skip to main content
Home  /  Publications



Gu, L; Li, M; Li, C M; Haratipour, P; Lingeman, R; Jossart, J; Gutova, M; Flores, L; Hyde, C; Kenjić, N; Li, H; Chung, V; Li, H; Lomenick, B; Von Hoff, D D; Synold, T W; Aboody, K S; Liu, Y; Horne, D; Hickey, R J; Perry, J J P; Malkas, L H. Small Molecule Targeting of Transcription-Replication Conflict for Selective Chemotherapy. Cell Chemical Biology 2023, 30, 1–13Jones, J., MacKrell, E. J., Wang, T.-Y., Lomenick, B., Roukes, M. L., & Chou, T.-F. Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization. BMC Bioinformatics 2023, 24(1), 239.Tan CH, Cheng KW, Park H, Sternberg PW, Chou TF. LINKIN-associated proteins necessary for tissue integrity during collective cell migration.
bioRxiv [Preprint].
2023 Feb 9:2023.02.08.527750. doi: 10.1101/2023.02.08.527750.
Wang GZ, Warren EA, Haas AL, Peña AS, Kiedrowski MR, Lomenick B, Chou TF, Bomberger JM, Tirrell DA, Limoli DH. Staphylococcal secreted cytotoxins are competition sensing signals for Pseudomonas aeruginosa.
bioRxiv [Preprint]
. 2023 Jan 29:2023.01.29.526047. doi: 10.1101/2023.01.29.526047.
Iijima, H., Gilmer, G., Wang, K., Bean, A. C., He, Y., Lin, H., Tang, W.-Y., Lamont, D., Tai, C., Ito, A., Jones, J. J., Evans, C., & Ambrosio, F. Age-related matrix stiffening epigenetically regulates α-Klotho expression and compromises chondrocyte integrity. Nature Communications 2023, 14(1), 18.


Guna A, Stevens TA, Inglis AJ, Replogle JM, Esantsi TK, Muthukumar G, Shaffer KCL, Wang ML, Pogson AN, Jones JJ, Lomenick B, Chou TF, Weissman JS, Voorhees RM. MTCH2 is a mitochondrial outer membrane protein insertase.
2022 Oct 21;378(6617):317-322. doi: 10.1126/science.add1856.
Spero MA, Jones J, Lomenick B, Chou TF, Newman DK. Mechanisms of chlorate toxicity and resistance in Pseudomonas aeruginosa.
Mol Microbiol.
2022 Oct;118(4):321-335. doi: 10.1111/mmi.14972.
Yang CI, Zhu Z, Jones JJ, Lomenick B, Chou TF, Shan SO. System-wide analyses reveal essential roles of N-terminal protein modification in bacterial membrane integrity.
2022 Jul 15;25(8):104756. doi: 10.1016/j.isci.2022.104756.
Ravanfar R, Sheng Y, Shahgholi M, Lomenick B, Jones J, Chou TF, Gray HB, Winkler JR. Surface cysteines could protect the SARS-CoV-2 main protease from oxidative damage.
J Inorg Biochem.
2022, 234:111886.

Wang F, Li S, Houerbi N, Chou TF. Temporal proteomics reveal specific cell cycle oncoprotein downregulation by p97/VCP inhibition.
Cell Chem. Biol
2022, 29(3), 1-13.

Puskar R, Du Truong C, Swain K, Chowdhury S, Chan KY, Li S, Cheng KW, Wang TY, Poh YP, Mazor Y, Liu H, Chou TF, Nannenga BL, Chiu PL. Molecular asymmetry of a photosynthetic supercomplex from green sulfur bacteria.
Nat Commun,
2022, 13(1):5824.

Wang F, Li S, Wang TY, Lopez GA, Antoshechkin I, Chou TF. P97/VCP ATPase inhibitors can rescue p97 mutation-linked motor neuron degeneration.
Brain Commun
. 2022, 4(4):fcac176.

Li S, Wang F, Zhang G, Chou TF. NMS-873 leads to Dysfunctional glycometabolism in a p97-Independent manner in HCT116 colon cancer cells.
. 2022, 14(4):764.

Wang F, Li S, Rosencrans WM, Cheng KW, Stott GM, Mroczkowski B, Chou TF. Sulforaphane is synergistic with CB-5083 and inhibits colony formation of CB-5083-resistant HCT116 cells.
. 2022, 17(11):e202200030.

Wang F, Li S, Cheng KW, Rosencrans WM, Chou TF. The p97 Inhibitor UPCDC-30245 Blocks Endo-Lysosomal Degradation.
Pharmaceuticals (Basel)
. 2022, 7;15(2):204.


Cheng YS, Zhang T, Ma X, Pratuangtham S, Zhang GC, Ondrus, AA, Mafi A, Lomenick B, Jones JJ, Ondrus AE. A proteome-wide map of 20(S)-hydroxycholesterol interactors in cell membranes
Nat Chem Biol 2021 17, 1271–1280.
Cheng KW, Li S, Wang F, Ruiz-Lopez NM, Houerbi N, Chou TF. Impacts of p97 on Proteome Changes in Human Cells during Coronaviral Replication
2021, 10(11), 2953.
Michels DE, Lomenick B, Chou TF, Sweredoski MJ, Pasulka A. Amino Acid Analog Induces Stress Response in Marine Synechococcus
Appl Environ Microbiol.
2021 July 13;87(15):e00200-21.
Zhang G, Li S, Wang F, Jones AC, Goldberg AFG, Lin B, Virgil S, Stoltz BM, Deshaies RJ, Chou TF. A Covalent p97/VCP ATPase Inhibitor can overcome resistance to CB-5083 and NMS-873 in colorectal cancer cells
Eur J Med Chem.
2021 March 5;213:113148.
Wang R, Mishra P, Garbis SD, Moradian A, Sweredoski MJ, Chan DC. Identification of new OPA1 cleavage site reveals that short isoforms regulate mitochondrial fusion
Mol Biol Cell.
2021 Jan 15;32:157-168.
Shin CS, Meng S, Garbis SD, Moradian A, Taylor RW, Sweredoski MJ, Lomenick B, Chan DC. LONP1 and mtHSP70 cooperate to promote mitochondrial protein folding
Nat Commun.
2021 Jan 11;12(1):265.
Wang F, Moen DR, Sauni C, Kan SH, Li S, Le SQ, Lomenick B, Zhang X, Ekins S, Singamsetty S, Wood J, Dickson PI, Chou TF. Enzyme Replacement Therapy for Mucopolysaccharidosis IIID using Recombinant Human α-N-Acetylglucosamine-6-Sulfatase in Neonatal Mice
Mol Pharm.
2021 Jan 4;18(1):214-227.


Ireland WT, Beeler SM, Flores-Bautista E, McCarty NS, Röschinger T, Belliveau NM, Sweredoski MJ, Moradian A, Kinney JB, Phillips R. Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time
2020, 9:e55308.
Dopie J, Sweredoski MJ, Moradian A, Belmont AS. Tyramide signal amplification mass spectrometry (TSA-MS) ratio identifies nuclear speckle proteins
J Cell Biol.
2020, 219(9):e201910207.
Morianos I, Trochoutsou AI, Papadopoulou G, Semitekolou M, Banos A, Konstantopoulos D, Manousopoulou A, Kapasa M, Wei P, Lomenick B, Belaidi E, Kalamatas T, Karageorgiou K, Doskas T, Sallusto F, Pan F, Garbis SD, Quintana FJ, Xanthou G.. Activin-A limits Th17 pathogenicity and autoimmune neuroinflammation via CD39 and CD73 ectonucleotidases and Hif1-α-dependent pathways
Proc Natl Acad Sci U S A.
2020, 117(22):12269-12280.
Kaplan M, Sweredoski MJ, Rodrigues JPGLM, Tocheva EI, Chang YW, Ortega DR, Beeby M, Jensen GJ. Bacterial flagellar motor PL-ring disassembly subcomplexes are widespread and ancient
Proc Natl Acad Sci U S A.
2020, 117(16):8941-8947.
Neubauer C, Crémière A, Wang XT, Thiagarajan N, Sessions AL, Adkins JF, Dalleska NF, Turchyn AV, Clegg JA, Moradian A, Sweredoski MJ, Garbis SD, Eiler JM. Stable Isotope Analysis of Intact Oxyanions Using Electrospray Quadrupole-Orbitrap Mass Spectrometry
Anal Chem.
2020, 92(4):3077-3085.
Reichermeier KM, Straube R, Reitsma JM, Sweredoski MJ, Rose CM, Moradian A, den Besten W, Hinkle T, Verschueren E, Petzold G, Thomä NH, Wertz IE, Deshaies RJ, Kirkpatrick DS. PIKES Analysis Reveals Response to Degraders and Key Regulatory Mechanisms of the CRL4 Network
Mol Cell.
2020, 77(5):1092-1106.


Hill S, Reichermeier K, Scott DC, Samentar L, Coulombe-Huntington J, Izzi L, Tang X, Ibarra R, Bertomeu T, Moradian A, Sweredoski MJ, Caberoy N, Schulman BA, Sicheri F, Tyers M, Kleiger G. Robust cullin-RING ligase function is established by a multiplicity of poly-ubiquitylation pathways
2019, 8:e51163.
Varuzhanyan G, Rojansky R, Sweredoski MJ, Graham RL, Hess S, Ladinsky MS, Chan DC. Mitochondrial fusion is required for spermatogonial differentiation and meiosis
2019, 8:e51601.
Reubsaet L, Sweredoski MJ, Moradian A, Lomenick B, Eggleston-Rangel R, Garbis SD. Nano volume fractionation strategy for dilute-and-shoot injections in off-line loss-less proteomic workflows for extensive protein identifications of ultra-low sample amounts
J Chromatogr A.
2020, 1609:460507.
Bergkessel M, Babin BM, VanderVelde D, Sweredoski MJ, Moradian A, Eggleston-Rangel R, Hess S, Tirrell DA, Artsimovitch I, Newman DK. The dormancy‐specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa
Mol Microbiol.
2019, 112(3):992-1009.
Sharon G, Cruz NJ, Kang DW, Gandal MJ, Wang B, Kim YM, Zink EM, Casey CP, Taylor BC, Lane CJ, Bramer LM, Isern NG, Hoyt DW, Noecker C, Sweredoski MJ, Moradian A, Borenstein E, Jansson JK, Knight R, Metz TO, Lois C, Geschwind DH, Krajmalnik-Brown R, Mazmanian SK. Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice
2019, 177(6):1600-1618.
Frankiw L, Majumdar D, Burns C, Vlach L, Moradian A, Sweredoski MJ, Baltimore D. BUD13 Promotes a Type I Interferon Response by Countering Intron Retention in Irf7
Mol Cell.
2019, 73(4):803-814.e6.


Reubsaet L, Sweredoski MJ, Moradian A. Data-Independent Acquisition for the Orbitrap Q Exactive HF: A Tutorial
J Proteome Res.
2019, 18(3):803-813.
Ekanger LA, Oyala PH, Moradian A, Sweredoski MJ, Barton JK. Nitric Oxide Modulates Endonuclease III Redox Activity by a 800 mV Negative Shift upon [Fe 4 S 4] Cluster Nitrosylation
J Am Chem Soc.
2018, 140(37):11800-11810.
Herman AB, Vrakas CN, Ray M, Kelemen SE, Sweredoski MJ, Moradian A, Haines DS, Autieri MV. FXR1 Is an IL-19-Responsive RNA-Binding Protein that Destabilizes Pro-inflammatory Transcripts in Vascular Smooth Muscle Cells
Cell Rep.
2018, 24(5):1176-1189.
Walkup WG 4th, Sweredoski MJ, Graham RL, Hess S, Kennedy MB. Phosphorylation of synaptic GTPase-activating protein (synGAP) by polo-like kinase (Plk2) alters the ratio of its GAP activity toward HRas, Rap1 and Rap2 GTPases
Biochem Biophys Res Commun
. 2018, 503(3):1599-1604.
Belliveau, N. M., Barnes, S. L., Ireland, W. T., Jones, D. L., Sweredoski, M. J., Moradian, A., Hess, S., Kinney, J. B., Phillips, R. Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria
Proc Natl Acad Sci U S A.
2018, 115(21):E4796-E4805.
McAvoy, C., Siegel, A., Piszkiewicz, S., Miaou, E., Yu, M., Nguyen, T., Moradian, A., Sweredoski, M. J., Hess, S., Shan, S. O. Two Distinct Sites of client protein interaction with the chaperone cpSRP43
J Biol Chem.
2018, 293(23):8861-8873.
Pasulka, A. L., Thamatrakoln, K., Kopf, S. H., Guan, Y., Poulos B., Moradian, A., Sweredoski, M. J., Hess, S., Sullivan, M. B., Bidle, K. D., Orphan, V. J. Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods
Environmental microbiology
, 2018, 20, 671-692.


Reitsma, J. M., Liu, X., Reichermeier, K. M., Moradian, A., Sweredoski, M. J., Hess, S., Deshaies, R. J. Composition and regulation of the cellular repertoire of SCF ubiquitin ligases
Cell, 2017, 171, 6, 1326-1339.
Li, J., Yakushi, T., Parlati, F., Mackinnon, A.L., Perez, C., Ma, Y., Carter, K. P., Colayco, S., Magnuson, G., Brown, B., Nguyen, K., Vasile, S., Suyama, E., Smith, L. H., Sergienko, E., Pinkerton, A. B., Chung, T. D. Y., Palmer, A. E., Pass, I., Hess, S., Cohen, S. M., Deshaies R. J. Capzimin is a potent and specific inhibitor of proteasome isopeptidase Rpn11
Nat. Chem. Bio., 2017, 13, 5, 486-493
Babin, B. M., Atangcho, L., van Eldijk, M. B., Sweredoski, M. J., Moradian, A., Hess, S., Tolker-Nielsen, T., Newman, D. K., Tirrell D. A. Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms
mBio, 2017, 8, 5, e01593-17.
Glenn, W. S., Stone, S. E., Ho, S. H., Sweredoski, M. J., Moradian, A., Hess, S., Bailey-Serres, J., Tirrell, D. A. Bioorthogonal noncanonical amino acid tagging (BONCAT) enables time-resolved analysis of protein synthesis in native plant tissue
Plant physiology, 2017, 173, 3, 1543-1553.
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, 292, 386-396.


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.
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 .
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.
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.
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
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
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
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
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
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
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
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
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
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


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
Walkup, W. G. IV, 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
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
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
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
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
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
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
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
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
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
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
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
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
Franco, C., and Hess, S. Recent proteomic advances in developmental, regeneration, and cancer governing signaling pathways.
Proteomics, 2015, 1014-1025


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
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
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
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
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
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
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.
Porras-Yakushi, T. R., and Hess, S.
Recent advances in defining the ubiquitylome.
Expert Rev Proteomics, 2014, 11, 477-490
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


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.
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/B55a holoenzyme
MCB, 2013, 33(16):3330-42.;288(19):13420-30.
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.
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.
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.
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
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.
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
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.
Hess, S.
Sample preparation guide for mass spectrometry-based proteomics
Spectroscopy/Current Trends in Mass Spectrometry, 2013, 7, 12-17
Kalli A, Smith GT, Sweredoski MJ, Hess, S.


Kalli A., Hess S.
Electron Capture Dissociation of Hydrogen Deficient Peptide Radical Cations
JASMS, 2012, 23, 10, 1729-1740
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
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
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.
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.
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.
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.
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.
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.
Hess S.
The emerging field of chemo- and pharmacoproteomics
Proteomics . Clin Appl, 2012 2012 Nov 26. doi: 10.1002/prca.201200091.


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.
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.
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.
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.
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.
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.


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


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


Publications where PEL provided support but was not an author:

Weaver SJ, Ortega DR, Sazinsky MH, Dalia TN, Dalia AB, Jensen GJ.
CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae.
Nat Commun. 2020, Oct 8;11(1):5080.
Joffrin AM, Hsieh-Wilson LC.
Photoaffinity Probes for the Identification of Sequence-Specific Glycosaminoglycan-Binding Proteins
J. Am. Chem. Soc. 2020, 142, 32, 13672–13676
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.


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