Mail - nrtdp-help@northwestern.edu

Publications

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

    2026

  • Lee AS, Fisher NP, Marunde MR, Su P, Khan LF, Ezell RJ, Gillespie ZB, GrahamB, Taylor HF, Onuoha UC, Su T, Jooß K, Schachner LF, Fuchs HA, Noll K, MeinersMJ, Cheek MA, Burg JM, Sun ZW, Musselman CA, Keogh MC, Kelleher NL. "Direct Readout of Multivalent Chromatin Reader-Nucleosome Interactions by Nucleosome Mass Spectrometry" ACS Cent Sci. 2026. 12(2) PubMed .
  • Kang KM, Vargas AL, Ferreira LA, Des Soye BJ, Corrigan M, Zhang CK, Wang F,Duan D, Kelleher NL, Hohmann AG, Liu D, Silverman RB. "Targeting Conformational Flexibility of a Reactive Intermediate to Enhance Selectivity of a GABA Aminotransferase Inactivator" J Am Chem Soc. 2026. 148(8) PubMed .
  • Fellers RT, Greer JB, Early BP, Hollas MAR, Robey MT, Kelleher NL, Durbin KR. "PSLite Online: A Portable, Modern Web Application to Analyze Top-Down Mass Spectrometry Fragmentation Data" J Mass Spectrom. 2026. 61(3) PubMed .
  • Ctortecka C, Jaishankar D, Su P, Huang CF, Pla I, Henning N, Hollas MAR,Callegari MA, Taylor ME, Lee YM, Daud A, Pinelli DF, Rohan V, Caldwell MA, ForteE, Sanchez A, Kelleher NL, Nadig SN. "Top-Down Proteomics in the Assessment of Kidney Donor Quality: a novel approach to increased organ utilization" medRxiv [Preprint]. 2026. PubMed .
  • Korchak JA, Stephen Yi S, Kelleher NL, Sahni N, Sheynkman GM. "Proteoform medicine: characterizing and targeting protein forms in human disease" Nat Rev Genet. 2026. 27(4) PubMed .
  • Sanchez A, Pla I, Huang CF, Kanchustambham VL, Hollas MAR, Greer JB, LadnerDP, Peterson KN, Fisher TD, Su T, Van Le NH, Mattamana BB, Faull PA, Polineni P,Barrios P, Banea TE, Melani RD, Caldwell MA, McGee JP, Forte E, Kelleher NL. "SPAP: Soluble Human Plasma Proteoform Analysis via Acetonitrile Precipitation and Top-Down Mass Spectrometry" J Am Soc Mass Spectrom. 2026. 37(1) PubMed .
  • Gould N, Wang Q, Agar JN, Brodbelt JS, Chen D, Cupp-Sutton KA, Domínguez-VegaE, Fang F, Fillet M, Fischer MS, Gaspar A, Ge Y, Gou MJ, GreguÅ¡ M, Gstöttner C,Hamidli N, Helms A, Hossain MA, Juetten KJ, Kelleher NL, Kraus T, Larson EJ,Mellors JS, Nagy C, Neusüß C, Redman EA, Schairer J, Wu S, Xu T, Zhao Z, Zhu G,Ivanov AR, Jooß K, Sun L. "Intact Proteoform Analysis by Capillary Electrophoresis-Mass Spectrometry" Are We There Yet? Angew Chem Int Ed Engl. 2026. 65(5) PubMed .
  • Fisher TD, Compton PD, Robey MT, Fellers RT, Durbin KR, Kelleher NL. "Automated Enzymatic Deglycosylation of Monoclonal Antibody with the SampleStream Platform" J Am Soc Mass Spectrom. 2026. 37(1) PubMed .

    • 2025

  • Marunde MR, Popova IK, Hall NW, Vaidya A, Bone JR, Boone BA, Brown PJ, EzellRJ, Firestone TM, Fuchs HA, Gibson E, Gillespie ZB, Gloor SL, Hickman AR, HowardSA, Husby NL, Hsiung VT, Johnstone AL, Khan LF, Krajewski K, Lee AS, McAnarneyET, Maier KE, Maryanski DN, McCuiston JL, Noll KE, Novitzky K, Patteson EF,Rodriguez KL, Sanchez JC, Schachner LF, Smith CE, Sun L, Taylor HF, Watson R,Willis HE, Musselman CA, Venters BJ, Cheek MA, Meiners MJ, Sun ZW, Kelleher NL,Cowles MW, Weinzapfel EN, Keogh MC, Burg JM. "Nucleosome context regulates chromatin reader preference" Nucleic Acids Res. 2025. 53(20) PubMed .
  • Huang CF, Su T, Flozak AS, Gottardi CJ, Kelleher NL. "Intact Mass Profiling Reveals Phospho-Proteoforms of the Catenins (85-110 kDa) Regulated by Actomyosin Contractility" Angew Chem Int Ed Engl. 2025. 64(52) PubMed .
  • Keogh MC, Almouzni G, Andrews AJ, Armache KJ, Arrowsmith CH, Baek SH,Bedford MT, Bernstein E, Côté J, David Y, Denu JM, Fierz B, Garcia BA, Glass KC,Gozani O, Helin K, Henikoff S, Jensen ON, Josefowicz SZ, Kelleher NL,Kutateladze TG, Lindner HH, Lu C, Luger K, Mallick P, Musselman CA, Muir TW,PaÅ¡a-Tolić L, Schneider R, Shi X, Shi Y, Sidoli S, Smith LM, Tyler JK, WolbergerC, Workman JL, Strahl BD, Young NL. "A needed nomenclature for nucleosomes" Mol Cell. 2025. 85(19) PubMed .
  • Skinner KA, Fisher TD, Lee A, Su T, Forte E, Sanchez A, Caldwell MA,Kelleher NL. "Next-generation protein sequencing and individual ion mass spectrometry enable complementary analysis of interleukin-6" Anal Bioanal Chem. 2025. 417(28) PubMed .
  • Huang CF, Su T, Flozak AS, Gottardi CJ, Kelleher NL. "Top-Down Individual Ion Mass Spectrometry Reveals 85-110 kDa Catenin Phospho-Proteoforms Regulated by Actomyosin Contractility" bioRxiv [Preprint]. 2025. .
  • Wainwright AAC, Madhoun K, Su P, Janisse SE, Besaw JE, Grewal HS, Ernst OP,Kafader JO, Kelleher NL, Miller RJD. "Wavelength Dependence of Intact Protein Extraction Using Femtosecond Laser Ablation" J Phys Chem Lett. 2025. 16(34) PubMed .
  • Naseri NN, Xu T, Chantarawong S, Patrie SM, Kelleher NL, Sharma M, Shalem O,Rhoades E. "Specific Combinations of Physiological Tau Phosphorylation Regulate Tau-Microtubule Interactions in Developing Neurons" bioRxiv [Preprint]. 2025. .
  • Lee AS, Fisher NP, Marunde MR, Su P, Khan LF, Graham B, Taylor HF, OnuohaUC, Su T, Jooß K, Schachner LF, Fuchs HA, Noll K, Cheek MA, Burg JM, Sun ZW,Musselman CA, Keogh MC, Kelleher NL. "Direct Readout of Multivalent Chromatin Reader-Nucleosome Interactions by Nucleosome Mass Spectrometry" bioRxiv [Preprint]. 2025. PubMed .
  • Liggett MR, Wang B, Dawood ZS, Zhang M, Jin G, Ho JW, Taylor ME, White V,Pla I, Sanchez A, Caldwell M, Kelleher NL, Liu B, Couchenour DC, Shaikh A, YaoY, Park KH, Ma J, Alam HB. "Treatment with MG53 ameliorates traumatic brain injury-associated acute kidney injury" J Trauma Acute Care Surg. 2025. 99(5) PubMed .
  • Lee AS, Huang CF, Su T, Bodner J, Kelleher NL, Foltz DR. "Replication stress alters CENP-A nucleosome stability during S phase" bioRxiv [Preprint]. 2025. .
  • Xu T, Su T, Soye BJD, Kandi S, Huang CF, Wilkins JT, Castellani RJ, KafaderJO, Patrie SM, Vassar R, Kelleher NL. "The Proteoform Landscape of Tau from the Human Brain" J Proteome Res. 2025. 24(6) .
  • Su P, Hollas MAR, Pla I, Rubakhin S, Butun FA, Greer JB, Early BP, FellersRT, Caldwell MA, Sweedler JV, Kafader JO, Kelleher NL. "Proteoform profiling of endogenous single cells from rat hippocampus at scale" Nat Biotechnol. 2025. PubMed .
  • Maciag AE, Yang Y, Sharma AK, Turner DM, DeHart CJ, Abdelkarim H, Fan L,Smith BP, Kumari V, Dyba M, Rigby M, Castillo Badillo JA, Adams L, Fornelli L,Fox S, Brafman A, Turbyville T, Gillette W, Messing S, Agamasu C, Wolfe AL,Gysin S, Chan AH, Simanshu DK, Esposito D, Chertov O, Stephen AG, Arkin M,Renslo A, Kelleher NL, Gaponenko V, Lightstone FC, Nissley DV, McCormick F. "Blocking C-terminal processing of KRAS4b via a direct covalent attack on the CaaX-box cysteine" Proc Natl Acad Sci U S A. 2025. 122(19) .
  • Gomes FP, Durbin KR, Schauer K, Nwachukwu JC, R Kobylski R, Njeri JW, SeathCP, Saviola AJ, McClatchy DB, Diedrich JK, Garrett PT, Papa AB, Ciolacu I,Kelleher NL, Nettles KW, Yates JR 3rd. "Native top-down proteomics enables discovery in endocrine-resistant breast cancer" Nat Chem Biol. 2025. 21(8) PubMed .
  • Liu Y, Piorczynski TB, Estrella B, Ricker EC, Pazos M, Gonzalez Y, Tolu SS,Ryu Tiger YK, Karan C, Cremers S, Nandakumar R, Honig B, Hwang H, Kelleher NL,Camarillo JM, Abshiru NA, Amengual JE. "Targeting Monoallelic CREBBP / EP300 Mutations in Germinal Center-Derived B-Cell Lymphoma with a First- in-Class Histone Acetyltransferase Activator" bioRxiv [Preprint]. 2025. .
  • Shull T, Bhimalli P, Welninski S, Cho BK, Mattamana B, Arivalagan J, TarhoniI, Goo YA, Schneider JA, Agrawal S, Bennett DA, Leurgans S, Patel MB, Ely EW,Kelleher NL, Borgia JA, Schneider JR, Al-Harthi L. "Elevated neuroinflammation, autoimmunity, and altered IgG glycosylation profile in the cerebral spinal fluid of severe COVID-19 patients" Brain Behav Immun. 2025. 128 PubMed .
  • Ives AN, Jooß K, Melani RD, Fellers RT, Janetzko J, Kelleher NL. "Capillary Zone Electrophoresis-Mass Spectrometry of Intact G Protein-Coupled Receptors Enables Proteoform Profiling" Anal Chem. 2025. 97(13) .
  • Börner K, Blood PD, Silverstein JC, Ruffalo M, Satija R, Teichmann SA,Pryhuber GJ, Misra RS, Purkerson JM, Fan J, Hickey JW, Molla G, Xu C, Zhang Y,Weber GM, Jain Y, Qaurooni D, Kong Y; HRA Team; Bueckle A, Herr BW 2nd. "Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage" Nat Methods. 2025. 22(4) PubMed .
  • Su T, Fellers RT, Greer JB, LeDuc RD, Thomas PM, Kelleher NL. "Proteoform- predictor: Increasing the Phylogenetic Reach of Top-Down Proteomics" J Proteome Res. 2025. 24(4) PubMed .
  • Skinner KA, Fisher TD, Lee A, Su T, Forte E, Sanchez A, Caldwell MA,Kelleher NL. "Next-Generation Protein Sequencing and individual ion mass spectrometry enable complementary analysis of interleukin-6" bioRxiv [Preprint]. 2025. PubMed .
  • Janisse SE, Fellers RT, Raab SA, Goodwin MP, Bowen KP, Lian ZJ, Durbin KR,Senko MW, Compton PD, Kafader JO, Kelleher NL. "A Robust and Automated Platform for Charge Detection Mass Spectrometry of Megadalton Biotherapeutics" Anal Chem. 2025. 97(8) PubMed .
  • Kelleher NL. "The Proteoform Program of Life: Deciphering Evolution at the Protein Level" J Proteome Res. 2025. 24(5) .
  • Nshanian M, Gruber JJ, Geller BS, Chleilat F, Lancaster SM, White SM,Alexandrova L, Camarillo JM, Kelleher NL, Zhao Y, Snyder MP. "Short-chain fatty acid metabolites propionate and butyrate are unique epigenetic regulatory elements linking diet, metabolism and gene expression" Nat Metab. 2025. 7(1) PubMed .
  • Su P, McGee JP, Hollas MAR, Fellers RT, Durbin KR, Greer JB, Early BP, YipPF, Zabrouskov V, Srzentić K, Senko MW, Compton PD, Kelleher NL, Kafader JO. "Standardized workflow for multiplexed charge detection mass spectrometry on orbitrap analyzers" Nat Protoc. 2025. 20(6) PubMed .
  • He F, Aebersold R, Baker MS, Bian X, Bo X, Chan DW, Chang C, Chen L, Chen X,Chen YJ, Cheng H, Collins BC, Corrales F, Cox J, E W, Van Eyk JE, Fan J, FaridiP, Figeys D, Gao GF, Gao W, Gao ZH, Goda K, Goh WWB, Gu D, Guo C, Guo T, He Y,Heck AJR, Hermjakob H, Hunter T, Iyer NG, Jiang Y, Jimenez CR, Joshi L, KelleherNL, Li M, Li Y, Lin Q, Liu CH, Liu F, Liu GH, Liu Y, Liu Z, Low TY, Lu B, MannM, Meng A, Moritz RL, Nice E, Ning G, Omenn GS, Overall CM, Palmisano G, Peng Y,Pineau C, Poon TCW, Purcell AW, Qiao J, Reddel RR, Robinson PJ, Roncada P,Sander C, Sha J, Song E, Srivastava S, Sun A, Sze SK, Tang C, Tang L, Tian R,Vizcaíno JA, Wang C, Wang C, Wang X, Wang X, Wang Y, Weiss T, Wilhelm M, WinklerR, Wollscheid B, Wong L, Xie L, Xie W, Xu T, Xu T, Yan L, Yang J, Yang X, YatesJ, Yun T, Zhai Q, Zhang B, Zhang H, Zhang L, Zhang L, Zhang P, Zhang Y, ZhengYZ, Zhong Q, Zhu Y; Ï€-HuB Consortium. "Author Correction: Ï€-HuB: the proteomic navigator of the human body" Nature. 2025. 637(8046) .

    • 2024

  • He F, Aebersold R, Baker MS, Bian X, Bo X, Chan DW, Chang C, Chen L, Chen X,Chen YJ, Cheng H, Collins BC, Corrales F, Cox J, E W, Van Eyk JE, Fan J, FaridiP, Figeys D, Gao GF, Gao W, Gao ZH, Goda K, Goh WWB, Gu D, Guo C, Guo T, He Y,Heck AJR, Hermjakob H, Hunter T, Iyer NG, Jiang Y, Jimenez CR, Joshi L, KelleherNL, Li M, Li Y, Lin Q, Liu CH, Liu F, Liu GH, Liu Y, Liu Z, Low TY, Lu B, MannM, Meng A, Moritz RL, Nice E, Ning G, Omenn GS, Overall CM, Palmisano G, Peng Y,Pineau C, Poon TCW, Purcell AW, Qiao J, Reddel RR, Robinson PJ, Roncada P,Sander C, Sha J, Song E, Srivastava S, Sun A, Sze SK, Tang C, Tang L, Tian R,Vizcaíno JA, Wang C, Wang C, Wang X, Wang X, Wang Y, Weiss T, Wilhelm M, WinklerR, Wollscheid B, Wong L, Xie L, Xie W, Xu T, Xu T, Yan L, Yang J, Yang X, YatesJ, Yun T, Zhai Q, Zhang B, Zhang H, Zhang L, Zhang L, Zhang P, Zhang Y, ZhengYZ, Zhong Q, Zhu Y; Ï€-HuB Consortium. "Ï€-HuB: the proteomic navigator of the human body" Nature. 2024. 636(8042) PubMed .
  • Nakagawa R, Llorian M, Varsani-Brown S, Chakravarty P, Camarillo JM, BarryD, George R, Blackledge NP, Duddy G, Kelleher NL, Klose RJ, Turner M, Calado DP. "Epi-microRNA mediated metabolic reprogramming counteracts hypoxia to preserve affinity maturation" Nat Commun. 2024. 15(1) PubMed .
  • Zou Y, Huang CF, Sturrock GR, Kelleher NL, Fitzgerald MC. "Top-Down Stability of Proteins from Rates of Oxidation (TD-SPROX) Approach for Measuring Proteoform-Specific Folding Stability" Anal Chem. 2024. 96(49) PubMed .
  • Forte E, Sanders JM, Pla I, Kanchustambham VL, Hollas MAR, Huang CF, SanchezA, Peterson KN, Melani RD, Huang A, Polineni P, Doll JM, Dietch Z, Kelleher NL,Ladner DP. "Top-Down Proteomics Identifies Plasma Proteoform Signatures of Liver Cirrhosis Progression" Mol Cell Proteomics. 2024. 23(12) .
  • Huang CF, Hollas MA, Sanchez A, Bhattacharya M, Ho G, Sundaresan A, CaldwellMA, Zhao X, Benz R, Siddiqui A, Kelleher NL. "Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-Down Proteomics" J Proteome Res. 2024. 23(10) PubMed .
  • Des Soye BJ, Melani RD, Hollas MAR, Duan J, Patrie SM, Fisher TD, MattamanaBB, Daud A, Pinelli DF, Ladner DP, Kelleher NL, Forte E. "Characterization of the Antibody Response to SARS-CoV-2 Infection in COVID-19 Transplant versus Nontransplant Recipients by Ig-MS" J Proteome Res. 2024. 23(9) .
  • Des Soye BJ, McGee JP, Hollas MAR, Forte E, Fellers RT, Melani RD, WilkinsJT, Compton PD, Kafader JO, Kelleher NL. "Automated Immunoprecipitation, Sample Preparation, and Individual Ion Mass Spectrometry Platform for Proteoforms" Anal Chem. 2024. .
  • Ayon NJ, Earp CE, Gupta R, Butun FA, Clements AE, Lee AG, Dainko D, RobeyMT, Khin M, Mardiana L, Longcake A, Rangel-Grimaldo M, Hall MJ, Probert MR,Burdette JE, Keller NP, Raja HA, Oberlies NH, Kelleher NL, Caesar LK. "Bioactivity-driven fungal metabologenomics identifies antiproliferative stemphone analogs and their biosynthetic gene cluster" Metabolomics. 2024. 20(5) PubMed .
  • Huang CF, Hollas MA, Sanchez A, Bhattacharya M, Ho G, Sundaresan A, CaldwellMA, Zhao X, Benz R, Siddiqui A, Kelleher NL. "Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-down Proteomics" bioRxiv [Preprint]. 2024. PubMed .
  • Devitt AN, Vargas AL, Zhu W, Des Soye BJ, Butun FA, Alt T, Kaley N, FerreiraGM, Moran GR, Kelleher NL, Liu D, Silverman RB. "Correction to "Design, Synthesis, and Mechanistic Studies of (R)-3-Amino-5,5-difluorocyclohex-1-ene-1-carboxylic Acid as an Inactivator of Human Ornithine Aminotransferase"" ACS Chem Biol. 2024. 19(8) .
  • Manley OM, Shriver TJ, Xu T, Melendrez IA, Palacios P, Robson SA, Guo Y,Kelleher NL, Ziarek JJ, Rosenzweig AC. "A multi-iron enzyme installs copper- binding oxazolone/thioamide pairs on a nontypeable Haemophilus influenzae virulence factor" Proc Natl Acad Sci U S A. 2024. 121(28) PubMed .
  • Forte E, Sanders JM, Pla I, Kanchustambham VL, Hollas MAR, Huang CF, SanchezA, Peterson KN, Melani RD, Huang A, Polineni P, Doll JM, Dietch Z, Kelleher NL,Ladner DP. "Top-Down Proteomics Identifies Plasma Proteoform Signatures of Liver Cirrhosis Progression" bioRxiv [Preprint]. 2024. .
  • Faizi M, Fellers RT, Lu D, Drown BS, Jambhekar A, Lahav G, Kelleher NL,Gunawardena J. "MSModDetector: a tool for detecting mass shifts and post- translational modifications in individual ion mass spectrometry data" Bioinformatics. 2024. 40(6) PubMed .
  • Habeck T, Brown KA, Des Soye B, Lantz C, Zhou M, Alam N, Hossain MA, Jung W,Keener JE, Volny M, Wilson JW, Ying Y, Agar JN, Danis PO, Ge Y, Kelleher NL, LiH, Loo JA, Marty MT, PaÅ¡a-Tolić L, Sandoval W, Lermyte F. "Top-down mass spectrometry of native proteoforms and their complexes: a community study" Nat Methods. 2024. 21(12) PubMed .
  • Devitt AN, Vargas AL, Zhu W, Des Soye BJ, Butun FA, Alt T, Kaley N, FerreiraGM, Moran GR, Kelleher NL, Liu D, Silverman RB. "Design, Synthesis, and Mechanistic Studies of (R)-3-Amino-5,5-difluorocyclohex-1-ene-1-carboxylic Acid as an Inactivator of Human Ornithine Aminotransferase" ACS Chem Biol. 2024. 19(5) PubMed .
  • Su P, Hollas MAR, Butun FA, Kanchustambham VL, Rubakhin S, Ramani N, GreerJB, Early BP, Fellers RT, Caldwell MA, Sweedler JV, Kafader JO, Kelleher NL. "Single Cell Analysis of Proteoforms" J Proteome Res. 2024. 23(6) .
  • Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F,Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, LiuH, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de PlasR, Vlachos IS, Zhou M; HuBMAP Consortium; Börner K, Snyder MP. "Author Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)" Nat Cell Biol. 2024. 26(5) PubMed .
  • Drown BS, Gupta R, McGee JP, Hollas MAR, Hergenrother PJ, Kafader JO,Kelleher NL. "Precise Readout of MEK1 Proteoforms upon MAPK Pathway Modulation by Individual Ion Mass Spectrometry" Anal Chem. 2024. 96(11) .
  • Nshanian M, Geller BS, Gruber JJ, Chleilat F, Camarillo JM, Kelleher NL,Zhao Y, Snyder MP. "Short-chain fatty acids propionate and butyrate control growth and differentiation linked to cellular metabolism" Res Sq [Preprint]. 2024. PubMed .
  • Park SC, Steffan BN, Yun Lim F, Gupta R, Ayaloglu Butun F, Chen H, Ye R,Decker T, Wu CC, Kelleher NL, Woo Bok J, Keller NP. "Terpenoid balance in Aspergillus nidulans unveiled by heterologous squalene synthase expression" Sci Adv. 2024. 10(8) PubMed .
  • Huang CF, Kline JT, Negrão F, Robey MT, Toby TK, Durbin KR, Fellers RT,Friedewald JJ, Levitsky J, Abecassis MMI, Melani RD, Kelleher NL, Fornelli L. "Targeted Quantification of Proteoforms in Complex Samples by Proteoform Reaction Monitoring" Anal Chem. 2024. 96(8) .
  • Nshanian M, Gruber JJ, Geller BS, Chleilat F, Lancaster S, White SM,Alexandrova L, Camarillo JM, Kelleher NL, Zhao Y, Snyder MP. "Short-chain fatty acid metabolites propionate and butyrate are unique epigenetic regulatory elements linking diet, metabolism and gene expression" bioRxiv [Preprint]. 2024. .
  • Goodwin MP, Grinfeld D, Yip P, Bowen KP, Kafader JO, Kelleher NL, Senko MW. "Improved Signal Processing for Mass Shifting Ions in Charge Detection Mass Spectrometry" J Am Soc Mass Spectrom. 2024. 35(4) PubMed .
  • Green JJ, Grimm C, Fristo A, Byrum J, Kelleher NL. "Parsing 20 Years of Public Data by AI Maps Trends in Proteomics and Forecasts Technology" J Proteome Res. 2024. 23(2) PubMed .

    • 2023

  • Huang CF, Su P, Fisher TD, Levitsky J, Kelleher NL, Forte E. "Mass spectrometry-based proteomics for advancing solid organ transplantation research" Front Transplant. 2023. 2 PubMed .
  • Weerawarna PM, Schiefer IT, Soares P, Fox S, Morimoto RI, Melani RD,Kelleher NL, Luan CH, Silverman RB. "Target Identification of a Class of Pyrazolone Protein Aggregation Inhibitor Therapeutics for Amyotrophic Lateral Sclerosis" ACS Cent Sci. 2023. 10(1) PubMed .
  • McGee JP, Su P, Durbin KR, Hollas MAR, Bateman NW, Maxwell GL, Conrads TP,Fellers RT, Melani RD, Camarillo JM, Kafader JO, Kelleher NL. "Author Correction: Automated imaging and identification of proteoforms directly from ovarian cancer tissue" Nat Commun. 2023. 14(1) PubMed .
  • Fisher NP, McGee JP, Bowen KP, Goodwin M, Senko MW, Kelleher NL, Kafader JO. "Determining Collisional Cross Sections from Ion Decay with Individual Ion Mass Spectrometry" J Am Soc Mass Spectrom. 2023. 34(12) PubMed .
  • Park SC, Steffan BN, Lim FY, Gupta R, Butun FA, Chen H, Ye R, Decker T, WuCC, Kelleher NL, Bok JW, Keller NP. "Terpenoid balance in Aspergillus nidulans unveiled by heterologous squalene synthase expression" bioRxiv [Preprint]. 2023. PubMed .
  • Kandi S, Cline EN, Rivera BM, Viola KL, Zhu J, Condello C, LeDuc RD, KleinWL, Kelleher NL, Patrie SM. "Amyloid β Proteoforms Elucidated by Quantitative LC/MS in the 5xFAD Mouse Model of Alzheimer's Disease" J Proteome Res. 2023. 22(11) PubMed .
  • McGee JP, Su P, Durbin KR, Hollas MAR, Bateman NW, Maxwell GL, Conrads TP,Fellers RT, Melani RD, Camarillo JM, Kafader JO, Kelleher NL. "Automated imaging and identification of proteoforms directly from ovarian cancer tissue" Nat Commun. 2023. 14(1) PubMed .
  • Robey MT, Utley D, Greer JB, Fellers RT, Kelleher NL, Durbin KR. "Advancing Intact Protein Quantitation with Updated Deconvolution Routines" Anal Chem. 2023. 95(40) PubMed .
  • McGee JP, Melani RD, Des Soye B, Croote D, Winton V, Quake SR, Kafader JO,Kelleher NL. "Immunocomplexed Antigen Capture and Identification by Native Top- Down Mass Spectrometry" J Am Soc Mass Spectrom. 2023. 34(10) PubMed .
  • Nakagawa R, Llorian M, Varsani-Brown S, Chakravarty P, Camarillo JM, BarryD, George R, Blackledge NP, Duddy G, Kelleher NL, Klose RJ, Turner M, Calado DP. "Epi-microRNA mediated metabolic reprogramming ensures affinity maturation" bioRxiv [Preprint]. 2023. PubMed .
  • Su T, Hollas MAR, Fellers RT, Kelleher NL. "Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics" Annu Rev Biomed Data Sci. 2023. 6 PubMed .
  • Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F,Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, LiuH, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de PlasR, Vlachos IS, Zhou M; HuBMAP Consortium; Börner K, Snyder MP. "Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)" Nat Cell Biol. 2023. 25(8) PubMed .
  • Quardokus EM, Saunders DC, McDonough E, Hickey JW, Werlein C, Surrette C,Rajbhandari P, Casals AM, Tian H, Lowery L, Neumann EK, Björklund F, NeelakantanTV, Croteau J, Wiblin AE, Fisher J, Livengood AJ, Dowell KG, Silverstein JC,Spraggins JM, Pryhuber GS, Deutsch G, Ginty F, Nolan GP, Melov S, Jonigk D,Caldwell MA, Vlachos IS, Muller W, Gehlenborg N, Stockwell BR, Lundberg E,Snyder MP, Germain RN, Camarillo JM, Kelleher NL, Börner K, Radtke AJ. "Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging" Nat Methods. 2023. 20(8) .
  • Moritz L, Schon SB, Rabbani M, Sheng Y, Agrawal R, Glass-Klaiber J, SultanC, Camarillo JM, Clements J, Baldwin MR, Diehl AG, Boyle AP, O'Brien PJ,Ragunathan K, Hu YC, Kelleher NL, Nandakumar J, Li JZ, Orwig KE, Redding S,Hammoud SS. "Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse protamine 1" Nat Struct Mol Biol. 2023. 30(8) PubMed .
  • Durbin KR, Robey MT, Voong LN, Fellers RT, Lutomski CA, El-Baba TJ, RobinsonCV, Kelleher NL. "ProSight Native: Defining Protein Complex Composition from Native Top-Down Mass Spectrometry Data" J Proteome Res. 2023. 22(8) PubMed .
  • Faizi M, Fellers RT, Lu D, Drown BS, Jambhekar A, Lahav G, Kelleher NL,Gunawardena J. "MSModDetector: A Tool for Detecting Mass Shifts and Post- Translational Modifications in Individual Ion Mass Spectrometry Data" bioRxiv [Preprint]. 2023. PubMed .
  • Zhu W, Butrin A, Melani RD, Doubleday PF, Ferreira GM, Tavares MT, HabeebMohammad TS, Beaupre BA, Kelleher NL, Moran GR, Liu D, Silverman RB. "Correction to "Rational Design, Synthesis, and Mechanism of (3S,4R)-3-Amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylic Acid: Employing a Second-Deprotonation Strategy for Selectivity of Human Ornithine Aminotransferase over GABA Aminotransferase"" J Am Chem Soc. 2023. 145(17) .
  • MacDonald KM, Nicholson-Puthenveedu S, Tageldein MM, Khasnis S, Arrowsmith CH, Harding SM. “Antecedent chromatin organization determines cGAS recruitment to ruptured micronuclei” Cell Stem Cell. 2023. 14(1). PubMed .
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  • Adams LM, DeHart CJ, Drown BS, Anderson LC, Bocik W, Boja ES, Hiltke TM, Hendrickson CL, Rodriguez H, Caldwell M, Vafabakhsh R, Kelleher NL. “Mapping the KRAS proteoform landscape in colorectal cancer identifies truncated KRAS4B that decreases MAPK signaling” J Biol Chem. 2023. 299(1). PubMed .
  • Chen YY, Chen S, Ok K, Duncan FE, O’Halloran TV, Woodruff TK. “Zinc dynamics regulate early ovarian follicle development” J Biol Chem. 2023. 299(1). PubMed .

    • 2022

  • Ash MK, Bhimalli PP, Cho BK, Mattamana BB, Gambut S, Tarhoni I, Fhied CL, Reyes AF, Welninski SJ, Arivalagan J, Negrão F, Goel R, Beck TL, Hope TJ, Sha BE, Goo YA, Al-Harthi L, Mamede JI, Borgia JA, Kelleher NL, Schneider JR. “Bulk IgG glycosylation predicts COVID-19 severity and vaccine antibody response” Cell reports. 2022. 41(11). PubMed .
  • Hegazy M, Koetsier JL, Huffine AL, Broussard JA, Godsel BM, Cohen-Barak E, Sprecher E, Wolfgeher DJ, Kron SJ, Godsel LM, Green KJ. “Epidermal stratification requires retromer-mediated desmoglein-1 recycling” Dev Cell. 2022. 57(24). PubMed .
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  • Ives AN, Dunn HA, Afsari HS, Seckler HDS, Foroutan MJ, Chavez E, Melani RD, Fellers RT, LeDuc RD, Thomas PM, Martemyanov KA, Kelleher NL, Vafabakhsh R. “Middle-Down Mass Spectrometry Reveals Activity-Modifying Phosphorylation Barcode in a Class C G Protein-Coupled Receptor” J Am Chem Soc. 2022. 144(50). PubMed .
  • McGee JP, Senko MW, Jooß K, Des Soye BJ, Compton PD, Kelleher NL, Kafader JO. “Automated Control of Injection Times for Unattended Acquisition of Multiplexed Individual Ion Mass Spectra” Anal Chem. 2022 . 94(48) PubMed .
  • Forte E, Des Soye BJ, Melani RD, Hollas MAR, Kafader JO, Sha BE, Schneider JR, Kelleher NL. “Divergent Antibody Repertoires Found for Omicron versus Wuhan SARS-CoV-2 Strains Using Ig-MS” J Proteome Res . 2022 . 21 (12) PubMed .
  • Rangel DL, Melani RD, Carvalho EL, Boldo JT, Gomes Dos Santos T, Kelleher NL, Pinto PM. “Venom characterization of the Brazilian Pampa snake Bothrops pubescens by top-down and bottom-up proteomics” Toxicon . 2022 . 220 PubMed .
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  • Schachner LF, Soye BD, Ro S, Kenney GE, Ives AN, Su T, Goo YA, Jewett MC, Rosenzweig AC, Kelleher NL. “Revving an Engine of Human Metabolism: Activity Enhancement of Triosephosphate Isomerase via Hemi-Phosphorylation” ACS Chem Biol. 2022 . 17(10) PubMed .
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  • Farooq Z, Kusuma F, Burke P, Dufour CR, Lee D, Tabatabaei N, Toboz P, Radovani E, Greenblatt JF, Rehman J, Class J, Khoutorsky A, Fonseca BD, Richner JM, Mercier E, Bourque G, Giguère V, Subramaniam AR, Han J, Tahmasebi S. “The amino acid sensor GCN2 suppresses terminal oligopyrimidine (TOP) mRNA translation via La-related protein 1 (LARP1)” J Biol Chem. 2022 . 298(9) PubMed .
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  • Zhu W, Butrin A, Melani RD, Doubleday PF, Ferreira GM, Tavares MT, Habeeb Mohammad TS, Beaupre BA, Kelleher NL, Moran GR, Liu D, Silverman RB. “Rational Design, Synthesis, and Mechanism of (3 S ,4 R )-3-Amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylic Acid: Employing a Second-Deprotonation Strategy for Selectivity of Human Ornithine Aminotransferase over GABA Aminotransferase” J Am Chem Soc. 2022 . 144(12) PubMed .
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  • Mammoto T, Hunyenyiwa T, Kyi P, Hendee K, Matus K, Rao S, Lee SH, Tabima DM, Chesler NC, Mammoto A. “Hydrostatic Pressure Controls Angiogenesis Through Endothelial YAP1 During Lung Regeneration” Front Bioeng Biotechnol. 2022 . PubMed .
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    • 2021

  • Melani RD, Des Soye BJ, Kafader JO, Forte E, Hollas M, Blagojevic V, Negrão F, McGee JP, Drown B, Lloyd-Jones C, Seckler HS, Camarillo JM, Compton PD, LeDuc RD, Early B, Fellers RT, Cho BK, Mattamana BB, Goo YA, Thomas PM, Ash MK, Bhimalli PP, Al-Harthi L, Sha BE, Schneider JR, Kelleher NL. “Next-Generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire” J Proteome Res . 2021. Online ahead of print. PubMed .
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  • Troyanovsky RB, Indra I, Kato R, Mitchell BJ, Troyanovsky SM. “Basolateral protein Scribble binds phosphatase PP1 to establish a signaling network maintaining apicobasal polarity” J Biol Chem. 2021 . 297(5) PubMed . PubMedCentral .
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  • Bhansali RS, Rammohan M, Lee P, Laurent AP, Wen Q, Suraneni P, Yip BH, Tsai YC, Jenni S, Bornhauser B, Siret A, Fruit C, Pacheco-Benichou A, Harris E, Besson T, Thompson BJ, Goo YA, Hijiya N, Vilenchik M, Izraeli S, Bourquin JP, Malinge S, Crispino JD. “DYRK1A regulates B cell acute lymphoblastic leukemia through phosphorylation of FOXO1 and STAT3” J Clin Invest . 2021 . 131(1) PubMed . PubMedCentral .
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  • Yusufova N, Kloetgen A, Teater M, Osunsade A, Camarillo JM, Chin CR, Doane AS, Venters BJ, Portillo-Ledesma S, Conway J, Phillip JM, Elemento O, Scott DW, Béguelin W, Licht JD, Kelleher NL, Staudt LM, Skoultchi AI, Keogh MC, Apostolou E, Mason CE, Imielinski M, Schlick T, David Y, Tsirigos A, Allis CD, Soshnev AA, Cesarman E, Melnick AM. “Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture” Nature . 2021 . 589(7841) p. 299-305 PubMed . PubMedCentral .
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    • 2020

  • Parsa S, Ortega-Molina A, Ying HY, Jiang M, Teater M, Wang J, Zhao C, Reznik E, Pasion JP, Kuo D, Mohan P, Wang S, Camarillo JM, Thomas PM, Jain N, Garcia-Bermudez J, Cho BK, Tam W, Kelleher NL, Socci N, Dogan A, De Stanchina E, Ciriello G, Green MR, Li S, Birsoy K, Melnick AM, Wendel HG. “The serine hydroxymethyltransferase-2 (SHMT2) initiates lymphoma development through epigenetic tumor suppressor silencing” Nat Cancer . 2020 . 1 p. 653-664 PubMed . PubMedCentral .
  • Liu X, De la Cruz E, Gu X, Balint L, Oxendine-Burns M, Terrones T, Ma W, Kuo HH, Lantz C, Bansal T, Thorp E, Burridge P, Jakus Z, Herz J, Cleaver O, Torres M, Oliver G. “Lymphoangiocrine signals promote cardiac growth and repair” Nature . 2020 . 588(7839) p. 705-711 PubMed . PubMedCentral .
  • An S, Camarillo JM, Huang TY, Li D, Morris JA, Zoltek MA, Qi J, Behbahani M, Kambhampati M, Kelleher NL, Nazarian J, Thomas PM, Saratsis AM. “Histone tail analysis reveals H3K36me2 and H4K16ac as epigenetic signatures of diffuse intrinsic pontine glioma” J Exp Clin Cancer Res . 2020 . 39(1) p. 261 PubMed . PubMedCentral .
  • Lee J, Robinson ME, Ma N, Artadji D, Ahmed MA, Xiao G, Sadras T, Deb G, Winchester J, Cosgun KN, Geng H, Chan LN, Kume K, Miettinen TP, Zhang Y, Nix MA, Klemm L, Chen CW, Chen J, Khairnar V, Wiita AP, Thomas-Tikhonenko A, Farzan M, Jung JU, Weinstock DM, Manalis SR, Diamond MS, Vaidehi N, Müschen M. “IFITM3 functions as a PIP3 scaffold to amplify PI3K signalling in B cells” Nature . 2020 . 588(7838) p. 491-497 PubMed . PubMedCentral .
  • Abshiru NA, Sikora JW, Camarillo JM, Morris JA, Compton PD, Lee T, Neelamraju Y, Haddox S, Sheridan C, Carroll M, Cripe LD, Tallman MS, Paietta EM, Melnick AM, Thomas PM, Garrett-Bakelman FE, Kelleher NL. “Targeted detection and quantitation of histone modifications from 1,000 cells” PLoS One . 2020 . 15(10) PubMed . PubMedCentral .
  • Deighan WI, Winton VJ, Melani RD, Anderson LC, McGee JP, Schachner LF, Barnidge D, Murray D, Alexander HD, Gibson DS, Deery MJ, McNicholl FP, McLaughlin J, Kelleher NL, Thomas PM. “Development of novel methods for non-canonical myeloma protein analysis with an innovative adaptation of immunofixation electrophoresis, native top-down mass spectrometry, and middle-down de novo sequencing” Clin Chem Lab Med . 2020 . 59(4) p. 653-661 PubMed .
  • Song X, Zhou Z, Li H, Xue Y, Lu X, Bahar I, Kepp O, Hung MC, Kroemer G, Wan Y. “Pharmacologic Suppression of B7-H4 Glycosylation Restores Antitumor Immunity in Immune-Cold Breast Cancers” Cancer Discov . 2020 . 10(12) p. 1872-1893 PubMed . PubMedCentral .
  • Srzentić K, Fornelli L, Tsybin YO, Loo JA, Seckler H, Agar JN, Anderson LC, Bai DL, Beck A, Brodbelt JS, van der Burgt YEM, Chamot-Rooke J, Chatterjee S, Chen Y, Clarke DJ, Danis PO, Diedrich JK, D’Ippolito RA, Dupré M, Gasilova N, Ge Y, Goo YA, Goodlett DR, Greer S, Haselmann KF, He L, Hendrickson CL, Hinkle JD, Holt MV, Hughes S, Hunt DF, Kelleher NL, Kozhinov AN, Lin Z, Malosse C, Marshall AG, Menin L, Millikin RJ, Nagornov KO, Nicolardi S, Paša-Tolić L, Pengelley S, Quebbemann NR, Resemann A, Sandoval W, Sarin R, Schmitt ND, Shabanowitz J, Shaw JB, Shortreed MR, Smith LM, Sobott F, Suckau D, Toby T, Weisbrod CR, Wildburger NC, Yates JR 3rd, Yoon SH, Young NL, Zhou M. “Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry” J Am Soc Mass Spectrom . 2020 . 31(9) p. 1783-1802 PubMed . PubMedCentral .
  • Weisbrod CR, Anderson LC, Greer JB, DeHart CJ, Hendrickson CL. “Increased Single-Spectrum Top-Down Protein Sequence Coverage in Trapping Mass Spectrometers with Chimeric Ion Loading” Anal Chem . 2020 . 92(18) p. 12193-12200 PubMed . PubMedCentral .
  • Lee K, Huang ZN, Mirkin CA, Odom TW. “Endosomal Organization of CpG Constructs Correlates with Enhanced Immune Activation” Nano Lett . 2020 . 20(8) p.6170-6175 PubMed . PubMedCentral .
  • Szczepanski AP, Zhao Z, Sosnowski T, Goo YA, Bartom ET, Wang L . “ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer” Genome Med . 2020 . 12(1) p. 63 PubMed . PubMedCentral .
  • McMahon KM, Calvert AE, Dementieva IS, Hussain S, Wilkins JT, Thaxton CS . “Interparticle Molecular Exchange of Surface Chemical Components of Native High-Density Lipoproteins to Complementary Nanoparticle Scaffolds” ACS Sens . 2020 . 5(10) p. 3019-3024 PubMed . PubMedCentral .
  • Takemori A, Butcher DS, Harman VM, Brownridge P, Shima K, Higo D, Ishizaki J, Hasegawa H, Suzuki J, Yamashita M, Loo JA, Loo RRO, Beynon RJ, Anderson LC, Takemori N. “PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry” J Proteome Res . 2020 . 19(9) p. 3779-3791 PubMed . PubMedCentral .
  • Zhou Y, Han C, Wang E, Lorch AH, Serafin V, Cho BK, Gutierrez Diaz BT, Calvo J, Fang C, Khodadadi-Jamayran A, Tabaglio T, Marier C, Kuchmiy A, Sun L, Yacu G, Filip SK, Jin Q, Takahashi YH, Amici DR, Rendleman EJ, Rawat R, Bresolin S, Paganin M, Zhang C, Li H, Kandela I, Politanska Y, Abdala-Valencia H, Mendillo ML, Zhu P, Palhais B, Van Vlierberghe P, Taghon T, Aifantis I, Goo YA, Guccione E, Heguy A, Tsirigos A, Wee KB, Mishra RK, Pflumio F, Accordi B, Basso G, Ntziachristos P. “Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia” Cancer Discov . 2020 . 10(9) p. 1388-1409 PubMed . PubMedCentral .
  • Béguelin W, Teater M, Meydan C, Hoehn KB, Phillip JM, Soshnev AA, Venturutti L, Rivas MA, Calvo-Fernández MT, Gutierrez J, Camarillo JM, Takata K, Tarte K, Kelleher NL, Steidl C, Mason CE, Elemento O, Allis CD, Kleinstein SH, Melnick AM. “Mutant EZH2 Induces a Pre-malignant Lymphoma Niche by Reprogramming the Immune Response” Cancer Cell . 2020 . 37(5) p. 655-673 PubMed . PubMedCentral .
  • Levine DC, Hong H, Weidemann BJ, Ramsey KM, Affinati AH, Schmidt MS, Cedernaes J, Omura C, Braun R, Lee C, Brenner C, Peek CB, Bass J. “NAD + Controls Circadian Reprogramming through PER2 Nuclear Translocation to Counter Aging” Mod Cell . 2020 . 78(5) p. 835-849 PubMed . PubMedCentral .
  • Zhang D, Kinloch AJ, Srinath A, Shenkar R, Girard R, Lightle R, Moore T, Koskimäki J, Mohsin A, Carrión-Penagos J, Romanos S, Shen L, Clark MR, Shi C, Awad IA. “Antibodies in cerebral cavernous malformations react with cytoskeleton autoantigens in the lesional milieu” J Autoimmun. 2020 . 113 PubMed . PubMedCentral .
  • Ruhland BR, Reniere ML. “YjbH Requires Its Thioredoxin Active Motif for the Nitrosative Stress Response, Cell-to-Cell Spread, and Protein-Protein Interactions in Listeria monocytogenes” J Bacteriol. 2020 . 202 (12) PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • Doubleday PF, Fornelli L, Kelleher NL. “Elucidating Proteoform Dynamics Underlying the Senescence Associated Secretory Phenotype” J Proteome Res . 2020 . 19(2) p. 938-948 PubMed . PubMedCentral .
  • Kaplan N, Dong Y, Wang S, Yang W, Park JK, Wang J, Fiolek E, Perez White B, Chandel NS, Peng H, Lavker RM. “FIH-1 engages novel binding partners to positively influence epithelial proliferation via p63” FASEB J . 2020 . 34(1) p. 525-539 PubMed . PubMedCentral .
  • Winer B, Edgel KA, Zou X, Sellau J, Hadiwidjojo S, Garver LS, McDonough CE, Kelleher NL, Thomas PM, Villasante E, Ploss A, Gerbasi VR. “Identification of Plasmodium falciparum proteoforms from liver stage models” Malar J . 2020 . 19(1) p. 10 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • Coden ME, Loffredo LF, Walker MT, Jeong BM, Nam K, Bochner BS, Abdala-Valencia H, Berdnikovs S. “Fibrinogen Is a Specific Trigger for Cytolytic Eosinophil Degranulation” J Immunol . 2020 . 204(2) p. 438-448 PubMed . PubMedCentral .
  • Schneider JR, Shen X, Orlandi C, Nyanhete T, Sawant S, Carias AM, Smith AD 4th, Kelleher NL, Veazey RS, Lewis GK, Tomaras GD, Hope TJ. “A MUC16 IgG Binding Activity Selects for a Restricted Subset of IgG Enriched for Certain Simian Immunodeficiency Virus Epitope Specificities” J Virol . 2020 . 94(5) PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .

    • 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 PubMed . PubMedCentral .
  • Watson ZL, Yamamoto TM, McMellen A, Kim H, Hughes CJ, Wheeler LJ, Post MD, Behbakht K, Bitler BG. “Histone methyltransferases EHMT1 and EHMT2 (GLP/G9A) maintain PARP inhibitor resistance in high-grade serous ovarian carcinoma” Clin Epigenetics . 2019 . 11(1) p. 165 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 Adv . 2019 . 5(1) eaat0456 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • Wilkins JT, Seckler HS. “HDL modification: recent developments and their relevance to atherosclerotic cardiovascular disease.” Curr Opin Lipidol . 2019 . 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 Protoc . 2019 . 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 Res . 2019 . 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 PubMed . PubMedCentral .

    • 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 PubMed . PubMedCentral .
  • 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) p: eaar5280. PubMed .
  • 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 .
  • 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 PubMed . PubMedCentral .
  • 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 .
  • 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 PubMed . PubMedCentral .
  • 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 .
  • 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 .
  • 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 PubMed . PubMedCentral .
  • 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 .
  • Fornelli L, Srzentić K, Huguet R, Mullen C, Sharma S, Zabrouskov V, Fellers RT, Durbin KR, Compton PD, Kelleher NL. “Accurate Sequence Analysis of a Monoclonal Antibody by Top-Down and Middle-Down Orbitrap Mass Spectrometry Applying Multiple Ion Activation Techniques” Anal Chem. 2018 . 90(14) p. 8421-8429 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • Smith LM, Kelleher NL. “Proteoforms as the next proteomics currency.” Science . 2018 . 359(6380) p. 1106-1107 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 PubMed . PubMedCentral .
  • 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 Proteomics . 2018. 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. Rep . 2017 . 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 PubMed . PubMedCentral .
  • 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. 2017 . PubMed . 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. 2017 . PubMed . 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 PubMed . PubMedCentral .
  • 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. p . 381-94 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.” Proteomics . 2016. 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. Chem . 2016. 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 Biology . 2016. 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 PubMed . PubMedCentral .

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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