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A Mutation in Histone H2B Represents a New Class of Oncogenic Driver.

Bennett RL, Bele A, Small EC, Will CM, Nabet B, Oyer JA, Huang X, Ghosh RP, Grzybowski AT, Yu T, Zhang Q, Riva A, Lele TP, Schatz GC, Kelleher NL, Ruthenburg AJ, Liphardt J, Licht JD.

Cancer Discov. 2019 Jul 23. pii: CD-19-0393. doi: 10.1158/2159-8290.CD-19-0393. [Epub ahead of print]


Coupling Fluorescence-Activated Cell Sorting and Targeted Analysis of Histone Modification Profiles in Primary Human Leukocytes.

Camarillo JM, Swaminathan S, Abshiru NA, Sikora JW, Thomas PM, Kelleher NL.

J Am Soc Mass Spectrom. 2019 Jul 8. doi: 10.1007/s13361-019-02255-x. [Epub ahead of print]


Mechanism of Inactivation of Ornithine Aminotransferase by (1S,3S)-3-Amino-4-(hexafluoropropan-2-ylidenyl)cyclopentane-1-carboxylic Acid.

Moschitto MJ, Doubleday PF, Catlin DS, Kelleher NL, Liu D, Silverman RB.

J Am Chem Soc. 2019 Jul 10;141(27):10711-10721. doi: 10.1021/jacs.9b03254. Epub 2019 Jun 28.


Best practices and benchmarks for intact protein analysis for top-down mass spectrometry.

Donnelly DP, Rawlins CM, DeHart CJ, Fornelli L, Schachner LF, Lin Z, Lippens JL, Aluri KC, Sarin R, Chen B, Lantz C, Jung W, Johnson KR, Koller A, Wolff JJ, Campuzano IDG, Auclair JR, Ivanov AR, Whitelegge JP, Paša-Tolić L, Chamot-Rooke J, Danis PO, Smith LM, Tsybin YO, Loo JA, Ge Y, Kelleher NL, Agar JN.

Nat Methods. 2019 Jul;16(7):587-594. doi: 10.1038/s41592-019-0457-0. Epub 2019 Jun 27. Review.


Defining the NSD2 interactome: PARP1 PARylation reduces NSD2 histone methyltransferase activity and impedes chromatin binding.

Huang X, LeDuc RD, Fornelli L, Schunter AJ, Bennett RL, Kelleher NL, Licht JD.

J Biol Chem. 2019 Aug 16;294(33):12459-12471. doi: 10.1074/jbc.RA118.006159. Epub 2019 Jun 27.


Native top-down mass spectrometry provides insights into the copper centers of membrane-bound methane monooxygenase.

Ro SY, Schachner LF, Koo CW, Purohit R, Remis JP, Kenney GE, Liauw BW, Thomas PM, Patrie SM, Kelleher NL, Rosenzweig AC.

Nat Commun. 2019 Jun 17;10(1):2675. doi: 10.1038/s41467-019-10590-6.


Identification and Quantification of Proteoforms by Mass Spectrometry.

Schaffer LV, Millikin RJ, Miller RM, Anderson LC, Fellers RT, Ge Y, Kelleher NL, LeDuc RD, Liu X, Payne SH, Sun L, Thomas PM, Tucholski T, Wang Z, Wu S, Wu Z, Yu D, Shortreed MR, Smith LM.

Proteomics. 2019 May;19(10):e1800361. doi: 10.1002/pmic.201800361. Review.


Precision Targeting with EZH2 and HDAC Inhibitors in Epigenetically Dysregulated Lymphomas.

Lue JK, Prabhu SA, Liu Y, Gonzalez Y, Verma A, Mundi PS, Abshiru N, Camarillo JM, Mehta S, Chen EI, Qiao C, Nandakumar R, Cremers S, Kelleher NL, Elemento O, Amengual JE.

Clin Cancer Res. 2019 Apr 12. doi: 10.1158/1078-0432.CCR-18-3989. [Epub ahead of print]


Standard Proteoforms and Their Complexes for Native Mass Spectrometry.

Schachner LF, Ives AN, McGee JP, Melani RD, Kafader JO, Compton PD, Patrie SM, Kelleher NL.

J Am Soc Mass Spectrom. 2019 Jul;30(7):1190-1198. doi: 10.1007/s13361-019-02191-w. Epub 2019 Apr 8.


Accurate Estimation of Context-Dependent False Discovery Rates in Top-Down Proteomics.

LeDuc RD, Fellers RT, Early BP, Greer JB, Shams DP, Thomas PM, Kelleher NL.

Mol Cell Proteomics. 2019 Apr;18(4):796-805. doi: 10.1074/mcp.RA118.000993. Epub 2019 Jan 15.


Measurement of Individual Ions Sharply Increases the Resolution of Orbitrap Mass Spectra of Proteins.

Kafader JO, Melani RD, Senko MW, Makarov AA, Kelleher NL, Compton PD.

Anal Chem. 2019 Feb 19;91(4):2776-2783. doi: 10.1021/acs.analchem.8b04519. Epub 2019 Jan 29.


A novel crosslinking protocol stabilizes amyloid β oligomers capable of inducing Alzheimer's-associated pathologies.

Cline EN, Das A, Bicca MA, Mohammad SN, Schachner LF, Kamel JM, DiNunno N, Weng A, Paschall JD, Bu RL, Khan FM, Rollins MG, Ives AN, Shekhawat G, Nunes-Tavares N, de Mello FG, Compton PD, Kelleher NL, Klein WL.

J Neurochem. 2019 Mar;148(6):822-836. doi: 10.1111/jnc.14647. Epub 2019 Jan 29.


A comprehensive pipeline for translational top-down proteomics from a single blood draw.

Toby TK, Fornelli L, Srzentić K, DeHart CJ, Levitsky J, Friedewald J, Kelleher NL.

Nat Protoc. 2019 Jan;14(1):119-152. doi: 10.1038/s41596-018-0085-7.


Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria.

Fisher OS, Kenney GE, Ross MO, Ro SY, Lemma BE, Batelu S, Thomas PM, Sosnowski VC, DeHart CJ, Kelleher NL, Stemmler TL, Hoffman BM, Rosenzweig AC.

Nat Commun. 2018 Oct 15;9(1):4276. doi: 10.1038/s41467-018-06681-5.


USP7 Cooperates with NOTCH1 to Drive the Oncogenic Transcriptional Program in T-Cell Leukemia.

Jin Q, Martinez CA, Arcipowski KM, Zhu Y, Gutierrez-Diaz BT, Wang KK, Johnson MR, Volk AG, Wang F, Wu J, Grove C, Wang H, Sokirniy I, Thomas PM, Goo YA, Abshiru NA, Hijiya N, Peirs S, Vandamme N, Berx G, Goosens S, Marshall SA, Rendleman EJ, Takahashi YH, Wang L, Rawat R, Bartom ET, Collings CK, Van Vlierberghe P, Strikoudis A, Kelly S, Ueberheide B, Mantis C, Kandela I, Bourquin JP, Bornhauser B, Serafin V, Bresolin S, Paganin M, Accordi B, Basso G, Kelleher NL, Weinstock J, Kumar S, Crispino JD, Shilatifard A, Ntziachristos P.

Clin Cancer Res. 2019 Jan 1;25(1):222-239. doi: 10.1158/1078-0432.CCR-18-1740. Epub 2018 Sep 17.


Stability of histone post-translational modifications in samples derived from liver tissue and primary hepatic cells.

Gruppuso PA, Boylan JM, Zabala V, Neretti N, Abshiru NA, Sikora JW, Doud EH, Camarillo JM, Thomas PM, Kelleher NL, Sanders JA.

PLoS One. 2018 Sep 7;13(9):e0203351. doi: 10.1371/journal.pone.0203351. eCollection 2018.


An activating mutation of the NSD2 histone methyltransferase drives oncogenic reprogramming in acute lymphocytic leukemia.

Swaroop A, Oyer JA, Will CM, Huang X, Yu W, Troche C, Bulic M, Durham BH, Wen QJ, Crispino JD, MacKerell AD Jr, Bennett RL, Kelleher NL, Licht JD.

Oncogene. 2019 Jan;38(5):671-686. doi: 10.1038/s41388-018-0474-y. Epub 2018 Aug 31.


Estimating the Distribution of Protein Post-Translational Modification States by Mass Spectrometry.

Compton PD, Kelleher NL, Gunawardena J.

J Proteome Res. 2018 Aug 3;17(8):2727-2734. doi: 10.1021/acs.jproteome.8b00150. Epub 2018 Jul 10.


The Value of Activated Ion Electron Transfer Dissociation for High-Throughput Top-Down Characterization of Intact Proteins.

Riley NM, Sikora JW, Seckler HS, Greer JB, Fellers RT, LeDuc RD, Westphall MS, Thomas PM, Kelleher NL, Coon JJ.

Anal Chem. 2018 Jul 17;90(14):8553-8560. doi: 10.1021/acs.analchem.8b01638. Epub 2018 Jul 5.


Natural products from thioester reductase containing biosynthetic pathways.

Mullowney MW, McClure RA, Robey MT, Kelleher NL, Thomson RJ.

Nat Prod Rep. 2018 Sep 19;35(9):847-878. doi: 10.1039/c8np00013a. Review.


Accurate Sequence Analysis of a Monoclonal Antibody by Top-Down and Middle-Down Orbitrap Mass Spectrometry Applying Multiple Ion Activation Techniques.

Fornelli L, Srzentić K, Huguet R, Mullen C, Sharma S, Zabrouskov V, Fellers RT, Durbin KR, Compton PD, Kelleher NL.

Anal Chem. 2018 Jul 17;90(14):8421-8429. doi: 10.1021/acs.analchem.8b00984. Epub 2018 Jun 28.


The unique biomineralization transcriptome and proteome of Lytechinus variegatus teeth.

Alvares K, DeHart CJ, Thomas PM, Kelleher NL, Veis A.

Connect Tissue Res. 2018 Dec;59(sup1):20-29. doi: 10.1080/03008207.2017.1408605.


Repurposed HisC Aminotransferases Complete the Biosynthesis of Some Methanobactins.

Park YJ, Kenney GE, Schachner LF, Kelleher NL, Rosenzweig AC.

Biochemistry. 2018 Jun 26;57(25):3515-3523. doi: 10.1021/acs.biochem.8b00296. Epub 2018 May 10.


β-Glucocerebrosidase Modulators Promote Dimerization of β-Glucocerebrosidase and Reveal an Allosteric Binding Site.

Zheng J, Chen L, Skinner OS, Ysselstein D, Remis J, Lansbury P, Skerlj R, Mrosek M, Heunisch U, Krapp S, Charrow J, Schwake M, Kelleher NL, Silverman RB, Krainc D.

J Am Chem Soc. 2018 May 9;140(18):5914-5924. doi: 10.1021/jacs.7b13003. Epub 2018 Apr 30.


A Targeted, Differential Top-Down Proteomic Methodology for Comparison of ApoA-I Proteoforms in Individuals with High and Low HDL Efflux Capacity.

Seckler HDS, Fornelli L, Mutharasan RK, Thaxton CS, Fellers R, Daviglus M, Sniderman A, Rader D, Kelleher NL, Lloyd-Jones DM, Compton PD, Wilkins JT.

J Proteome Res. 2018 Jun 1;17(6):2156-2164. doi: 10.1021/acs.jproteome.8b00100. Epub 2018 Apr 27.


Identification of the First Diketomorpholine Biosynthetic Pathway Using FAC-MS Technology.

Robey MT, Ye R, Bok JW, Clevenger KD, Islam MN, Chen C, Gupta R, Swyers M, Wu E, Gao P, Thomas PM, Wu CC, Keller NP, Kelleher NL.

ACS Chem Biol. 2018 May 18;13(5):1142-1147. doi: 10.1021/acschembio.8b00024. Epub 2018 Apr 17.


Precise characterization of KRAS4b proteoforms in human colorectal cells and tumors reveals mutation/modification cross-talk.

Ntai I, Fornelli L, DeHart CJ, Hutton JE, Doubleday PF, LeDuc RD, van Nispen AJ, Fellers RT, Whiteley G, Boja ES, Rodriguez H, Kelleher NL.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4140-4145. doi: 10.1073/pnas.1716122115. Epub 2018 Apr 2.


Proteoforms as the next proteomics currency.

Smith LM, Kelleher NL.

Science. 2018 Mar 9;359(6380):1106-1107. doi: 10.1126/science.aat1884. Epub 2018 Mar 8. No abstract available.


Total Synthesis of Tambromycin Enabled by Indole C-H Functionalization.

Miley GP, Rote JC, Silverman RB, Kelleher NL, Thomson RJ.

Org Lett. 2018 Apr 20;20(8):2369-2373. doi: 10.1021/acs.orglett.8b00700. Epub 2018 Mar 27.


Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids.

Martin RW, Des Soye BJ, Kwon YC, Kay J, Davis RG, Thomas PM, Majewska NI, Chen CX, Marcum RD, Weiss MG, Stoddart AE, Amiram M, Ranji Charna AK, Patel JR, Isaacs FJ, Kelleher NL, Hong SH, Jewett MC.

Nat Commun. 2018 Mar 23;9(1):1203. doi: 10.1038/s41467-018-03469-5.


The biosynthesis of methanobactin.

Kenney GE, Dassama LMK, Pandelia ME, Gizzi AS, Martinie RJ, Gao P, DeHart CJ, Schachner LF, Skinner OS, Ro SY, Zhu X, Sadek M, Thomas PM, Almo SC, Bollinger JM Jr, Krebs C, Kelleher NL, Rosenzweig AC.

Science. 2018 Mar 23;359(6382):1411-1416. doi: 10.1126/science.aap9437.


Interrogation of Benzomalvin Biosynthesis Using Fungal Artificial Chromosomes with Metabolomic Scoring (FAC-MS): Discovery of a Benzodiazepine Synthase Activity.

Clevenger KD, Ye R, Bok JW, Thomas PM, Islam MN, Miley GP, Robey MT, Chen C, Yang K, Swyers M, Wu E, Gao P, Wu CC, Keller NP, Kelleher NL.

Biochemistry. 2018 Jun 12;57(23):3237-3243. doi: 10.1021/acs.biochem.8b00076. Epub 2018 Mar 20.


Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics.

Parkinson EI, Tryon JH, Goering AW, Ju KS, McClure RA, Kemball JD, Zhukovsky S, Labeda DP, Thomson RJ, Kelleher NL, Metcalf WW.

ACS Chem Biol. 2018 Apr 20;13(4):1029-1037. doi: 10.1021/acschembio.7b01089. Epub 2018 Mar 13.


Top-Down Proteomics Enables Comparative Analysis of Brain Proteoforms Between Mouse Strains.

Davis RG, Park HM, Kim K, Greer JB, Fellers RT, LeDuc RD, Romanova EV, Rubakhin SS, Zombeck JA, Wu C, Yau PM, Gao P, van Nispen AJ, Patrie SM, Thomas PM, Sweedler JV, Rhodes JS, Kelleher NL.

Anal Chem. 2018 Mar 20;90(6):3802-3810. doi: 10.1021/acs.analchem.7b04108. Epub 2018 Feb 26.


How many human proteoforms are there?

Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B.

Nat Chem Biol. 2018 Feb 14;14(3):206-214. doi: 10.1038/nchembio.2576.


ProForma: A Standard Proteoform Notation.

LeDuc RD, Schwämmle V, Shortreed MR, Cesnik AJ, Solntsev SK, Shaw JB, Martin MJ, Vizcaino JA, Alpi E, Danis P, Kelleher NL, Smith LM, Ge Y, Agar JN, Chamot-Rooke J, Loo JA, Pasa-Tolic L, Tsybin YO.

J Proteome Res. 2018 Mar 2;17(3):1321-1325. doi: 10.1021/acs.jproteome.7b00851. Epub 2018 Feb 14.


Mutant-IDH1-dependent chromatin state reprogramming, reversibility, and persistence.

Turcan S, Makarov V, Taranda J, Wang Y, Fabius AWM, Wu W, Zheng Y, El-Amine N, Haddock S, Nanjangud G, LeKaye HC, Brennan C, Cross J, Huse JT, Kelleher NL, Osten P, Thompson CB, Chan TA.

Nat Genet. 2018 Jan;50(1):62-72. doi: 10.1038/s41588-017-0001-z. Epub 2017 Nov 27.


Top-down characterization of endogenous protein complexes with native proteomics.

Skinner OS, Haverland NA, Fornelli L, Melani RD, Do Vale LHF, Seckler HS, Doubleday PF, Schachner LF, Srzentić K, Kelleher NL, Compton PD.

Nat Chem Biol. 2018 Jan;14(1):36-41. doi: 10.1038/nchembio.2515. Epub 2017 Nov 13.


A cryptic Tudor domain links BRWD2/PHIP to COMPASS-mediated histone H3K4 methylation.

Morgan MAJ, Rickels RA, Collings CK, He X, Cao K, Herz HM, Cozzolino KA, Abshiru NA, Marshall SA, Rendleman EJ, Sze CC, Piunti A, Kelleher NL, Savas JN, Shilatifard A.

Genes Dev. 2017 Oct 1;31(19):2003-2014. doi: 10.1101/gad.305201.117.


Correction to Selective Targeting by a Mechanism-Based Inactivator against Pyridoxal 5'-Phosphate-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover.

Mascarenhas R, Le HV, Clevenger KD, Lehrer HJ, Ringe D, Kelleher NL, Silverman RB, Liu D.

Biochemistry. 2017 Oct 31;56(43):5844-5845. doi: 10.1021/acs.biochem.7b00961. Epub 2017 Oct 18. No abstract available.


Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability.

Rickels R, Herz HM, Sze CC, Cao K, Morgan MA, Collings CK, Gause M, Takahashi YH, Wang L, Rendleman EJ, Marshall SA, Krueger A, Bartom ET, Piunti A, Smith ER, Abshiru NA, Kelleher NL, Dorsett D, Shilatifard A.

Nat Genet. 2017 Nov;49(11):1647-1653. doi: 10.1038/ng.3965. Epub 2017 Oct 2.


Native Electron Capture Dissociation Maps to Iron-Binding Channels in Horse Spleen Ferritin.

Skinner OS, McAnally MO, Van Duyne RP, Schatz GC, Breuker K, Compton PD, Kelleher NL.

Anal Chem. 2017 Oct 17;89(20):10711-10716. doi: 10.1021/acs.analchem.7b01581. Epub 2017 Oct 4.


A synthetic biology approach to probing nucleosome symmetry.

Ichikawa Y, Connelly CF, Appleboim A, Miller TC, Jacobi H, Abshiru NA, Chou HJ, Chen Y, Sharma U, Zheng Y, Thomas PM, Chen HV, Bajaj V, Müller CW, Kelleher NL, Friedman N, Bolon DN, Rando OJ, Kaufman PD.

Elife. 2017 Sep 12;6. pii: e28836. doi: 10.7554/eLife.28836.


Diversity of Amyloid-beta Proteoforms in the Alzheimer's Disease Brain.

Wildburger NC, Esparza TJ, LeDuc RD, Fellers RT, Thomas PM, Cairns NJ, Kelleher NL, Bateman RJ, Brody DL.

Sci Rep. 2017 Aug 25;7(1):9520. doi: 10.1038/s41598-017-10422-x.


Cell Surface Proteomics of N-Linked Glycoproteins for Typing of Human Lymphocytes.

Haverland NA, Waas M, Ntai I, Keppel T, Gundry RL, Kelleher NL.

Proteomics. 2017 Oct;17(19). doi: 10.1002/pmic.201700156.


Selective Targeting by a Mechanism-Based Inactivator against Pyridoxal 5'-Phosphate-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover.

Mascarenhas R, Le HV, Clevenger KD, Lehrer HJ, Ringe D, Kelleher NL, Silverman RB, Liu D.

Biochemistry. 2017 Sep 19;56(37):4951-4961. doi: 10.1021/acs.biochem.7b00499. Epub 2017 Sep 6. Erratum in: Biochemistry. 2017 Oct 31;56(43):5844-5845.


Colibactin assembly line enzymes use S-adenosylmethionine to build a cyclopropane ring.

Zha L, Jiang Y, Henke MT, Wilson MR, Wang JX, Kelleher NL, Balskus EP.

Nat Chem Biol. 2017 Oct;13(10):1063-1065. doi: 10.1038/nchembio.2448. Epub 2017 Aug 7.


A scalable platform to identify fungal secondary metabolites and their gene clusters.

Clevenger KD, Bok JW, Ye R, Miley GP, Verdan MH, Velk T, Chen C, Yang K, Robey MT, Gao P, Lamprecht M, Thomas PM, Islam MN, Palmer JM, Wu CC, Keller NP, Kelleher NL.

Nat Chem Biol. 2017 Aug;13(8):895-901. doi: 10.1038/nchembio.2408. Epub 2017 Jun 12.


Proteoforms in Peripheral Blood Mononuclear Cells as Novel Rejection Biomarkers in Liver Transplant Recipients.

Toby TK, Abecassis M, Kim K, Thomas PM, Fellers RT, LeDuc RD, Kelleher NL, Demetris J, Levitsky J.

Am J Transplant. 2017 Sep;17(9):2458-2467. doi: 10.1111/ajt.14359. Epub 2017 Jun 27.


High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer.

Cleland TP, DeHart CJ, Fellers RT, VanNispen AJ, Greer JB, LeDuc RD, Parker WR, Thomas PM, Kelleher NL, Brodbelt JS.

J Proteome Res. 2017 May 5;16(5):2072-2079. doi: 10.1021/acs.jproteome.7b00043. Epub 2017 Apr 19.

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