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BUD13 Promotes a Type I Interferon Response by Countering Intron Retention in Irf7.

Frankiw L, Majumdar D, Burns C, Vlach L, Moradian A, Sweredoski MJ, Baltimore D.

Mol Cell. 2018 Dec 28. pii: S1097-2765(18)31030-X. doi: 10.1016/j.molcel.2018.11.038. [Epub ahead of print]


Data-independent Acquisition for the Orbitrap Q Exactive HF. A tutorial.

Reubsaet L, Sweredoski MJ, Moradian A.

J Proteome Res. 2018 Dec 17. doi: 10.1021/acs.jproteome.8b00845. [Epub ahead of print]


Nitric Oxide Modulates Endonuclease III Redox Activity by a 800 mV Negative Shift upon [Fe4S4] Cluster Nitrosylation.

Ekanger LA, Oyala PH, Moradian A, Sweredoski MJ, Barton JK.

J Am Chem Soc. 2018 Sep 19;140(37):11800-11810. doi: 10.1021/jacs.8b07362. Epub 2018 Sep 6.


FXR1 Is an IL-19-Responsive RNA-Binding Protein that Destabilizes Pro-inflammatory Transcripts in Vascular Smooth Muscle Cells.

Herman AB, Vrakas CN, Ray M, Kelemen SE, Sweredoski MJ, Moradian A, Haines DS, Autieri MV.

Cell Rep. 2018 Jul 31;24(5):1176-1189. doi: 10.1016/j.celrep.2018.07.002.


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.

Walkup WG 4th, Sweredoski MJ, Graham RL, Hess S, Kennedy MB.

Biochem Biophys Res Commun. 2018 Sep 10;503(3):1599-1604. doi: 10.1016/j.bbrc.2018.07.087. Epub 2018 Jul 24.


Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria.

Belliveau NM, Barnes SL, Ireland WT, Jones DL, Sweredoski MJ, Moradian A, Hess S, Kinney JB, Phillips R.

Proc Natl Acad Sci U S A. 2018 May 22;115(21):E4796-E4805. doi: 10.1073/pnas.1722055115. Epub 2018 May 4.


Two distinct sites of client protein interaction with the chaperone cpSRP43.

McAvoy CZ, Siegel A, Piszkiewicz S, Miaou E, Yu M, Nguyen T, Moradian A, Sweredoski MJ, Hess S, Shan SO.

J Biol Chem. 2018 Jun 8;293(23):8861-8873. doi: 10.1074/jbc.RA118.002215. Epub 2018 Apr 18.


Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods.

Pasulka AL, Thamatrakoln K, Kopf SH, Guan Y, Poulos B, Moradian A, Sweredoski MJ, Hess S, Sullivan MB, Bidle KD, Orphan VJ.

Environ Microbiol. 2018 Feb;20(2):671-692. doi: 10.1111/1462-2920.13996. Epub 2017 Dec 14.


Composition and Regulation of the Cellular Repertoire of SCF Ubiquitin Ligases.

Reitsma JM, Liu X, Reichermeier KM, Moradian A, Sweredoski MJ, Hess S, Deshaies RJ.

Cell. 2017 Nov 30;171(6):1326-1339.e14. doi: 10.1016/j.cell.2017.10.016. Epub 2017 Nov 2.


Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms.

Babin BM, Atangcho L, van Eldijk MB, Sweredoski MJ, Moradian A, Hess S, Tolker-Nielsen T, Newman DK, Tirrell DA.

MBio. 2017 Oct 24;8(5). pii: e01593-17. doi: 10.1128/mBio.01593-17.


Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) Enables Time-Resolved Analysis of Protein Synthesis in Native Plant Tissue.

Glenn WS, Stone SE, Ho SH, Sweredoski MJ, Moradian A, Hess S, Bailey-Serres J, Tirrell DA.

Plant Physiol. 2017 Mar;173(3):1543-1553. doi: 10.1104/pp.16.01762. Epub 2017 Jan 19.


Co-evolution of Two GTPases Enables Efficient Protein Targeting in an RNA-less Chloroplast Signal Recognition Particle Pathway.

Chandrasekar S, Sweredoski MJ, Sohn CH, Hess S, Shan SO.

J Biol Chem. 2017 Jan 6;292(1):386-396. doi: 10.1074/jbc.M116.752931. Epub 2016 Nov 28.


Identification of Mechanism-Based Inactivation in P450-Catalyzed Cyclopropanation Facilitates Engineering of Improved Enzymes.

Renata H, Lewis RD, Sweredoski MJ, Moradian A, Hess S, Wang ZJ, Arnold FH.

J Am Chem Soc. 2016 Sep 28;138(38):12527-33. doi: 10.1021/jacs.6b06823. Epub 2016 Sep 14.


A conserved quality-control pathway that mediates degradation of unassembled ribosomal proteins.

Sung MK, Porras-Yakushi TR, Reitsma JM, Huber FM, Sweredoski MJ, Hoelz A, Hess S, Deshaies RJ.

Elife. 2016 Aug 23;5. pii: e19105. doi: 10.7554/eLife.19105.


Ribosomal proteins produced in excess are degraded by the ubiquitin-proteasome system.

Sung MK, Reitsma JM, Sweredoski MJ, Hess S, Deshaies RJ.

Mol Biol Cell. 2016 Sep 1;27(17):2642-52. doi: 10.1091/mbc.E16-05-0290. Epub 2016 Jul 6.


Improved 6-Plex Tandem Mass Tags Quantification Throughput Using a Linear Ion Trap-High-Energy Collision Induced Dissociation MS(3) Scan.

Liu JM, Sweredoski MJ, Hess S.

Anal Chem. 2016 Aug 2;88(15):7471-5. doi: 10.1021/acs.analchem.6b01067. Epub 2016 Jul 13.


Structural and kinetic analysis of the COP9-Signalosome activation and the cullin-RING ubiquitin ligase deneddylation cycle.

Mosadeghi R, Reichermeier KM, Winkler M, Schreiber A, Reitsma JM, Zhang Y, Stengel F, Cao J, Kim M, Sweredoski MJ, Hess S, Leitner A, Aebersold R, Peter M, Deshaies RJ, Enchev RI.

Elife. 2016 Mar 31;5. pii: e12102. doi: 10.7554/eLife.12102.


Engineered Aminoacyl-tRNA Synthetase for Cell-Selective Analysis of Mammalian Protein Synthesis.

Mahdavi A, Hamblin GD, Jindal GA, Bagert JD, Dong C, Sweredoski MJ, Hess S, Schuman EM, Tirrell DA.

J Am Chem Soc. 2016 Apr 6;138(13):4278-81. doi: 10.1021/jacs.5b08980. Epub 2016 Mar 25.


Glutamine Triggers Acetylation-Dependent Degradation of Glutamine Synthetase via the Thalidomide Receptor Cereblon.

Nguyen TV, Lee JE, Sweredoski MJ, Yang SJ, Jeon SJ, Harrison JS, Yim JH, Lee SG, Handa H, Kuhlman B, Jeong JS, Reitsma JM, Park CS, Hess S, Deshaies RJ.

Mol Cell. 2016 Mar 17;61(6):809-20. doi: 10.1016/j.molcel.2016.02.032.


Time-resolved proteomic analysis of quorum sensing in Vibrio harveyi.

Bagert JD, van Kessel JC, Sweredoski MJ, Feng L, Hess S, Bassler BL, Tirrell DA.

Chem Sci. 2016 Mar 1;7(3):1797-1806. Epub 2015 Nov 23.


SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa.

Babin BM, Bergkessel M, Sweredoski MJ, Moradian A, Hess S, Newman DK, Tirrell DA.

Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):E597-605. doi: 10.1073/pnas.1514412113. Epub 2016 Jan 19.


PYCR1 and PYCR2 Interact and Collaborate with RRM2B to Protect Cells from Overt Oxidative Stress.

Kuo ML, Lee MB, Tang M, den Besten W, Hu S, Sweredoski MJ, Hess S, Chou CM, Changou CA, Su M, Jia W, Su L, Yen Y.

Sci Rep. 2016 Jan 6;6:18846. doi: 10.1038/srep18846.


A Targeted MRM Approach for Tempo-Spatial Proteomics Analyses.

Moradian A, Porras-Yakushi TR, Sweredoski MJ, Hess S.

Methods Mol Biol. 2016;1394:75-85. doi: 10.1007/978-1-4939-3341-9_6.


A Trichomonas vaginalis Rhomboid Protease and Its Substrate Modulate Parasite Attachment and Cytolysis of Host Cells.

Riestra AM, Gandhi S, Sweredoski MJ, Moradian A, Hess S, Urban S, Johnson PJ.

PLoS Pathog. 2015 Dec 18;11(12):e1005294. doi: 10.1371/journal.ppat.1005294. eCollection 2015 Dec.


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.

Ramkumar P, Lee CM, Moradian A, Sweredoski MJ, Hess S, Sharrocks AD, Haines DS, Reddy EP.

J Biol Chem. 2015 Dec 4;290(49):29617-28. doi: 10.1074/jbc.M115.664649. Epub 2015 Oct 14.


Vectored antibody gene delivery mediates long-term contraception.

Li J, Olvera AI, Akbari OS, Moradian A, Sweredoski MJ, Hess S, Hay BA.

Curr Biol. 2015 Oct 5;25(19):R820-2. doi: 10.1016/j.cub.2015.08.002.


High resolution parallel reaction monitoring with electron transfer dissociation for middle-down proteomics.

Sweredoski MJ, Moradian A, Raedle M, Franco C, Hess S.

Anal Chem. 2015 Aug 18;87(16):8360-6. doi: 10.1021/acs.analchem.5b01542. Epub 2015 Jul 28.


ETD Outperforms CID and HCD in the Analysis of the Ubiquitylated Proteome.

Porras-Yakushi TR, Sweredoski MJ, Hess S.

J Am Soc Mass Spectrom. 2015 Sep;26(9):1580-7. doi: 10.1007/s13361-015-1168-0. Epub 2015 May 21.


The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3.

McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco M, Burghard C, Moradian A, Sweredoski MJ, Shishkin AA, Su J, Lander ES, Hess S, Plath K, Guttman M.

Nature. 2015 May 14;521(7551):232-6. doi: 10.1038/nature14443. Epub 2015 Apr 27.


Cell-specific proteomic analysis in Caenorhabditis elegans.

Yuet KP, Doma MK, Ngo JT, Sweredoski MJ, Graham RL, Moradian A, Hess S, Schuman EM, Sternberg PW, Tirrell DA.

Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2705-10. doi: 10.1073/pnas.1421567112. Epub 2015 Feb 17.


Oxidation of p53 through DNA charge transport involves a network of disulfides within the DNA-binding domain.

Schaefer KN, Geil WM, Sweredoski MJ, Moradian A, Hess S, Barton JK.

Biochemistry. 2015 Jan 27;54(3):932-41. doi: 10.1021/bi501424v. Epub 2015 Jan 13.


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.

Walkup WG 4th, Washburn L, Sweredoski MJ, Carlisle HJ, Graham RL, Hess S, Kennedy MB.

J Biol Chem. 2015 Feb 20;290(8):4908-27. doi: 10.1074/jbc.M114.614420. Epub 2014 Dec 22.


Degradation of the deubiquitinating enzyme USP33 is mediated by p97 and the ubiquitin ligase HERC2.

Chan NC, den Besten W, Sweredoski MJ, Hess S, Deshaies RJ, Chan DC.

J Biol Chem. 2014 Jul 11;289(28):19789-98. doi: 10.1074/jbc.M114.569392. Epub 2014 May 22.


Quantitative, time-resolved proteomic analysis by combining bioorthogonal noncanonical amino acid tagging and pulsed stable isotope labeling by amino acids in cell culture.

Bagert JD, Xie YJ, Sweredoski MJ, Qi Y, Hess S, Schuman EM, Tirrell DA.

Mol Cell Proteomics. 2014 May;13(5):1352-8. doi: 10.1074/mcp.M113.031914. Epub 2014 Feb 21.


F-box protein FBXL16 binds PP2A-B55α and regulates differentiation of embryonic stem cells along the FLK1+ lineage.

Honarpour N, Rose CM, Brumbaugh J, Anderson J, Graham RL, Sweredoski MJ, Hess S, Coon JJ, Deshaies RJ.

Mol Cell Proteomics. 2014 Mar;13(3):780-91. doi: 10.1074/mcp.M113.031765. Epub 2014 Jan 5.


Comprehensive proteomic profiling of outer membrane vesicles from Campylobacter jejuni.

Jang KS, Sweredoski MJ, Graham RL, Hess S, Clemons WM Jr.

J Proteomics. 2014 Feb 26;98:90-8. doi: 10.1016/j.jprot.2013.12.014. Epub 2013 Dec 29.


Identification of secreted bacterial proteins by noncanonical amino acid tagging.

Mahdavi A, Szychowski J, Ngo JT, Sweredoski MJ, Graham RL, Hess S, Schneewind O, Mazmanian SK, Tirrell DA.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):433-8. doi: 10.1073/pnas.1301740111. Epub 2013 Dec 17.


The top-down, middle-down, and bottom-up mass spectrometry approaches for characterization of histone variants and their post-translational modifications.

Moradian A, Kalli A, Sweredoski MJ, Hess S.

Proteomics. 2014 Mar;14(4-5):489-97. doi: 10.1002/pmic.201300256. Epub 2013 Dec 16. Review.


Prometastatic GPCR CD97 is a direct target of tumor suppressor microRNA-126.

Lu YY, Sweredoski MJ, Huss D, Lansford R, Hess S, Tirrell DA.

ACS Chem Biol. 2014 Feb 21;9(2):334-8. doi: 10.1021/cb400704n. Epub 2013 Nov 25.


Perturbations to the ubiquitin conjugate proteome in yeast δubx mutants identify Ubx2 as a regulator of membrane lipid composition.

Kolawa N, Sweredoski MJ, Graham RL, Oania R, Hess S, Deshaies RJ.

Mol Cell Proteomics. 2013 Oct;12(10):2791-803. doi: 10.1074/mcp.M113.030163. Epub 2013 Jun 22.


Activation of p107 by fibroblast growth factor, which is essential for chondrocyte cell cycle exit, is mediated by the protein phosphatase 2A/B55α holoenzyme.

Kurimchak A, Haines DS, Garriga J, Wu S, De Luca F, Sweredoski MJ, Deshaies RJ, Hess S, Graña X.

Mol Cell Biol. 2013 Aug;33(16):3330-42. doi: 10.1128/MCB.00082-13. Epub 2013 Jun 17.


O-linked glycosylation sites profiling in Mycobacterium tuberculosis culture filtrate proteins.

Smith GT, Sweredoski MJ, Hess S.

J Proteomics. 2014 Jan 31;97:296-306. doi: 10.1016/j.jprot.2013.05.011. Epub 2013 May 20.


Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: focus on LTQ-Orbitrap mass analyzers.

Kalli A, Smith GT, Sweredoski MJ, Hess S.

J Proteome Res. 2013 Jul 5;12(7):3071-86. doi: 10.1021/pr3011588. Epub 2013 May 31.


Cand1 promotes assembly of new SCF complexes through dynamic exchange of F box proteins.

Pierce NW, Lee JE, Liu X, Sweredoski MJ, Graham RL, Larimore EA, Rome M, Zheng N, Clurman BE, Hess S, Shan SO, Deshaies RJ.

Cell. 2013 Mar 28;153(1):206-15. doi: 10.1016/j.cell.2013.02.024. Epub 2013 Feb 28.


Data-dependent middle-down nano-liquid chromatography-electron capture dissociation-tandem mass spectrometry: an application for the analysis of unfractionated histones.

Kalli A, Sweredoski MJ, Hess S.

Anal Chem. 2013 Apr 2;85(7):3501-7. doi: 10.1021/ac303103b. Epub 2013 Mar 12.


Comprehensive profiling of N-linked glycosylation sites in HeLa cells using hydrazide enrichment.

Malerod H, Graham RL, Sweredoski MJ, Hess S.

J Proteome Res. 2013 Jan 4;12(1):248-59. doi: 10.1021/pr300859k. Epub 2012 Dec 4.


Dopaminergic modulation of the hippocampal neuropil proteome identified by bioorthogonal noncanonical amino acid tagging (BONCAT).

Hodas JJ, Nehring A, Höche N, Sweredoski MJ, Pielot R, Hess S, Tirrell DA, Dieterich DC, Schuman EM.

Proteomics. 2012 Aug;12(15-16):2464-76. doi: 10.1002/pmic.201200112.


Designer reagents for mass spectrometry-based proteomics: clickable cross-linkers for elucidation of protein structures and interactions.

Sohn CH, Agnew HD, Lee JE, Sweredoski MJ, Graham RL, Smith GT, Hess S, Czerwieniec G, Loo JA, Heath JR, Deshaies RJ, Beauchamp JL.

Anal Chem. 2012 Mar 20;84(6):2662-9. doi: 10.1021/ac202637n. Epub 2012 Mar 5.


Protein interaction profiling of the p97 adaptor UBXD1 points to a role for the complex in modulating ERGIC-53 trafficking.

Haines DS, Lee JE, Beauparlant SL, Kyle DB, den Besten W, Sweredoski MJ, Graham RL, Hess S, Deshaies RJ.

Mol Cell Proteomics. 2012 Jun;11(6):M111.016444. doi: 10.1074/mcp.M111.016444. Epub 2012 Feb 14.

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