., Marotti, L.A., Kiang, L., Torres, M.P., Borchers, C.H. Dohlman, H.G., Phosphorylation of the RGS Protein Sst2 by the MAP kinase Fus3 and use of Sst2 as a Model to Analyze Determninats of Substrate Specificity. Biochemistry, 44(22): 8159-66 (2005)

Warren, E.N., Jiang, J., Parker, C.E., Borchers C.H., Absolute Quantitation of Cancer-related Proteins using an MS-based Peptide Chip. BioTechniques, 38: S7-S11 (2005)

Loiselle, D.R., Thelin, W.R., Parker, C.E., Dicheva, N.N., Kesner, B.A., Mocanu, V., Wang, F., Milgram, S.L., Warren, M.R.E., Borchers, C.H. Improved Protein Identification through the Use of Unstained Gels. Journal of Proteome Research, 4(3): 992-997 (2005)

Petrotchenko, E.V., Olkhovik, V.K., Borchers, C.H. Isotopically-Coded Cleavable Crosslinker for Studying Protein-Protein Interaction and Protein Complexes. Molecular and Cellular Proteomics, 4(8): 1167-1179 (2005)

Warren, M.R.E., Parker, C.E., Mocanu, V., Klapper, D., Borchers C.H., Electrospray Ionization Tandem Mass Spectrometry of Model Peptides Reveals Diagnostic Fragment Ions for Protein Ubiquitination. Rap. Commun. Mass Spectrom., 19: 1-9 (2005)

2004

Borchers, C.H. Marquez, V.E., Schroeder, G.K., Short, S.A., Snider, M.J., Speir, P.K., Wolfenden, R., Fourier Transform Ion Cyclotron Resonance MS Reveals the Presence of a Water Molecule in an Enzyme Transition-State Analogue Complex. PNAS, 101(43): 15341-15345 (2004)

Hall, M.C., Warren, E.N., Borchers C.H., Multi-Kinase Phosphorylation of the APC/C Activator Cdh1 Revealed by Mass Spectrometry. Cell Cycle, 3: 1278-1284 (2004)

Warren, E.N., Elms, P.J., Parker, C.E, Borchers, C. H., Development of a Protein Chip: A MS-based Method for Quantitation of Protein Expression and Modification Levels using an Immunoaffinity Approach. Analytical Chemistry, 76: 4082-4092 (2004)

Howell, M., Borchers, C., Milgram, S.L., Heterogeneous Nuclear Ribonuclear Protein U Associates with YAP and Regulates Its Co-activation of Bax Transcription. JBC, 25: 26300-263006 (2004)

Huang, C., Borchers, C.H. Schaller, M.D., Jacobson, K., Phosphorylation of paxillin by p38mapk is involved in the neurite outgrowth of PC-12 cells. Journal of Cell Biology, 164(4): 593-602 (2004)

2003

Furukawa, M., He, Y.J., Borchers, C., Xiong, Y., Targeting of protein ubiquitination by BTB-Cullin 3-Roc1 ubiquitin ligases. Nature Cell Biology, 5(11): 1001-1007 (2003)

Xiao, T., Hall, H., Kizer, K., Sabata, Y., Hall, M., Borchers, C.H. Strahl, B.D., Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes & Dev., 17: 654-663 (2003)

Huang, C., Rajfur,Z., Schaller, M., Borchers C., Jacobson K., Phosphorylation of Serine 178 on Paxillin by JNK1 can regulate Cell Migration. Nature, 424(6945): 219-223 (2003)

Hall, M.C., Torres, M.P., Schroeder, G., Borchers, C.H. Mnd2 and Swm1 are Core Subunits of the Saccharomyces cerevisiae Anaphase-Promoting Complex. J. Biol. Chem., 19: 16698-16705 (2003)

Raska, C.S., Parker C.E., Sunnarborg, S.W., Pope, R. M., Lee D.L., Glish, G.L., Borchers, C.H. Rapid and Sensitive Identification of Epitope-Containing Peptides by Direct Matrix Assisted Laser Desorption Ionization Tandem Mass Spectrometry of Peptides Affinity-bound to Antibody Beads. J. Am. Soc. Mass Spectrom., 14: 1076-1085 (2003)

Kast, J., Parker, C.E., Drift, K.v.d., Dial, J.M., Milgram, S.L., Wilm, M., Howell, M., Borchers, C.H. Matrix-assisted laser desorption/ionization directed nano-electrospray ionization tandem mass spectrometric analysis for protein Identification. Rap. Commun. Mass Spectrom., 17: 1825-1834 (2003)

Hall, M.C., Shcherbakova, P.V., Borchers, C.H. Dial, J.M., Tomer, K.B., Kunkel, T.A., DNA binding by yeast Mlh1 and Pms1: implications for DNA mismatch repair. Nucleic Acids Research, 31(8): 2025-2034 (2003)

Zheng, L., Dominski, Z., Yang, X-C., Elms, P., Raska, C., Borchers, C.H. Marzluff, W.F., Phosphorylation of SLBP on two threonines triggers degradation of SLBP, the sole cell-cycle regulated factor required for regulation of histone mRNA processing, at the end of S-phase. Mol. Cell. Bio., 23(5): 1590-1601 (2003)

2002

Jun, H., Pope, R.M., Borchers, C., Graves, L.M., Mapping of Protein Phosphorylation by Dual Enzyme Digestion on MALDI-QoTOF-MS. Anal. Biochem., 310(2): 214-218 (2002)

Dominski, Z., Yang, X., Raska, C.S., Santiago, C., Borchers, C.H. Duronio, R.J., Marzluff, W.F., 3'end processing of Drosophila histone pre-mRNAs: Requirement for phosphorylated dSLBP and co-evolution of the histone pre-mRNA processing system. Mol. Cell Bio., 22(18): 6648-6660 (2002)

Bruno, M.E., Borchers, C.H. Dial, M.J., Walker, N.J., Hartis, J.E., Wetmore, B.A., Barrett, J.C., Tomer, K.B., Merrick, B.A., Effects of TCDD upon I?B and IKK Subunits Localized in Microsomes by Proteomics. Arch. Biochem. Biophy., 406(2): 153-164 (2002)

Raska, C.S., Parker, C.E., Huang, C., Han. J., Glish, G.L., Pope, R.M., Borchers, C.H. Pseudo-MS3 in a MALDI Orthogonal Quadrupole-time of Flight Mass Spectrometer. Journal of the American Society for Mass Spectrometry, 13: 1034-1041 (2002)

Raska, C.S., Parker, C.E., Glish, G.L., Dominski, Z., Marzluff, W.F., Pope, R.M., Borchers, C.H. Direct MALDI-MS/MS of Phosphopeptides Affinity-Bound to IMAC Beads. Analytical Chemistry, 74: 3429-3433 (2002)

Wine, R.N., Dial, J.M., Tomer, K.B., Borchers, C.H. Identification of Components of Protein Complexes Using a Fluorescent Photo-Cross-Linker and Mass Spectrometry. Analytical Chemistry, 74: 1939-1945 (2002)

Borchers, C., Boer, R., Klemm, K., Figala, V., Witte, S., Denzinger, T., Ulrich, W.R., Haas, S., Ise, W., Gekeler, V., Przybylski,M., Characterization of the Dexnigulpidine Binding Site in the Multidrug Resistance-Related Transport Protein P-Glycoprotein by Photoaffinity Labelling and Mass Spectrometry. Molecular Pharmacology, 61: 1366-1376 (2002)

2001

Wang, H., Cao, R., Xia, L., Erdjument-Bromage, H., Borchers, C., Tempst, P., Zhang Y., Purification and Functional Characterization of a Histone H3-Lysine 4-Specific Methyltransferase. Molecular Cell, 8(6): 1207-1217 (2001)

Chapin, R.E., Wine, R.N., Harris, M.W., Borchers, C.H. Haseman, J.K., The Structure of a Cell-Cell Adhesion Complex Associated with Spermiation in Rat Seminiferous Epithelium. J. Andrology, 22: 1030-1052 (2001)

Petrotchenko, E.V., Pedersen, L.C., Borchers, C.H. Tomer, K.B., Negishi, M., The Dimerization Motif of Cytosolic Sulfotransferase. FEBS Letters, 490: 39-43 (2001)

Merrick, B.A., Zhou, W., Martin, K.J., Jeyarajah, S., Parker,C.E., Selkirk, J.K., Tomer, K.B., Borchers, C.H. Site-Specific Phosphorylation of Human P53 Protein Determined by Mass Spectrometry. Biochemistry, 39: 11194-11204 (2001)

2000

Xuegong, Z., Borchers, C., Bienstock, R.J., Tomer, K.B., Mass Spectrometric Characterization of the Glycosylation Pattern of HIV-gp120 Expressed in CHO Cells. Biochemistry, 39: 11194-11204 (2000)

Hochleitner, E.O., Borchers C., Parker C., Bienstock, R.J., Tomer, K.B., Characterization of a Discontinuous Epitope of the HIV Core Protein HIV-p24 by Epitope Excision and Differential Modification followed by Mass Spectrometric Peptide Mapping. Protein Science, 9(3): 487-496 (2000)

Borchers, C., Peter, J.F., Hall, M.C., Kunkel, T.A., Tomer, K.B., Identification of In-Gel Digested Proteins by Complementary Peptide-Mass Fingerprinting and Tandem Mass Spectrometry Data obtained on an Electrospray Ionization Quadrupole Time-of-flight Mass Spectrometer. Analytical Chemistry, 72(6): 1163-1168 (2000)

Book Chapters

Ouvry-Patat, S.A., Torres, M.P. Gelfand, G., Easterling, M., Speir, J. P., Borchers, C.H. Top-down Proteomics on a High-field Fourier Transform Ion Cyclotron Resonance Mass spectrometer. In: Methods in Molecular Biology, Editor: Pasa-Tolic, L, Humana Press, NJ, accepted for publication (2007)

Parker, C. E.; Mocanu, V.; Warren, M. R.; Greer, S. F., Borchers, C.H. Mass Spectrometric Determination of Protein Ubiquitination. In: Methods in Molecular Biology, Editor: Patterson, W. C., Humana Press, NJ, Vol. 103, 153-173 (2005)

Parker, C. E.; Warren, M. R.; Loiselle, D., Dicheva, N.N., Scarlett, C.O., Borchers, C.H. Identification of Components of Protein Complexes. In: Methods in Molecular Biology, Editor: Patterson, W. C., Humana Press, NJ, Vol. 103, 117-151 (2005)

Borchers, C.H. Chen, T., Neamati, N., Application of Proteomics in Basic Biological Sciences and Cancer. In: Molecular Carcinogenesis and the Molecular Biology of Human Cancer, CRC press, Editor: Warshawsky D., Landolph, J.R., CRC, 263-288 (2005)

Borchers, C., Automation and integration strategies in high-throughput genomics; Editorial advisory Board Member Commentaries. In High-Throughput Genomics: Maximizing Efficiency and Productivity for Drug Discovery and Development, Editor S.J. Walker, T.D. Howard, G.A. Hawkins, K.E. Vrana J.A., D. Lockwood & M.A. Branca; Cambridge Healthtech Institute: 118-119 (2001).

M. Przybylski, C. Borchers, M. Jetschke, R. Schuhmacher, W. Fiedler, M. Mak, M.O. Glocker, Molecular Approaches for the Characterization of Protein Tertiary Structures by Selective Chemical Modification and Mass Spectrometric Peptide Mapping. In: Peptides-Chemistry, Structure and Biology, Editor Hodges, R.S., & Smith, J.A., Escom Science Publ., Leiden; 254-256 (1994)