Publications

Below are the current list of peer-reviewed publications which have benefited from our support.

    2020

  • McGee JP, Melani RD, Goodwin M, McAlister G, Huguet R, Senko MW, Compton PD, Kelleher NL. “Voltage Rollercoaster Filtering of Low-Mass Contaminants During Native Protein Analysis” J Am Soc Mass Spectrom. 2020. 31(3) p. 763-767 PubMed
  • Kafader JO, Melani RD, Durbin KR, Ikwuagwu B, Early BP, Fellers RT, Beu SC, Zabrouskov V, Makarov AA, Maze JT, Shinholt DL, Yip PF, Tullman-Ercek D, Senko MW, Compton PD, Kelleher NL. “Multiplexed mass spectrometry of individual ions improves measurement of proteoforms and their complexes” Nat Meth. 2020. 17(4) p. 391-394 PubMedPubMedCentral.  
  • Kafader JO, Durbin KR, Melani RD, Des Soye BJ, Schachner LF, Senko MW, Compton PD, Kelleher NL. “Individual Ion Mass Spectrometry Enhances the Sensitivity and Sequence Coverage of Top-Down Mass Spectrometry” J Proteome Res. 2020. 19(3) p. 1346-1350 PubMedPubMedCentral.  
  • Doubleday PF, Fornelli L, Kelleher NL. “Elucidating Proteoform Dynamics Underlying the Senescence Associated Secretory Phenotype” J Proteome Res. 2020. 19(2) p. 938-948 PubMedPubMedCentral.  
  • Salvi A, Amrine CSM, Austin JR, Kilpatrick K, Russo A, Lantvit D, Calderon-Gierszal E, Mattes Z, Pearce CJ, Grinstaff MW, Colby AH, Oberlies NH, Burdette JE. “Verticillin A Causes Apoptosis and Reduces Tumor Burden in High-Grade Serous Ovarian Cancer by Inducing DNA Damage” Mol Cancer Ther. 2020. 19(1) p. 89-100 PubMedPubMedCentral.  
  • Park HM, Winton VJ, Drader JJ, Manalili Wheeler S, Lazar GA, Kelleher NL, Liu Y, Tran JC, Compton PD. “Novel Interface for High-Throughput Analysis of Biotherapeutics by Electrospray Mass Spectrometry” Mol Cell Proteom. 2020. 92(2) p. 2186-2193 PubMedPubMedCentral.  
  • Cable CJ, Kaplan N, Getsios S, Thomas PM, Perez White BE. “Biotin Identification Proteomics in Three-Dimensional Organotypic Human Skin Cultures” Methods Mol Biol. 2020. 2109 p. 185-197 PubMedPubMedCentral.  
  • Fornelli L, Srzentić K, Toby TK, Doubleday PF, Huguet R, Mullen C, Melani RD, Dos Santos Seckler H, DeHart CJ, Weisbrod CR, Durbin KR, Greer JB, Early BP, Fellers RT, Zabrouskov V, Thomas PM, Compton PD, Kelleher NL. “Thorough Performance Evaluation of 213 nm Ultraviolet Photodissociation for Top-down Proteomics” Mol Cell Proteom. 2020. 19(2) p. 405-420 PubMedPubMedCentral.  
  •  

    2019

  • Henning NF, LeDuc RD, Even KA, Laronda MM. “Proteomic analyses of decellularized porcine ovaries identified new matrisome proteins and spatial differences across and within ovarian compartments” Sci Rep. 2019. 9(1) p. 20001 PubMedPubMedCentral.  
  • Poropatich K, Paunesku T, Zander A, Wray B, Schipma M, Dalal P, Agulnik M, Chen S, Lai B, Antipova O, Maxey E, Brown K, Wanzer MB, Gursel D, Fan H, Rademaker A, Woloschak GE, Mittal BB. “Elemental Zn and its Binding Protein Zinc-α2-Glycoprotein are Elevated in HPV-Positive Oropharyngeal Squamous Cell Carcinoma.” Sci Rep. 2019. 9(1) p. 16965 PubMedPubMedCentral.  
  • Huguet R, Mullen C, Srzentić K, Greer JB, Fellers RT, Zabrouskov V, Syka JEP, Kelleher NL, Fornelli L. “Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms.” Anal Chem. 2019. 91(24) p. 15732-15739 PubMedPubMedCentral.  
  • Des Soye BJ, Gerbasi VR, Thomas PM, Kelleher NL, Jewett MC. “A Highly Productive, One-Pot Cell-Free Protein Synthesis Platform Based on Genomically Recoded Escherichia coli.” Cell Chem Biol. 2019. 26(12) p. 1743-1754 PubMedPubMedCentral.  
  • Melani RD, Srzentić K, Gerbasi VR, McGee JP, Huguet R, Fornelli L, Kelleher NL. “Direct measurement of light and heavy antibody chains using ion mobility and middle-down mass spectrometry.” MAbs. 2019. 11(8) p. 1351-1357 PubMedPubMedCentral.  
  • Parker BW, Goncz EJ, Krist DT, Statsyuk AV, Nesvizhskii AI, Weiss EL. “Mapping low-affinity/high-specificity peptide-protein interactions using ligand-footprinting mass spectrometry.” Proc Natl Acad Sci U S A. 2019. 116(42) p. 21001-21011 PubMedPubMedCentral.  
  • Park HM, Satta R, Davis RG, Goo YA, LeDuc RD, Fellers RT, Greer JB, Romanova EV, Rubakhin SS, Tai R, Thomas PM, Sweedler JV, Kelleher NL, Patrie SM, Lasek AW. “Multidimensional Top-Down Proteomics of Brain-Region-Specific Mouse Brain Proteoforms Responsive to Cocaine and Estradiol.” J Proteome Res. 2019. 18(11) p. 3999-4012 PubMedPubMedCentral.  
  • Kafader JO, Beu SC, Early BP, Melani RD, Durbin KR, Zabrouskov V, Makarov AA, Maze JT, Shinholt DL, Yip PF, Kelleher NL, Compton PD, Senko MW. STORI Plots Enable Accurate Tracking of Individual Ion Signals.” J Am Soc Mass Spectrom. 2019. 30(11) p. 2200-2203 PubMedPubMedCentral.  
  • Smith LM, Thomas PM, Shortreed MR, Schaffer LV, Fellers RT, LeDuc RD, Tucholski T, Ge Y, Agar JN, Anderson LC, Chamot-Rooke J, Gault J, Loo JA, Paša-Tolić L, Robinson CV, Schlüter H, Tsybin YO, Vilaseca M, Vizcaíno JA, Danis PO, Kelleher NL. “A five-level classification system for proteoform identifications.” Nat Meth.. 2019. 16(10) p. 939-940 PubMedPubMedCentral.  
  • Bhowmik D, Culver KSB, Liu T, Odom TW. “Resolving Single-Nanoconstruct Dynamics during Targeting and Nontargeting Live-Cell Membrane Interactions.” ACS Nano.. 2019. 13(12) p. 13637-13644 PubMed.
  • 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. “A Mutation in Histone H2B Represents a New Class of Oncogenic Driver.” Cancer Discov. 2019. 9(10) p. 1438-1451 PubMedPubMedCentral.  
  • Sundaravel S, Kuo WL, Jeong JJ, Choudhary GS, Gordon-Mitchell S, Liu H, Bhagat TD, McGraw KL, Gurbuxani S, List AF, Verma A, Wickrema A. “Loss of Function of DOCK4 in Myelodysplastic Syndromes Stem Cells is Restored by Inhibitors of DOCK4 Signaling Networks.” Clin Cancer Res. 2019. 25(18) p. 5638-5349 PubMedPubMedCentral.  
  • Camarillo JM, Swaminathan S, Abshiru NA, Sikora JW, Thomas PM, Kelleher NL. “Coupling Fluorescence-Activated Cell Sorting and Targeted Analysis of Histone Modification Profiles in Primary Human Leukocytes” J Am Soc Mass Spectrom. 2019. 30(12) p. 2526-2534 PubMedPubMedCentral.  
  • 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. “Best practices and benchmarks for intact protein analysis for top-down mass spectrometry.” Nat Meth. 2019. 16(7) p. 587-594 PubMedPubMedCentral.  
  • Huang X, LeDuc RD, Fornelli L, Schunter AJ, Bennett RL, Kelleher NL, Licht JD. “Defining the NSD2 interactome: PARP1 PARylation reduces NSD2 histone methyltransferase activity and impedes chromatin binding” J Biol Chem. 2019. 294(33) p. 12459-12471 PubMedPubMedCentral.  
  • Diebold LP, Gil HJ, Gao P, Martinez CA, Weinberg SE, Chandel NS. “Mitochondrial complex III is necessary for endothelial cell proliferation during angiogenesis” Nat Metab. 2019. 1(1) p. 158-171 PubMedPubMedCentral.  
  • 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. “Identification and Quantification of Proteoforms by Mass Spectrometry.” Proteomics. 2019. 19(10) p. e1800361 PubMedPubMedCentral.  
  • 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. “Precision Targeting with EZH2 and HDAC Inhibitors in Epigenetically Dysregulated Lymphomas” Clin Cancer Res. 2019. 25(17) p. 5271-5283 PubMedPubMedCentral.  
  • Schachner LF, Ives AN, McGee JP, Melani RD, Kafader JO, Compton PD, Patrie SM, Kelleher NL. “Standard Proteoforms and Their Complexes for Native Mass Spectrometry” J Am Soc Mass Spectrom. 2019. 30(7) p. 1190-1198 PubMedPubMedCentral.  
  • LeDuc RD, Fellers RT, Early BP, Greer JB, Shams DP, Thomas PM, Kelleher NL. “Accurate Estimation of Context-Dependent False Discovery Rates in Top-Down Proteomics.” Mol Cell Proteomics. 2019. 18(4) p. 796-805 PubMed
  • May JL, Kouri FM, Hurley LA, Liu J, Tommasini-Ghelfi S, Ji Y, Gao P, Calvert AE, Lee A, Chandel NS, Davuluri RV, Horbinski CM, Locasale JW, Stegh AH. “IDH3α Regulates One-Carbon Metabolism in Glioblastoma.” Sci Adv2019. 5(1) eaat0456 PubMedPubMedCentral.
  • 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. “A Novel Crosslinking Protocol Stabilizes Amyloid β Oligomers Capable of Inducing Alzheimer’s-Associated Pathologies.” J Neurochem. 2019. 148(6) p. 822-836 PubMedPubMedCentral.  
  • Wilkins JT, Seckler HS. “HDL modification: recent developments and their relevance to atherosclerotic cardiovascular disease.” Curr Opin Lipidol2019. 30(1) p. 24-29 PubMed
  • Toby TK, Fornelli L, Srzentić K, DeHart CJ, Levitsky J, Friedewald J, Kelleher NL. “A comprehensive pipeline for translational top-down proteomics from a single blood draw.” Nat Protoc2019. 14(1) p. 119-152 PubMed.  
  • 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. “USP7 Cooperates with NOTCH1 to Drive the Oncogenic Transcriptional Program in T-Cell Leukemia.” Clin Cancer Res2019. 25(1) p. 222-239 PubMed. PubMedCentral
  • 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. “An Activating Mutation of the NSD2 Histone Methyltransferase Drives Oncogenic Reprogramming in Acute Lymphocytic Leukemia.” Oncogene. 2019. 38(5) p. 671-686 PubMedPubMedCentral
  •  

    2018

  • Saleiro D, Blyth GT, Kosciuczuk EM, Ozark PA, Majchrzak-Kita B, Arslan AD, Fischietti M, Reddy NK, Horvath CM, Davis RJ, Fish EN, Platanias LC. “IFN-γ-inducible antiviral responses require ULK1-mediated activation of MLK3 and ERK5.” Sci Signal. 2018. 11(557) p. eaap9921 PubMedPubMedCentral
  • Agarwal D, Fellers RT, Early BP, Lu D, DeHart CJ, Compton PD, Thomas PM, Lahav G, Kelleher NL, Gunawardena J. “Analysing protein post-translational modform regions by linear programming.” bioRxiv. 2018. preprint. doi: BioRxiv.
  • DeHart CJ, Fornelli L, Anderson LC, Fellers RT, Lu D, Hendrickson CL, Lahav G, Gunawardena J, Kelleher NL, “A Multi-modal Proteomics Strategy for Characterizing Posttranslational Modifications of Tumor Suppressor p53 Reveals many Sites but Few Modified Forms.”, bioRxiv, 2018, preprint. doi: bioRxiv.
  • Ting SY, Bosch DE, Mangiameli SM, Radey MC, Huang S, Park YJ, Kelly KA, Filip SK, Goo YA, Eng JK, Allaire M, Veesler D, Wiggins PA, Peterson SB, Mougous JD. “Bifunctional Immunity Proteins Protect Bacteria against FtsZ-Targeting ADP-Ribosylating Toxins.” Cell. 2018. 175(5) p. 1380-1392. PubMed
  • Killinger BA, Madaj Z, Sikora JW, Rey N, Haas AJ, Vepa Y, Lindqvist D, Chen H, Thomas PM, Brundin P, Brundin L, Labrie V. “The Vermiform Appendix Impacts the Risk of Developing Parkinson’s Disease.” Sci Transl Med. 2018. 10(465) pii: eaar5280. PubMed
  • 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. “Characterization of a Long Overlooked Copper Protein from Methane- and Ammonia-Oxidizing Bacteria.” Nat Commun. 2018. 9(1) p. 4276 PubMedPubMedCentral
  • Moehring F, Waas M, Keppel TR, Rathore D, Cowie AM, Stucky CL, Gundry RL. “Quantitative Top-Down Mass Spectrometry Identifies Proteoforms Differentially Released during Mechanical Stimulation of Mouse Skin.” J Proteome Res. 2018. 17(8) p. 2635-2648 PubMedPubMedCentral
  • Blair KM, Mears KS, Taylor JA, Fero J, Jones LA, Gafken PR, Whitney JC, Salama NR. “The Helicobacter pylori Cell Shape Promoting Protein Csd5 Interacts with the Cell Wall, MurF, and the Bacterial Cytoskeleton.” Mol Microbiol. 2018. 110(1) p. 114-127 PubMed
  • Gruppuso PA, Boylan JM, Zabala V, Neretti N, Abshiru NA, Sikora JW, Doud EH, Camarillo JM, Thomas PM, Kelleher NL, Sanders JA. “Stability of Histone Post-Translational Modifications in Samples Derived from Liver Tissue and Primary Hepatic Cells.” PLoS One. 2018. 13(9) e0203351  PubMedPubMedCentral
  • Compton PD, Kelleher NL, Gunawardena J. “Estimating the Distribution of Protein Post-Translational Modification States by Mass Spectrometry.” J Proteome Res. 2018. 17(8) p. 2727-2734 PubMed
  • Riley NM, Sikora JW, Seckler HS, Greer JB, Fellers RT, LeDuc RD, Westphall MS, Thomas PM, Kelleher NL, Coon JJ. “The Value of Activated Ion Electron Transfer Dissociation for High-Throughput Top-Down Characterization of Intact Proteins.” Anal Chem. 2018. 90(14) p. 8553-8560 PubMed
  • Fischietti M, Arslan AD, Sassano A, Saleiro D, Majchrzak-Kita B, Ebine K, Munshi HG, Fish EN, Platanias LC. “Slfn2 Regulates Type I Interferon Responses by Modulating the NF-κB Pathway”. Mol Cell Biol. 2018. 38(16) p. e00053-18 PubMedPubMedCentral
  • Park YJ, Kenney GE, Schachner LF, Kelleher NL, Rosenzweig AC. “Repurposed HisC Aminotransferases Complete the Biosynthesis of Some Methanobactins.” Biochemistry. 2018. 57(25) p. 3515-3523 PubMed
  • 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. “A Targeted, Differential Top-Down Proteomic Methodology for Comparison of ApoA-I Proteoforms in Individuals with High and Low HDL Efflux Capacity.” J Proteome Res. 2018. 17(6) p. 2156-2164 PubMedPubMedCentral
  • 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. “Precise Characterization of KRAS4b Proteoforms in Human Colorectal Cells and Tumors Reveals Mutation/Modification Cross-Talk.” Proc Natl Acad Sci U S A. 2018. 115(16) p. 4140-4145 PubMedPubMedCentral
  • 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. “Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids.” Nat Commun. 2018. 9(1) p. 1203 PubMedPubMedCentral
  • 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. “The Biosynthesis of Methanobactin.” Science. 2018. 359(6382) p. 1411-1416 PubMedPubMedCentral.  
  • Smith LM, Kelleher NL. “Proteoforms as the next proteomics currency.” Science. 2018. 359(6380) p. 1106-1107 PubMedPubMedCentral.  
  • 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. “Top-Down Proteomics Enables Comparative Analysis of Brain Proteoforms Between Mouse Strains.” Anal. Chem. 2018.  90(6) p. 3802-3810 PubMed. PubMedCentral
  • 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. “How many human proteoforms are there?” Nat. Chem. Biol. 2018. 14(3) p. 206-214 PubMed. PubMedCentral.
  • 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. “ProForma: A Standard Proteoform Notation.” J. Proteome. Res.2018. 17(3) p. 1321-1325 PubMed. PubMedCentral.
  • 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. “Mutant-IDH1-dependent chromatin state reprogramming, reversibility, and persistence.” Nat. Genet. 2018. 50(1) p. 62-72 PubMed. PubMedCentral.
  • Skinner OS, Haverland NA, Fornelli L, Melani RD, Do Vale LHF, Seckler HS, Doubleday PF, Schachner LF, Srzentić K, Kelleher NL, Compton PD “Top-down characterization of endogenous protein complexes with native proteomics.” Nat. Chem. Biol. 2018. 14(1) p. 36-41 PubMed. PubMedCentral.
  • Lyon YA, Riggs D, Fornelli L, Compton PD, Julian RR, “The Ups and Downs of Repeated Cleavage and Internal Fragment Production in Top-Down Proteomics.” J. AM. Soc. Mass. Spectrom.2018. 29(1) p. 150-157 PubMed. PubMedCentral.
  • Fornelli L, Toby TK, Schachner LF, Doubleday PF, Srzentić K, Dehart CJ, Kelleher NL. “Top-down Proteomics: Where we are, where we are going?” Journal of Proteomics2018. 175: p. 3-4 PubMed. PubMedCentral.
  •  

    2017

  • 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, “A Cryptic Tudor Domain Links BRWD2/PHIP to COMPASS-Mediated Histone H3K4 Methylation.” Nat. Chem. Biol. 2017. 31(19) p. 2003-2014 PubMed. PubMedCentral.
  • Ezponda T, Dupéré-Richer D, Will CM, Small EC, Varghese N, Patel T, Nabet B, Popovic R, Oyer J, Bulic M, Zheng Y, Huang X, Shah MY, Maji S, Riva A, Occhionorelli M, Tonon G, Kelleher N, Keats J, Licht JD, “UTX/KDM6A Loss Enhances the Malignant Phenotype of Multiple Myeloma and Sensitizes Cells to EZH2 inhibition.” Cell. Rep2017. 21(3) p. 628-640 PubMed. PubMedCentral.
  • 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. “Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability.” Nat Genet. 2017. 49(11) p. 1647-1653 PubMedPubMedCentral
  • 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, “A Synthetic Biology Approach to Probing Nucleosome Symmetry.” Elife. 2017PubMed. PubMedCentral.
  • Sharma AI, Olson CL, Engman DM, “The Lipid Raft Proteome of African Trypanosomes Contains Many Flagellar Proteins.” Pathogens. 2017. 6(3) PubMed. PubMedCentral.
  • Wildburger NC, Esparza TJ, LeDuc RD, Fellers RT, Thomas PM, Cairns NJ, Kelleher NL, Bateman RJ, Brody DL, “Diversity of Amyloid-beta Proteoforms in the Alzheimer’s Disease Brain.” Sci. Rep. 2017. 7(1) p. 9520 PubMed. PubMedCentral.
  • Puvar K, Zhou Y, Qiu J, Luo ZQ, Wirth MJ1, Das C, “Ubiquitin Chains Modified by the Bacterial Ligase SdeA Are Protected from Deubiquitinase Hydrolysis.” Pathogens. 2017. 56(36) p. 4762-4766 PubMed. PubMedCentral.
  • Whitney JC, Peterson SB, Kim J, Pazos M, Verster AJ, Radey MC, Kulasekara HD, Ching MQ, Bullen NP, Bryant D, Goo YA, Surette MG, Borenstein E, Vollmer W, Mougous JD, “A Broadly Distributed Toxin Family Mediates Contact-Dependent Antagonism Between Gram-Positive Bacteria.” Elife. 2017PubMed. PubMedCentral.
  • Larkin MEM, Place AR, “Running the Stop Sign: Readthrough of a Premature UAG Termination Signal in the Translation of a Zebrafish (Danio rerio) Taurine Biosynthetic Enzyme.” Mar. Drugs. 2017. 15(6) PubMed. PubMedCentral.
  • Toby TK, Abecassis M, Kim K, Thomas PM, Fellers RT, LeDuc RD, Kelleher NL, Demetris J, Levitsky J, Place AR, “Proteoforms in Peripheral Blood Mononuclear Cells as Novel Rejection Biomarkers in Liver Transplant Recipients.” Am. J. Transplant. 2017. 17(9) p. 2458-2467 PubMed. PubMedCentral.
  • Ansó E, Weinberg SE, Diebold LP, Thompson BJ, Malinge S, Schumacker PT, Liu X, Zhang Y, Shao Z, Steadman M, Marsh KM, Xu J, Crispino JD, Chandel NS, “The mitochondrial respiratory chain is essential for haematopoietic stem cell function.” Nat. Cell. Biol.2017. 19(6) p. 614-625 PubMed. PubMedCentral.
  • Cleland TP, DeHart CJ, Fellers RT, VanNispen AJ, Greer JB, LeDuc RD, Parker WR, Thomas PM, Kelleher NL, Brodbelt JS, “High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer.” J. Proteome. Res. 2017. 16(5) p. 2072-2079 PubMed. PubMedCentral.
  • DiChiara T, DiNunno N, Clark J, Bu RL, Cline EN, Rollins MG, Gong Y, Brody DL, Sligar SG, Velasco PT, Viola KL, Klein WL. “Alzheimer’s Toxic Amyloid Beta Oligomers:
    Unwelcome Visitors to the Na/K ATPase alpha3 Docking Station.” Yale. J. Biol. Med. 2017. 90(1) p. 45-61 PubMed. PubMedCentral.
  • Greer SM, Holden DD, Fellers R, Kelleher NL, Brodbelt JS. “Modulation of Protein Fragmentation Through Carbamylation of Primary Amines.” J. Proteome Res. 2017. 28(8) p. 1587-1599 PubMed. PubMedCentral.
  • Piunti A, Hashizume R, Morgan MA, Bartom ET, Horbinski CM, Marshall SA, Rendleman EJ, Ma Q, Takahashi YH, Woodfin AR, Misharin AV, Abshiru NA, Lulla RR, Saratsis AM, Kelleher NL, James CD, Shilatifard A. “Therapeutic Targeting of polycomb and BET bromodomain proteins in diffuse intrinsic pontine gliomas.” Nat. Med. 2017. 23(4) p. 493-500 PubMed. PubMedCentral.
  • “Open Science Cyber Risk Profile.” Open Science Cyber Risk Profile. Web. 15 Feb. 2017. Github
  • Schroeter ER., Dehart CJ, Cleland TP, Zheng W, Thomas PM, Kelleher NL, Bern M, Schweitzer MH. “Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein.” Journal of Proteome Research. 2017. 16(2) p. 920-32 PubMedPubMedCentral.
  • Dehart CJ, Fellers RT, Fornelli L, Kelleher NL, Thomas PM. “Bioinformatics Analysis of Top-Down Mass Spectrometry Data with ProSight Lite.” Protein Bioinformatics Methods in Molecular Biology. 2017. p381-94 PubMed. PubMedCentral.
  • Meydan S, Klepacki D, Karthikeyan S, Margus T, Thomas PM, Jones JE, Khan Y, Briggs J, Dinman JD, Vázquez-Laslop N, Mankin AS. “Programmed Ribosomal Frameshifting Generates a Copper Transporter and a Copper Chaperone from the Same Gene.” Molecular Cell. 2017. 65(2) p. 207-19 PubMed. PubMedCentral.
  • Gan R, Perez JG, Carlson ED, Ntai I, Isaacs FJ, Kelleher NL, Jewett MC. “Translation System Engineering in Escherichia Coli Enhances Non-Canonical Amino Acid Incorporation into Proteins.” Biotechnol Bioeng. 2017. 114(5) p. 1074-1086 PubMed. PubMedCentral
  • Zhou Y, Zhang X, Fornelli L, Compton PD, Kelleher NL, Wirth MJ. “Chromatographic efficiency and selectivity in top-down proteomics of histones.” J. Chrom. B. 2017. 1044-1045 p. 47-53 PubMed. PubMedCentral.
  • Fornelli L, Durbin KR, Fellers RT, Early BP, Greer JB, LeDuc RD, Compton PD, Kelleher NL. “Advancing Top-down Analysis of the Human Proteome Using a Benchtop Quadrupole-Orbitrap Mass Spectrometer.” Journal of Proteome Research. 2017. 16(2) p. 609-18 PubMed. PubMedCentral.
  • Anderson LC, Dehart CJ, Kaiser NK, Fellers RT, Smith DF, Greer JB, LeDuc RD, Blakney GT, Thomas PM, Kelleher NL, Hendrickson CL. “Identification and Characterization of Human Proteoforms by Top-Down LC-21 Tesla FT-ICR Mass Spectrometry.” Journal of Proteome Research. 2017. 16(2) p. 1087-096 PubMed. PubMedCentral.
  • White BE, Perez RV, Kaplan N, Cable CJ, Thomas PM, Getsios S. “EphA2 Proteomics in Human Keratinocytes Reveals a Novel Association with Afadin and Epidermal Tight Junctions.” Journal of Cell Science. 2017. 130(1) p. 111-18 PubMed. PubMedCentral.
  •  

    2016

  • Skinner OS, Schachner LF, Kelleher NL. “The Search Engine for Multi-Proteoform Complexes: An Online Tool for the Identification and Stoichiometry Determination of Protein Complexes.” Current Protocols in Bioinformatics. 2016. 56:13.30.1-13.30.11 PubMed. PubMedCentral.
  • Savaryn JP, Toby TK, Kelleher NL. “A Researcher’s Guide to Mass Spectrometry-Based Proteomics.” Proteomics2016. 16(18) p. 435-443 PubMed. PubMedCentral.
  • Toby TK, Fornelli L, Kelleher NL. “Progress in Top-Down Proteomics and the Analysis of Proteoforms.” Annu. Rev. Anal. Chem2016. 9(1) p. 499-519 PubMed. PubMedCentral.
  • Kenney GE, Goering AW, Ross MO, Dehart CJ, Thomas PM, Hoffman BM, Kelleher NL, Rosenzweig AC. “Characterization of Methanobactin from Methylosinussp. LW4.” Journal of the American Chemical Society. 2016. 138(35) p. 1124-1127 PubMed. PubMedCentral.
  • Zheng Y, Huang X, Kelleher NL. “Epiproteomics: Quantitative Analysis of Histone Marks and Codes by Mass Spectrometry.” Current Opinion in Chemical Biology2016. 33(1) p. 142-50 PubMed. PubMedCentral.
  • Savaryn JP, Toby TK, Catherman AD, Fellers RT, LeDuc RD, Thomas PM, Friedewald JJ, Salomon DR, Abecassis MM, Kelleher NL. “Comparative Top Down Proteomics of Peripheral Blood Mononuclear Cells from Kidney Transplant Recipients with Normal Kidney Biopsies or Acute Rejection.” Proteomics. 2016. 16(14) p. 2048-058 PubMed. PubMedCentral.
  • Durbin KR, Fornelli L, Fellers RT, Doubleday PF, Narita M, Kelleher NL. “Quantitation and Identification of Thousands of Human Proteoforms below 30 kDa.” J Proteome Res. 2016 15(3) 976-82 PubMed. PubMedCentral.
  • Ntai I, Toby TK, LeDuc RD, Kelleher NL. “A Method for Label-Free, Differential Top-Down Proteomics.” Methods Mol Biol. 2016. p. 121-33 PubMed. PubMedCentral.
  • Zheng Y, Fornelli L, Compton PD, Sharma S, Canterbury J, Mullen C, Zabrouskov V, Fellers RT, Thomas PM, Licht JD, Senko MW, Kelleher NL. “Unabridged Analysis of Human Histone H3 by Differential Top-Down Mass Spectrometry Reveals Hypermethylated Proteoforms from MMSET/NSD2 Overexpression.” Mol Cell Proteomics. 2016. 15(3) p. 776-90 PubMed. PubMedCentral.
  •  

     2015

  • Lorenzatto KR, Kim K, Ntai I, Paludo GP, Camargo de Lima J, Thomas PM, Kelleher NL, Ferreira HB. “Top Down Proteomics Reveals Mature Proteoforms Expressed in Subcellular Fractions of the Echinococcus granulosus Preadult Stage.” J Proteome Res. 2015 14(11) p. 4805-14 PubMed. PubMedCentral.
  • Young DJ, Guydosh NR, Zhang F, Hinnebusch AG, Green R. “Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3’UTRs In Vivo.” Cell. 2015. 162(4) p. 872-84 PubMedPubMedCentral

Acknowledging the Resource

Please acknowledge work performed within the NRTDP with text similar to this: This research was carried out in collaboration with the National Resource for Translational and Developmental Proteomics under Grant P41 GM108569 from the National Institute of General Medical Sciences, National Institutes of Health and supported by the Sherman Fairchild Foundation.

 

 

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