Proteome Exploration Laboratory
Publications

This site lists all PEL publications

    2017

  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. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 2015

  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. Franco, C., and Hess, S. Recent proteomic advances in developmental, regeneration, and cancer governing signaling pathways.
    Proteomics, 2015, 1014-1025
  33. 2014

  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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.
  41. Porras-Yakushi, T. R., and Hess, S.
    Recent advances in defining the ubiquitylome.
    Expert Rev Proteomics, 2014, 11, 477-490
  42. 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
  43. 2013

  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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
  50. 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.
  51. 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
  52. 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.
  53. Hess, S.
    Sample preparation guide for mass spectrometry-based proteomics
    Spectroscopy/Current Trends in Mass Spectrometry, 2013, 7, 12-17
  54. 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)
  55. 2012

  56. Kalli A., Hess S.
    Electron Capture Dissociation of Hydrogen Deficient Peptide Radical Cations
    JASMS, 2012, 23, 10, 1729-1740
  57. 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
  58. 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
  59. 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.
  60. 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.
  61. 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.
  62. 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.
  63. 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.
  64. 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.
  65. Hess S.
    The emerging field of chemo- and pharmacoproteomics
    Proteomics . Clin Appl, 2012 2012 Nov 26. doi: 10.1002/prca.201200091.
  66. 2011

  67. 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.
  68. 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.
  69. 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.
  70. 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.
  71. 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.
  72. 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.
  73. 2010

  74. 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.
  75. Lloyd JR, Hess S.
    Peptide Fragmentation by Corona Discharge Induced Electrochemical Ionization
    JASMS, 2010, 21(12):2051-61.
  76. 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.
  77. 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.
  78. Graham RLJ, Hess S.
    Mass Spectrometry in the Elucidation of the Glycoproteome of Bacterial Pathogens
    Current Proteomics, 2010, 7(1): 57-81.
  79. 2009

  80. Lloyd JR, Hess S.
    A Corona Discharge Initiated Electrochemical Electrospray Ionization Technique
    JASMS, 2009, 20: 1988-1996.

Others

    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.