Proteome Exploration Laboratory
For a most up-to-date list of publications, please visit GOOGLE SCHOLAR

Journal Articles


  1. Chandrasekar, S., Sweredoski, M.J., Sohn, C.H., Hess, S., Shan. S.O.*
    Co-evolution of two GTPases enables efficient protein targeting in an RNA-less chloroplast Signal Recognition Particle pathway
    J. Biol. Chem., 2017, DOI: 10.1074/jbc.M116.752931.
  2. 2016

  3. Xue, L., Blythe, E. E., Freiberger, E. C., Mamrosh, J. L., Hebert, A. S., Reitsma, J. M., Hess, S., Coon, J. J., and Deshaies, R.J.
    Valosin-containing protein (VCP)-Adaptor Interactions are Exceptionally Dynamic and Subject to Differential Modulation by a VCP Inhibitor.
    Mol Cell Proteomics, 2016, 15, 2970-2986.
  4. Sung, M. K., Reitsma, J. M., Sweredoski, M. J., Hess, S., and Deshaies, R. J.
    Ribosomal proteins produced in excess are degraded by the ubiquitin-proteasome system.
    Mol Biol Cell, 2016, 27, 2642-2652 .
  5. Sung, M. K., Porras-Yakushi, T. R., Reitsma, J. M., Huber, F. M., Sweredoski, M. J., Hoelz, A., Hess, S., and Deshaies, R. J.
    A conserved quality-control pathway that mediates degradation of unassembled ribosomal proteins.
    Elife, 2016, 5, e19105.
  6. Renata, H., Lewis, R. D., Sweredoski, M. J., Moradian, A., Hess, S., Wang, Z. J., and Arnold, F. H.
    Identification of Mechanism-Based Inactivation in P450-Catalyzed Cyclopropanation Facilitates Engineering of Improved Enzymes.
    J Am Chem Soc , 2016, 138, 12527-12533.
  7. Nguyen, T. V., Lee, J. E., Sweredoski, M. J., Yang, S. J., Jeon, S. J., Harrison, J. S., Yim, J. H., Lee, S. G., Handa, H., Kuhlman, B., Jeong, J. S., Reitsma, J. M., Park, C. S., Hess, S., and Deshaies, R. J.
    Glutamine Triggers Acetylation-Dependent Degradation of Glutamine Synthetase via the Thalidomide Receptor Cereblon.
    Mol Cell , 2016, 61, 809-820
  8. Mosadeghi, R., Reichermeier, K. M., Winkler, M., Schreiber, A., Reitsma, J. M., Zhang, Y., Stengel, F., Cao, J., Kim, M., Sweredoski, M. J., Hess, S., Leitner, A., Aebersold, R., Peter, M., Deshaies, R. J., and Enchev, R. I.
    Structural and kinetic analysis of the COP9-Signalosome activation and the cullin-RING ubiquitin ligase deneddylation cycle
    Elife , 2016, e12102
  9. Mahdavi, A., Hamblin, G. D., Jindal, G. A., Bagert, J. D., Dong, C., Sweredoski, M. J., Hess, S., Schuman, E. M., and Tirrell, D. A.
    Engineered Aminoacyl-tRNA Synthetase for Cell-Selective Analysis of Mammalian Protein Synthesis.
    J Am Chem Soc, 2016,138, 4278-4281
  10. Liu, J. M., Sweredoski, M. J., and Hess, S.
    Improved 6-Plex Tandem Mass Tags Quantification Throughput Using a Linear Ion Trap-High-Energy Collision Induced Dissociation MS(3) Scan.
    Anal Chem, 2016,138, 7471-7475
  11. Kuo, M. L., Lee, M. B., Tang, M., den Besten, W., Hu, S., Sweredoski, M. J., Hess, S., Chou, C. M., Changou, C. A., Su, M., Jia, W., Su, L., and Yen, Y.
    PYCR1 and PYCR2 Interact and Collaborate with RRM2B to Protect Cells from Overt Oxidative Stress.
    Sci Rep 6, 2016, 6, 18846
  12. Crowe, B. L., Larue, R. C., Yuan, C., Hess, S., Kvaratskhelia, M., and Foster, M. P.
    Structure of the Brd4 ET domain bound to a C-terminal motif from gamma-retroviral integrases reveals a conserved mechanism of interaction.
    Proc Natl Acad Sci U S A, 2016, 113, 2086-2091
  13. Chen, C. L., Uthaya Kumar, D. B., Punj, V., Xu, J., Sher, L., Tahara, S. M., Hess, S., and Machida, K.
    NANOG Metabolically Reprograms Tumor-Initiating Stem-like Cells through Tumorigenic Changes in Oxidative Phosphorylation and Fatty Acid Metabolism.
    Cell Metab, 2016, 23, 206-219
  14. Bagert, J. D., van Kessel, J. C., Sweredoski, M. J., Feng, L., Hess, S., Bassler, B. L., and Tirrell, D. A
    Time-resolved proteomic analysis of quorum sensing in Vibrio harveyi.
    Chem Sci, 2016, 7, 1797-1806
  15. Babin, B. M., Bergkessel, M., Sweredoski, M. J., Moradian, A., Hess, S., Newman, D. K., and Tirrell, D. A.
    SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa.
    Proc Natl Acad Sci U S A, 2016, 113, E597-605
  16. 2015

  17. Yuet, K. P., Doma, M. K., Ngo, J. T., Sweredoski, M. J., Graham, R. L., Moradian, A., Hess, S., Schuman, E. M., Sternberg, P. W., and Tirrell, D. A.Babin, B. M., Bergkessel, M., Sweredoski, M. J., Moradian, A., Hess, S., Newman, D. K., and Tirrell, D. A.
    Cell-specific proteomic analysis in Caenorhabditis elegans.
    Proc Natl Acad Sci U S A, 2015, 112, 2705-2710
  18. Walkup, W. G. t., Washburn, L., Sweredoski, M. J., Carlisle, H. J., Graham, R. L., Hess, S., and Kennedy, M. B.
    Phosphorylation of synaptic GTPase-activating protein (synGAP) by Ca2+/calmodulin-dependent protein kinase II (CaMKII) and cyclin-dependent kinase 5 (CDK5) alters the ratio of its GAP activity toward Ras and Rap GTPases.
    J Biol Chem , 2015, 290, 4908-4927
  19. Sweredoski, M. J., Moradian, A., Raedle, M., Franco, C., and Hess, S.
    High resolution parallel reaction monitoring with electron transfer dissociation for middle-down proteomics.
    Anal Chem, 2015, 87, 8360-8366
  20. Schaefer, K. N., Geil, W. M., Sweredoski, M. J., Moradian, A., Hess, S., and Barton, J. K.
    Oxidation of p53 through DNA charge transport involves a network of disulfides within the DNA-binding domain.
    Biochemistry, 2015, 54, 932-941
  21. Riestra, A. M., Gandhi, S., Sweredoski, M. J., Moradian, A., Hess, S., Urban, S., and Johnson, P. J.
    A Trichomonas vaginalis Rhomboid Protease and Its Substrate Modulate Parasite Attachment and Cytolysis of Host Cells.
    PLoS Pathog, 2015, 11, e1005294
  22. Ramkumar, P., Lee, C. M., Moradian, A., Sweredoski, M. J., Hess, S., Sharrocks, A. D., Haines, D. S., and Reddy, E. P.
    JNK-associated Leucine Zipper Protein Functions as a Docking Platform for Polo-like Kinase 1 and Regulation of the Associating Transcription Factor Forkhead Box Protein K1.
    J Biol Chem, 2015, 290, 29617-29628
  23. Porras-Yakushi, T. R., Sweredoski, M. J., and Hess, S.
    ETD Outperforms CID and HCD in the Analysis of the Ubiquitylated Proteome.
    J Am Soc Mass Spectrom, 2015, 26, 1580-1587
  24. McHugh, C. A., Chen, C. K., Chow, A., Surka, C. F., Tran, C., McDonel, P., Pandya-Jones, A., Blanco, M., Burghard, C., Moradian, A., Sweredoski, M. J., Shishkin, A. A., Su, J., Lander, E. S., Hess, S., Plath, K., and Guttman, M.
    The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3.
    Nature, 2015, 521, 232-236
  25. Li, J., Olvera, A. I., Akbari, O. S., Moradian, A., Sweredoski, M. J., Hess, S., and Hay, B. A.
    Vectored antibody gene delivery mediates long-term contraception
    Curr Biol, 2015, 25, R820-822
  26. Karkashon, S., Raghupathy, R., Bhatia, H., Dutta, A., Hess, S., Higgs, J., Tifft, C. J., and Little, J. A.
    Intermediaries of branched chain amino acid metabolism induce fetal hemoglobin, and repress SOX6 and BCL11A, in definitive erythroid cells.
    Blood Cells Mol Dis, 2015, 55, 161-167
  27. Jang, K. S., Nani, R. R., Kalli, A., Levin, S., Muller, A., Hess, S., Reisman, S. E., and Clemons, W. M., Jr.
    A cationic cysteine-hydrazide as an enrichment tool for the mass spectrometric characterization of bacterial free oligosaccharides.
    Anal Bioanal Chem, 2015,407, 6181-6190
  28. Gristick, H. B., Rome, M. E., Chartron, J. W., Rao, M., Hess, S., Shan, S. O., and Clemons, W. M., Jr
    Mechanism of Assembly of a Substrate Transfer Complex during Tail-anchored Protein Targeting.
    J Biol Chem, 2015, 30006-30017
  29. 2014

  30. Chan, N. C., den Besten, W., Sweredoski, M. J., Hess, S., Deshaies, R. J., and Chan, D. C.
    Degradation of the deubiquitinating enzyme USP33 is mediated by p97 and the ubiquitin ligase HERC2
    J Biol Chem, 2014, 289, 19789-19798
  31. Dissinger, N., Shkriabai, N., Hess, S., Al-Saleem, J., Kvaratskhelia, M., and Green, P. L.
    Identification and characterization of HTLV-1 HBZ post-translational modifications.
    PLoS O, 2014, e112762
  32. Jang KS, Sweredoski MJ, Graham RLJ, Hess S, Clemens WM Jr
    Comprehensive proteomic profiling and functional annotations of outer membrane vesicles from Campylobacter jejuni
    Journal of Proteomics, 2014, 98, 90-98
  33. Honarpour N, Rose C, Brumbaugh J, Anderson J, Graham RLJ, Sweredoski MJ, Hess S, Coon JJ, Deshaies RJ.
    F-box protein FBXL16 binds PP2A-B55alpha and regulates differentiation of embryonic stem cells along the FLK1+ lineage
    MCP, 2014, mcp. M113. 031765
  34. Bagert, J. D., Xie, Y. J., Sweredoski, M. J., Qi, Y., Hess, S., Schuman, E. M., and Tirrell, D. A.
    Quantitative, time-resolved proteomic analysis by combining bioorthogonal noncanonical amino acid tagging and pulsed stable isotope labeling by amino acids in cell culture.
    MCP, 2014, mcp. M113. 031914
  35. Mahdavi A, Szychowski J, Sweredoski MJ, Graham RLJ, Hess S, Schneewind O, Mazmanian SK, Tirrell DA.
    Identification of secreted bacterial proteins by non-canonical amino acid tagging
    PNAS, 2014, 111 (1), 433-438
  36. Lu YY, Sweredoski MJ, Huss D, Lansford R, Hess S, Tirrell DA.
    Prometastatic GPCR CD97 Is a Direct Target of Tumor Suppressor microRNA-126.
    ACS Chem Biol., 2014, accepted Nov 25 2013; epub ahead of print.
  37. 2013

  38. Kolawa, N, Sweredoski MJ, Graham RLJ, Oania R, Verma R, Hess S, Deshaies RJ.
    Perturbations to the Ubiquitin Conjugate Proteome in DELTAubx Mutants Identify Ubx2 as a Regulator of Membrane Lipid Composition
    Mol Cell Proteomics, 2013, 12(10):2791-2803.
  39. Kurimchack A, Haines DS, Garriga J, Wu S, De Luca F, Sweredoski MJ, Deshaies RJ, Hess S, Grana X
    Activation of p107 by FGF, which is essential for chondrocyte cell cycle exit, is mediated by the PP2A/B55? holoenzyme s
    MCB, 2013, 33(16):3330-42.;288(19):13420-30.
  40. Smith GT, Sweredoski MJ and Hess S
    O-linked glycosylation sites profiling in Mycobacterium tuberculosis culture filtrate proteins
    Journal of Proteomics, 2014, DOI:pii: S1874-3919(13)00252-2.
  41. Kalli A, Smith GT, Sweredoski MJ, Hess S
    Tutorial: Evaluation and Optimization of Mass Spectrometric Settings during Data-Dependent Acquisition Mode: Focus on LTQ-Orbitrap Mass Analyzers
    Journal of Prot. Res., 2013, 12(7):3071-86.
  42. Nguyen TX, Jaru-Ampornpan P, Lam VQ, Cao P, Piszkiewicz S, Hess S, Shan SO.
    Mechanism of an ATP-independent protein disaggregase. I. Structure of a membrane protein aggregate reveals a mechanism of recognition by its chaperone.
    J Biol. Chem., 2013, 288(19):13420-30.
  43. Kalli A, Sweredoski MJ, Hess S
    Data Dependent Middle-Down nano-Liquid Chromatography-Electron Capture Dissociation Tandem Mass Spectrometry: An Application for the Analysis of Unfractionated Histones
    Anal Chem., 2013,85(7), 3501-3507
  44. Pierce NW, Lee JE, Liu X, Sweredoski MJ, Graham RLJ, Lariomore EA, Rome M, Zheng N, Clurman BE, Hess S, Shan S-o, Deshaies RJ
    Cand1 Promotes Assembly of New SCF Complexes through Dynamic Exchange of F Box Proteins
    Cell, 2013, 153(1), 206-2015. Faculty 1000 recommendation.
  45. Eidahl J, Crowe BL, McKee CJ, Plumb M, Shkriabai N, Graham RLJ, North JA,. Poirier MG, Gorelick RJ, Hess S, Foster MP, Kvaratskhelia M.
    Structural basis for high affinity binding of LEDGF PWWP with mononucleosomes
    Nucleic Acids Res, 2013, 41(6), 3924-3936
  46. Malerod H., Graham RLJ, Sweredoski MJ, Hess S.
    Comprehensive profiling of N-linked glycosylation sites in HeLa cells using hydrazide enrichment
    J. Proteome Res., 2013,12(1):248-59. doi: 10.1021/pr300859k.
  47. 2012

  48. Kalli A., Hess S.
    Electron Capture Dissociation of Hydrogen Deficient Peptide Radical Cations
    JASMS, 2012, 23, 10, 1729-1740
  49. Hodas JJ, Nehring A, Höche N, Sweredoski MJ, Pielot R, Hess S, Tirrell DA, Dieterich DC, Schuman EM.
    Dopaminergic modulation of the hippocampal neuropil proteome identified by bio-orthogonal non-canonical amino-acid tagging (BONCAT)
    Proteomics, 2012, 12(15-16):2464-76
  50. Sohn CH, Agnew HD, Lee JE, Sweredoski MJ, Graham RL, Smith GT, Hess S, Czerwieniec G, Loo JA, Heath JR, Deshaies RJ, and Beauchamp JL.
    Designer Reagents for Mass Spectrometry-Based Proteomics: Clickable Cross-Linkers for Elucidation of Protein Structures and Interactions
    Anal Chem, 2012, 84(6):2662-9
  51. Haines DS, Lee JE, Beauparlant SL, Kyle DB, den Besten W, Sweredoski MJ, Graham RLJ, Hess S, Deshaies RJ.
    Protein interaction profiling of the p97 adaptor UBXD1 points to a role for the complex in modulating ERGIC-53 trafficking
    MCP, 2012, accepted, doi:10.1074/mcp.M111.016444.
  52. Sohn CH, Lee JE, Sweredoski MJ, Graham RLJ, Smith GT, Hess S, Czerwieniec G, Loo JA, Deshaies RJ, and Beauchamp JL.
    Click Chemistry Facilitates Formation of Reporter Ions and Simplified Synthesis of Amine-Reactive Multiplexed Isobaric Tags for Protein Quantification
    J Am Chem Soc, 2012, 134(5):2672-80.
  53. Kalli A, Hess, S.
    Effect of Mass Spectrometric Parameters on Peptide and Protein Identification Rates for Shotgun Proteomic Experiments on an LTQ-Orbitrap Mass Analyzer
    Proteomics, 2012, 12(1):21-31. doi:10.1002/pmic.201100464.
  54. Kalli A, Hess, S.
    Fragmentation of Singly, Doubly and Triply Charged Hydrogen Deficient Peptide Radical Cations in Infrared Multiphoton Dissociation and Electron Induced Dissociation
    JASMS, 2012, 23(2), 244-263/pmcid:pmc3221448.
  55. Bell C, Smith GT, Sweredoski MJ, Hess S.
    Characterization of the Mycobacterium tuberculosis membrane proteome by liquid chromatography mass spectrometry-based proteomics techniques: a comprehensive resource for Tuberculosis research
    J. Prot. Res., 2012, 11(1), 119-130.
  56. 2011

  57. Sweredoski MJ, Smith GT, Kalli A, Graham RLJ, Hess, S.
    LogViewer: A software tool to visualize quality control parameters to optimize proteomics experiments using Orbitrap and LTQ-FT masss spectrometers
    Journal of Biomolecular Techniques, 2011, 22(4): 122-126.
  58. Gomez TA, Kolawa N, Gee M, Sweredoski MJ, Deshaies RJ.
    Identification of a functional docking site in the Rpn1 LRR domain for the UBA-UBL domain protein Ddi1.
    BMC Biol., 2011, May 31;9:33.
  59. Zhang D, Sweredoski MJ, Graham RLJ, Hess S, Shan S.-o.
    Novel Proteomic Tools Reveal Essential Roles of SRP and Importance of Proper Membrane Protein Biogenesis
    Mol Cell Proteomics, 2011, mcp.M111.011585.
  60. Chan NC, Salazar AM, Pham AH, Sweredoski MJ, Kolawa NJ, Graham RL, Hess S, Chan DC.
    Broad Activation of the ubiquitin-proteasome system by Parkin is critical for mitophagy
    Hum Mol Genet, 2011, 20(9):1726-37. Faculty 1000 recommendation.
  61. 2010

  62. Lee JE, Sweredoski MJ, Graham RLJ, Kolawa NJ, Smith GT, Hess S, Deshaies RJ.
    The steady-state repertoire of human SCF ubiquitin ligase complexes does not require ongoing Nedd8 conjugation
    Mol Cell Proteomics, 2010, mcp.M110.006460. Faculty 1000 recommendation.
  63. Lloyd JR, Hess S.
    Peptide Fragmentation by Corona Discharge Induced Electrochemical Ionization
    JASMS, 2010, 21(12):2051-61.
  64. Raghavendra NK, Shkriabai N, Graham R, Hess S, Kvaratskhelia M, Wu L.
    Identification of host proteins associated with HIV-1 preintegration complexes isolated from infected cells
    Retrovirology, 2010, 7: 66.
  65. Matsumoto T, Hess S, Kajiyama H, Sakairi T, Saleem MA, Mathieson P, Nojima Y, Kopp JB.
    Proteomic analysis identifies insulin-like growth factor binding protein-related protein 1 as a podocyte product
    Am J Physiol - Renal Physiol, 2010, 299(4):F776-84.
  66. Huettenhain R, Hess S.
    A combined top-down and bottom-up mass spectrometry approach for the characterization of hemoglobin variants in rhesus monkeys
    Proteomics, 2010, 10(20):3657-68.
  67. Berger C, Ho JTC, Hess S, Gawrisch K and Yeliseev A.
    Preparation of stable isotope-labeled peripheral cannabinoid receptor CB2 by bacterial fermentation
    Protein Expression and Purification, 2010, 70(2): 236-47.
  68. 2009 and earlier

  69. Lloyd JR, Hess S.
    A Corona Discharge Initiated Electrochemical Electrospray Ionization Technique
    JASMS, 2009, 20: 1988-1996.
  70. Kessl JJ, Eidahl JO, Shkriabai N, Zhao Z, McKee CJ, Hess S, Burke Jr TR, Kvaratskhelia M.
    An allosteric mechanism for inhibiting HIV-1 integrase with a small molecule compound
    Pharmacol, 2009, 76: 824-832.
  71. Chen X, Hunt D, Cushman SW, Hess S.
    Proteomic Characterization of thiazolidinedione regulation of obese adipose secretome in Zucker obese rats
    Proteomics Clinical Applications, 2009, 3(9): 1099-1111.
  72. Thompson J, Jakubovics N, Abraham B, Hess S, and Pikis A.
    The sim Operon Facilitates the Transport and Metabolism of Sucrose Isomers in Lactobacillus casei ATCC 334
    J. Bacteriol. 2008, (190)9: 3362-3373 Cover.
  73. Ho JT, White JF, Grisshammer R, Hess S.
    Analysis of a G protein-coupled receptor for neurotensin by liquid chromatography-electrospray ionization-mass spectrometry
    Anal. Biochem. 2008 376(1): 13-24.
  74. Reinhardt C, von Bruehl ML, Manukyan D, Grahl L, Lorenz M, Altmann B, Dlugai S, Hess S, Konrad I, Orschiedt L, Mackman N, Ruddock L, Massberg S, Engelmann B.
    Protein Disulfide Isomerase Acts as in Injury Response Signal that Enhances Fibrin Generation Via Tissue Factor Activation
    J. Clin. Invest. 2008 (118):1110-1122.
  75. Mans J, Natarajan K, Balbo A, Schuck P, Eikel D, Hess S, Robinson H, Simic H, Jonjic S, Tiemessen CT, Margulies DH.
    Cellular expression and crystal structure of the murine cytomegalovirus MHC-Iv glycoprotein, m153
    J. Biol. Chem. 2007 (282)48:35247-35258.
  76. P. Chen, J.O. Cisar, S Hess, J TC Ho and K.P. Leung.
    Amended Description of the Genes for Synthesis of Actinomyces naeslundii T14V Type 1 Fimbriae and Associated Adhesin
    Infection and Immunity 2007 75(8):4181-5.
  77. Jérôme Deval, Claudia D'Abramo, Zhuojun Zhao, Suzanne McCormick, Dimitrios Coutsinos, Sonja Hess, Mamuka Kvaratskhelia, and Matthias Götte*.
    High Resolution Footprinting of the Hepatitis C Virus Polymerase NS5B in complex with RNA
    J Biol Chem. 2007 282(23):16907-16.
  78. Nag N, Peterson K, Wyatt K, Hess S, Ray S, Favor J, Bogani D, Lyon M, Wistow G.
    Endogenous retroviral insertion in Cryge in the mouse No3 cataract mutant
    Genomics. 2007 89(4):512-20.
  79. Grijkowski A, Austin C., Kauffman JS, Snyder J, Hess S, Lloyd JR, Beaucage SL.
    Solid-phase synthesis of thermolytic DNA oligonucleotides functionalized with a single 4-hydroxy-1-butyl or 4-phosphato-/thiophosphato-1-butyl thiophosphate protecting group
    J Org Chem. 2007 Feb 2;72(3):805-15.
  80. Alteri CJ, Hess, S, Olin GC, Giron JA, Friedman RL.
    Mycobacterium tuberculsosi Produces Pili During Human Infection, PNAS 2007,104(12):5145-50. Faculty 1000 recommendation
    selected by Editor's Choice in Science.
  81. Pikis A, Hess S, Arnold I, Erni B, Thompson J.
    Genetic Requirements for Growth of Escherichia coli K-12 on Methyl-alpha-D-glucopyranoside, and the Five alpha-D-glucosyl-D-fructose Isomers of Sucrose
    J. Biol. Chem. 2006 281(26):17900-8.
  82. Shkriabai N, Datta SAK, Zhao Z, Hess S, Rein A, Kvaratskhelia M.
    Interactions of HIV-1 Gag with Assembly Cofactors
    Biochemistry, 2006 45(13):4077-4083.
  83. Baraniuk JN, Casado B, Maibach H, Clauw DJ, Pannell LK, and Hess S.
    A Chronic Fatigue Syndrome - Related Proteome in Human Cerebrospinal Fluid
    BMC Neurology, 2005 Dec 1,5:22 Editor's choice of the year; highly accessed.
  84. Liu Y, Kvaratskhelia M, Hess S, Qu Y, Zou Y.
    Modulation of replication protein A function by its hyperphosphorylation-induced conformational change involving DNA binding domain B
    J. Biol. Chem., 2005 23;280(38):32775-83.
  85. Andrzej Grajkowski, Joao Pedras-Vasconcelos, Christina Ausin, Sonja Hess, Daniela Verthelyi, Serge L. Beaucage.
    Thermolytic CpG-containing DNA Oligonucleotides as Potential Immunotherapetic Prodrugs
    Nucleic Acid Research 2005, 33(11):3550-6.
  86. X. Chen, S.W. Cushman, L.K. Pannell, S. Hess.
    Quantitative proteomic analysis of the secretory proteins from rat adipose cells using a 2D liquid chromatography-MS/MS approach
    J. Proteome Res. 2005, 4(2):570-7.
  87. Shell SM, Hess S, Kvaratskhelia M, Zou Y.
    Mass Spectrometric Identification of Lysines Involved in the Interaction of Human Replication Protein A with Single-Stranded DNA
    Biochemistry, 2005, 44, 971-978.
  88. Williams KL, Zhang Y, Shkriabai N, Karki RG, Nicklaus MC, Kotrikadze N, Hess S, LeGrice SF, Craigie R, Pathak VK, Kvaratskhelia M.
    Mass spectrometric analysis of the HIV-1 integrase:Pyridoxal-5'-phosphate complex reveals a new binding site for a nucleotide inhibitor
    J Biol Chem. 2005, 280(9):7949-55.
  89. Kvaratskhelia M, Clark PK, Hess S, Melder DC, Federspiel MJ, Hughes SH.
    Identification of glycosylation sites in the SU component of the Avian Sarcoma/Leukosis virus Envelope Glycoprotein (Subgroup A) by mass spectrometry
    Virology 2004, 326, 171-81.
  90. Oku N, Gustafson KR, Cartner LK, Wilson JA, Shigematsu N, Hess S, Pannell LK, Boyd MR, McMahon JB.
    Neamphamide A, a new HIV-inhibitory depsipeptide from the Papua New Guinea marine sponge Neamphius huxleyi
    J. Nat. Prod. 2004, 67, 1407-11.
  91. N. Shkriabai, S.S. Patil, S. Hess, S.R. Budihas, R. Craigie, T.R. Burke Jr., S.F. LeGrice, M. Kvaratskhelia.
    Identification of an inhibitor-binding site to HIV-1 integrase with affinity acetylation and mass spectrometry
    PNAS 2004, 101, 6894-6899.
  92. J. Thompson*, S. Hess, A. Pikis.
    Genes malh and pagl of Clostridium acetobutylicum ATCC 824 encode NAD+ and Mn2+-dependent phospho-alpha-glucosidase(s)
    J. Biol. Chem. 2004, 279, 1553-1561.
  93. M. Davies-Coleman*, T. M. Dzeha, C. A. Gray, S. Hess, L.K. Pannell, D. Hendricks, C. Arendse.
    Isolation of Homodolastatin 16, a New Cyclic Despipeptide from a Kenyan Collection of Lyngbya majuscula
    J. Nat. Prod. 2003, 66, 712-715.
  94. S. Hess*, K. Gustafson, M. Lipton, L.K. Pannell.
    Chirality determination of unusual amino acids using precolumn derivatization and HPLC-ESI-MS
    J. Chromat. A 2004 1035(2):211-9.
  95. B. Schumacher, S. Scholle, J. Hölzl, N. Khudeir, S. Hess, C.E. Müller*.
    Lignans Isolated from Valerian: Identification and Characterization of a New Olivil Derivative with Partial Agonistic Activitiy at A1 Adenosine Receptors
    J. Nat. Prod. 2002, 65(10), 1479-1485.
  96. A. Hofmann*, S. Hess, A.A. Noegel, M. Schleicher, A. Wlodawer.
    Crystallization of Cyclase Associated Protein from Dictyostelium discoideum
    Acta crystallogr. D Biol. Crystallogr. 2002, D58, 1858-1861.
  97. A. Hofmann*, H. Iwai, S. Hess, A. Plueckthun, A. Wlodaver.
    Crystal structure of cyclized green fluorescent protein
    Acta crystallogr. D Biol. Crystallogr. 2002, D58, 1400-1406.
  98. J.D. van Beek* , S. Hess, F. Vollrath, B.H. Meier.
    The molecular structure of spider dragline silk: folding and orientation of the protein backbone
    Proc. Natl. Acad. Sci. USA 2002, 99(16), 10266-10271 Cover.
  99. S. Hess*, J.D. van Beek, L. K. Pannell.
    Acid hydrolysis of silk fibroins and determination of the enrichment of isotopically labeled amino acids using precolumn derivatization and HPLC-ESI-MS
    Anal. Biochemistry 2002, 311, 19-26.
  100. A. Hofmann*, S. Ruvinov, S. Hess, R. Schantz, D.P. Delmer, A. Wlodawer.
    Plant annexins form calcium-independent oligomers in solution
    Protein Science 2002, 11, 2033-2040.
  101. S. Hess*, F. Cassels, L.K. Pannell.
    Identification and characterization of hydrophobic Escherichia coli virulence proteins by liquid chromatography-electrospray ionization mass spectrometry
    Anal. Biochemistry 2002, 302, 123-130.
  102. F.J. Blanco, S. Hess, L.K. Pannell, N. Rizzo, R. Tycko*.
    Solid state NMR data support a helix-loop-helix structural model for the N-terminal half of HIV-1 Rev in fibrillar form
    J. Mol. Biol. 2001, 313(4), 845-859
  103. S. Hess*, J. Ortwein, U. Teubert and K. Eger.
    Profiling indomethacin impurities using high-performance liquid chromatography and nuclear magnetic resonance
    Eur. J. Pharm. Sci. 2001, 14 (4), 301-311.
  104. Y.-F. Li, S. Hess, L. K. Pannell, C.W. Tabor and H. Tabor*.
    In Vivo Mechansim-Based Inactivation of S-Adenosylmethionine Decarboxylases from Escherichia coli, Salmonella typhimurium, and Saccharomyces cerevisiae
    Proceed. Natl. Acad. Sci. USA 2001, 98(19), 10578-10583.
  105. S. Hess*, M. A. Akermann, S. Wnendt, K. Zwingenberger, and K. Eger.
    Synthesis and immunological activity of water-soluble thalidomide prodrugs
    Bioorg. Med. Chem. 2001, 9(5), 1279-1291.
  106. D. Eschke, A. Brand, P. Scheibler, S. Hess, K. Eger, C. Allgaier, K. Nieber*.
    Effects of a novel adenosine A1 receptor ligand on hypoxia-induced changes of membrane properties and neurotransmitter release in rat brain
    Neurochem. Int. 2001, 38, 391-398.
  107. S. Hess*, M. Dölker, D. Haferburg, H.P. Kertscher, F.-M. Matysik, J. Ortwein, U. Teubert, W. Zimmermann, K. Eger.
    Separation, analyses and syntheses of trimethoprim impurities
    Pharmazie 2001, 56(4), 306-310.
  108. S. Hess*, M. Akermann, D. Ropte, K. Eger.
    Rapid and sensitive high performance liquid chromatographic separation of new trimethoprim impurities
    J. Pharm. Biomed. Anal. 2001, 25(3-4), 531-538.
  109. S. Hess*, C. E. Müller, W. Frobenius, U. Reith, K.-N. Klotz, K. Eger.
    7-Deazaadenines bearing polar substituents: structure-activity relationships of a new A1 and A3 adenosine receptor antagonists
    J. Med. Chem. 2000, 43, 4636-4646.

Book Chapters

  1. Moradian, A., Porras-Yakushi, T. R., Sweredoski, M. J., and Hess, S.
    A Targeted MRM Approach for Tempo-Spatial Proteomics Analyses
    Methods Mol Biol, 2016,1394, 75-85
  2. Graham RLJ, Kalli A, Smith GT, Sweredoski MJ, Hess, S.
    Tips from the Bench: Avoiding Pitfalls in Proteomics Sample Preparation.
    In Biomacromolecular Mass Spectrometry2012, 4(2), 261-272.
  3. Sonja Hess.
    A universal HPLC-MS method to determine the stereochemistry of common and unusual amino acids.
    In Methods in Molecular Biology, Amino Acids Protocols 2011.
  4. Sonja Hess, Xiaoli Chen.
    Applications of proteomics to the study of adipose tissue
    In Methods in Molecular Biology, Adipose Tissue Protocols -Second Edition 2008.


  1. Sweredoski, M. J., Second, T. P., Broeker, J., Moradian, A., and Hess, S.
    High resolution data-independent acquisition with electron transfer dissociation mass spectrometry: Multiplexed analysis of post-translationally modified proteins.
    International Journal of Mass Spectrometry, 2015, 390, 155-162
  2. Moradian, A., Franco, C., Sweredoski, M. J., and Hess, S.
    Middle-down electron capture dissociation and electron transfer dissociation for histone analysis.
    Journal of Analytical Science and Technology, 2015, 6, 1-7
  3. Franco, C., and Hess, S.
    Recent proteomic advances in developmental, regeneration, and cancer governing signaling pathways.
    Proteomics, 2015, 1014-1025
  4. Porras-Yakushi, T. R., and Hess, S.
    Recent advances in defining the ubiquitylome.
    Expert Rev Proteomics, 2014, 11, 477-490
  5. Moradian A, Kalli A, Sweredoski MJ, Hess S.
    The top-down, middle-down, and bottom-up mass spectrometry approaches for characterization of histone variants and their post-translational modifications
    Proteomics, 2014, 14, 489-497
  6. Hess, S.
    Sample preparation guide for mass spectrometry-based proteomics
    Spectroscopy/Current Trends in Mass Spectrometry, 2013, 7, 12-17
  7. Kalli A, Smith GT, Sweredoski MJ, Hess, S.
    Evaluation and Optimization of Mass Spectrometric Settings during Data-Dependent Acquisition Mode: Focus on LTQ-Orbitrap Mass Analyzers
    J Prot. Res., 2013 12(7):3071-86. (Tutorial)
  8. Hess S.
    The emerging field of chemo- and pharmacoproteomics
    Proteomics . Clin Appl, 2012 2012 Nov 26. doi: 10.1002/prca.201200091.
  9. Graham RLJ, Sweredoski MJ, Hess S.
    Stable Isotope Labeling of Amino Acids in Cell Culture: An Introduction for Biologists
    Current Proteomics, 2011, 4, 1-15.
  10. Graham RLJ, Hess S.
    Mass Spectrometry in the Elucidation of the Glycoproteome of Bacterial Pathogens
    Current Proteomics, 2010, 7(1): 57-81.
  11. X. Chen, S. Hess.
    Adipose proteome analysis: the focus on mediators of insuline resistance(Invited Review)
    Exp. Rev. Proteomics, 2008, 5(6): 827-39.
  12. S. Hess*.
    Recent advances in adenosine receptor antagonist research (Invited Review), Exp. Opin. Ther. Patents
    2001, 11(10): 1533-1561.
  13. M. Weiss, S. Hess*.
    Neuroaktive Steroide: Wirkungen und Risiken (Neuroactive Steroids: Effects and Risks)
    Pharm. uns. Zeit, 2000, 6: 372-376.


    Publications where PEL provided support but was not an author:

  • Tai HC, Besche H, Goldberg AL, Schuman EM.
    Characterization of the brain 26S proteasome and its interacting proteins.
    Frontiers in Molecular Neuroscience, 2010,3(12), 1-19.
  • Chica RA, Moore MM, Allen BD, Mayo SL.
    Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries.
    Proc Natl Acad Sci U S A., 2010, 107(47), 20257-62.
  • Szychowski J, Mahdavi A, Hodas JJ, Bagert JD, Ngo JT, Landgraf P, Dieterich DC, Schuman EM, Tirrell DA.
    Cleavable Biotin Probes for Labeling of Biomolecules via Azide-Alkyne Cycloaddition.
    J Am Chem Soc., 2010, 132(51):18351-60.
  • Patents

    • Single Electrode Corona Discharge Electrochemical/Electrospray Ionization;
      issued in July 2010
    • Use of Methionine-sulfoxide reductase A and B in proteomics applications;
      filed in November 2016; currently in negotiations with Thermo Fisher for licensing.

  • Pharmacopoeia contributions
  • Conference contributions