Publications

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

2023

• 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.
• Álvarez Z, Ortega JA, Sato K, Sasselli IR, Kolberg-Edelbrock AN, Qiu R, Marshall KA, Nguyen TP, Smith CS, Quinlan KA, Papakis V, Syrgiannis Z, Sather NA, Musumeci C, Engel E, Stupp SI, Kiskinis E. “Artificial extracellular matrix scaffolds of mobile molecules enhance maturation of human stem cell-derived neurons” Nat Commun. 2023. 30(2). PubMed.
• Amici DR, Cingoz H, Alasady MJ, Alhayek S, Phoumyvong CM, Sahni N, Yi SS, Mendillo ML. “The HAPSTR2 retrogene buffers stress signaling and resilience in mammals” Nat Commun. 2023. 14(1). PubMed.
• 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.
• Burgdorf JS, Yoon S, Dos Santos M, Lammert CR, Moskal JR, Penzes P. “An IGFBP2-derived peptide promotes neuroplasticity and rescues deficits in a mouse model of Phelan-McDermid syndrome” Mol Psychiatry. 2022. 144(50) PubMed.
• 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. 
• Logeswaran D, Li Y, Akhter K, Podlevsky JD, Olson TL, Forsberg K, Chen JJ. “Biogenesis of telomerase RNA from a protein-coding mRNA precursor” Proc Natl Acad Sci U S A. 2022. 119(41) PubMed. 
• Mondal C, Gacha-Garay MJ, Larkin KA, Adikes RC, Di Martino JS, Chien CC, Fraser M, Eni-Aganga I, Agullo-Pascual E, Cialowicz K, Ozbek U, Naba A, Gaitas A, Fu TM, Upadhyayula S, Betzig E, Matus DQ, Martin BL, Bravo-Cordero JJ. “A proliferative to invasive switch is mediated by srGAP1 downregulation through the activation of TGF-β2 signaling” Cell Rep. 2022. 40(12) PubMed. 
• Ranava D, Scheidler CM, Pfanzelt M, Fiedler M, Sieber SA, Schneider S, Yap MF. “Bidirectional sequestration between a bacterial hibernation factor and a glutamate metabolizing protein” Proc Natl Acad Sci U S A. 2022. 119(39) PubMed. 
• Trautmann HS, Ramsey KM. “A Ribosomal Protein Homolog Governs Gene Expression and Virulence in a Bacterial Pathogen” J Bacteriol. 2022. 204(10) PubMed. 
• Wilkins JT, Rohatgi A. “Resolution of apolipoprotein A1 and A2 proteoforms: their cardiometabolic correlates and implications for future research” Curr Opin Lopidol. 2022. 33(4) PubMed. 
• Campbell JA, Cianciotto NP. “Legionella pneumophila Cas2 Promotes the Expression of Small Heat Shock Protein C2 That Is Required for Thermal Tolerance and Optimal Intracellular Infection” Infect Immun. 2022. 90(10) PubMed. 
• Aoi Y, Shah AP, Ganesan S, Soliman SHA, Cho BK, Goo YA, Kelleher NL, Shilatifard A. “SPT6 functions in transcriptional pause/release via PAF1C recruitment” Mol Cell. 2022. 82(18) PubMed. 
• 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. 
• Su P, McGee JP, Durbin KR, Hollas MAR, Yang M, Neumann EK, Allen JL, Drown BS, Butun FA, Greer JB, Early BP, Fellers RT, Spraggins JM, Laskin J, Camarillo JM, Kafader JO, Kelleher NL. “Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry” Sci Adv. 2022. 8(32) PubMed. 
• 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. 
• Amici DR, Ansel DJ, Metz KA, Smith RS, Phoumyvong CM, Gayatri S, Chamera T, Edwards SL, O’Hara BP, Srivastava S, Brockway S, Takagishi SR, Cho BK, Goo YA, Kelleher NL, Ben-Sahra I, Foltz DR, Li J, Mendillo ML. “C16orf72/HAPSTR1 is a molecular rheostat in an integrated network of stress response pathways” Proc Natl Acad Sci U S A. 2022. 119(27) PubMed. 
• Ali ES, Lipońska A, O’Hara BP, Amici DR, Torno MD, Gao P, Asara JM, Yap MF, Mendillo ML, Ben-Sahra I. “The mTORC1-SLC4A7 axis stimulates bicarbonate import to enhance de novo nucleotide synthesis” Mol Cell. 2022. 82(17) PubMed. 
• Jooß K, McGee JP, Kelleher NL. “Native Mass Spectrometry at the Convergence of Structural Biology and Compositional Proteomics” Acc Chem Res. 2022. 55(14) PubMed. 
• Ranji Charna A, Des Soye BJ, Ntai I, Kelleher NL, Jewett MC. “An efficient cell-free protein synthesis platform for producing proteins with pyrrolysine-based noncanonical amino acids” Biotechnol J. 2022. 17(9) PubMed. 
• Yang M, Hu H, Su P, Thomas PM, Camarillo JM, Greer JB, Early BP, Fellers RT, Kelleher NL, Laskin J. “Proteoform-Selective Imaging of Tissues Using Mass Spectrometry” Angew Chem Int Ed Engl. 2022. 61(29) PubMed. 
• Drown BS, Jooß K, Melani RD, Lloyd-Jones C, Camarillo JM, Kelleher NL. “Mapping the Proteoform Landscape of Five Human Tissues” J Proteome Res. 2022. 21(5) PubMed. 
• Cherny KE, Balaji A, Mukherjee J, Goo YA, Hauser AR, Ozer E, Satchell KJF, Bachta KER, Kochan TJ, Mitra SD, Kociolek LK. “Identification of Clostridium innocuum hypothetical protein that is cross-reactive with C. difficile anti-toxin antibodies” Anaerobe. 2022. 75 PubMed. 
• Saleiro D, Wen JQ, Kosciuczuk EM, Eckerdt F, Beauchamp EM, Oku CV, Blyth GT, Fischietti M, Ilut L, Colamonici M, Palivos W, Atsaves PA, Tan D, Kocherginsky M, Weinberg RS, Fish EN, Crispino JD, Hoffman R, Platanias LC. “Discovery of a signaling feedback circuit that defines interferon responses in myeloproliferative neoplasms” Nat Commun. 2022. 13(1) PubMed. 
• Park YJ, Jodts RJ, Slater JW, Reyes RM, Winton VJ, Montaser RA, Thomas PM, Dowdle WB, Ruiz A, Kelleher NL, Bollinger JM Jr, Krebs C, Hoffman BM, Rosenzweig AC. “A mixed-valent Fe(II)Fe(III) species converts cysteine to an oxazolone/thioamide pair in methanobactin biosynthesis” Proc Natl Acad Sci U S A. 2022. 119(13) PubMed. 
• Teplensky MH, Distler ME, Kusmierz CD, Evangelopoulos M, Gula H, Elli D, Tomatsidou A, Nicolaescu V, Gelarden I, Yeldandi A, Batlle D, Missiakas D, Mirkin CA. “Spherical nucleic acids as an infectious disease vaccine platform” Proc Natl Acad Sci U S A. 2022. 119(14) PubMed. 
• 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. 
• LeDuc RD, Deutsch EW, Binz PA, Fellers RT, Cesnik AJ, Klein JA, Van Den Bossche T, Gabriels R, Yalavarthi A, Perez-Riverol Y, Carver J, Bittremieux W, Kawano S, Pullman B, Bandeira N, Kelleher NL, Thomas PM, Vizcaíno JA. “Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms” J Proteome Res. 2022. 21(4) PubMed. 
• Greer JB, Early BP, Durbin KR, Patrie SM, Thomas PM, Kelleher NL, LeDuc RD, Fellers RT. “ProSight Annotator: Complete control and customization of protein entries in UniProt XML files” Proteomics. 2022. 22(11-12) PubMed. 
• 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. 
• Plubell DL, Käll L, Webb-Robertson BJ, Bramer LM, Ives A, Kelleher NL, Smith LM, Montine TJ, Wu CC, MacCoss MJ. “Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?” J Proteome Res. 2022. 21(4) PubMed. 
• Melani RD, Gerbasi VR, Anderson LC, Sikora JW, Toby TK, Hutton JE, Butcher DS, Negrão F, Seckler HS, Srzentić K, Fornelli L, Camarillo JM, LeDuc RD, Cesnik AJ, Lundberg E, Greer JB, Fellers RT, Robey MT, DeHart CJ, Forte E, Hendrickson CL, Abbatiello SE, Thomas PM, Kokaji AI, Levitsky J, Kelleher NL. “The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells” Science. 2022. 375(6579) PubMed. 
• Hollas MAR, Robey MT, Fellers RT, LeDuc RD, Thomas PM, Kelleher NL. “The Human Proteoform Atlas: a FAIR community resource for experimentally derived proteoforms” Nucleic Acids Res. 2022. 50(D1) PubMed. 
• Kunder R, Velyunskiy M, Dunne SF, Cho BK, Kanojia D, Begg L, Orriols AM, Fleming-Trujillo E, Vadlamani P, Vialichka A, Bolin R, Perrino JN, Roth D, Clutter MR, Zielinski-Mozny NA, Goo YA, Cristofanilli M, Mendillo ML, Vassilopoulos A, Horiuchi D. “Synergistic PIM kinase and proteasome inhibition as a therapeutic strategy for MYC-overexpressing triple-negative breast cancer” Cell Chem Biol. 2022. 29(3) PubMed. 

 

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. 
• Smith LM, Agar JN, Chamot-Rooke J, Danis PO, Ge Y, Loo JA, Paša-Tolić L, Tsybin YO, Kelleher NL; Consortium for Top-Down Proteomics. “The Human Proteoform Project: Defining the human proteome” Sci Adv. 2021. 7(46) PubMed. 
• 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. 
• Hayes OG, Partridge BE, Mirkin CA. “Encoding hierarchical assembly pathways of proteins with DNA” Proc Natl Acad Sci U S A. 2021. 118(40)  PubMed. 
• Mandel-Brehm C, Fichtner ML, Jiang R, Winton VJ, Vazquez SE, Pham MC, Hoehn KB, Kelleher NL, Nowak RJ, Kleinstein SH, Wilson MR, DeRisi JL, O’Connor KC. “Elevated N-Linked Glycosylation of IgG V Regions in Myasthenia Gravis Disease Subtypes” J Immunol. 2021. 207(8) p. 2005-2014  PubMed. 
• Schachner LF, Tran DP, Lee A, McGee JP, Jooss K, Durbin K, Seckler HDS, Adams L, Cline E, Melani R, Ives AN, Des Soye B, Kelleher NL, Patrie SM. “Reassembling protein complexes after controlled disassembly by top-down mass spectrometry in native mode” Int J Mass Spectrom. 2021.  PubMed. 
• Park YJ, Roberts GM, Montaser R, Kenney GE, Thomas PM, Kelleher NL, Rosenzweig AC. “Characterization of a Copper-Chelating Natural Product from the Methanotroph Methylosinus sp. LW3″ Biochemistry. 2021. 60(38) p. 2845-2850 PubMed. 
• Vincent MP, Karabin NB, Allen SD, Bobbala S, Frey MA, Yi S, Yang Y, Scott EA. “The Combination of Morphology and Surface Chemistry Defines the Immunological Identity of Nanocarriers in Human Blood” Adv THer (Weinh). 2021. 4(4) PubMed. 
• Aoi Y, Takahashi YH, Shah AP, Iwanaszko M, Rendleman EJ, Khan NH, Cho BK, Goo YA, Ganesan S, Kelleher NL, Shilatifard A. “SPT5 stabilization of promoter-proximal RNA polymerase II” Mol Cell. 2021. 81(21) p. 4413-4424 PubMed. 
• Wilkins JT, Seckler HS, Rink J, Compton PD, Fornelli L, Thaxton CS, LeDuc R, Jacobs D, Doubleday PF, Sniderman A, Lloyd-Jones DM, Kelleher NL. “Spectrum of Apolipoprotein AI and Apolipoprotein AII Proteoforms and Their Associations With Indices of Cardiometabolic Health: The CARDIA Study” J Am Heart Assoc. 2021. 10(17) PubMed. 
• Zhao Z, Szczepanski AP, Tsuboyama N, Abdala-Valencia H, Goo YA, Singer BD, Bartom ET, Yue F, Wang L. “PAX9 Determines Epigenetic State Transition and Cell Fate in Cancer” Cancer Res. 2021. 81(18) p. 4696-4708 PubMed. PubMedCentral.
• Melani RD, Soye BJD, 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” MedRxiv. 2021. PubMed. PubMedCentral.
• Lipońska A, Yap MF. “Hibernation-Promoting Factor Sequesters Staphylococcus aureus Ribosomes to Antagonize RNase R-Mediated Nucleolytic Degradation” mBio. 2021. 12(4) PubMed. PubMedCentral.
• Doubleday PF, Fornelli L, Ntai I, Kelleher NL. “Oncogenic KRAS creates an aspartate metabolism signature in colorectal cancer cells” FEBS J. 2021. 188(23) p. 6683-6699 PubMed. 
• Alfaro JA, Bohländer P, Dai M, Filius M, Howard CJ, van Kooten XF, Ohayon S, Pomorski A, Schmid S, Aksimentiev A, Anslyn EV, Bedran G, Cao C, Chinappi M, Coyaud E, Dekker C, Dittmar G, Drachman N, Eelkema R, Goodlett D, Hentz S, Kalathiya U, Kelleher NL, Kelly RT, Kelman Z, Kim SH, Kuster B, Rodriguez-Larrea D, Lindsay S, Maglia G, Marcotte EM, Marino JP, Masselon C, Mayer M, Samaras P, Sarthak K, Sepiashvili L, Stein D, Wanunu M, Wilhelm M, Yin P, Meller A, Joo C. “The emerging landscape of single-molecule protein sequencing technologies” Nat Methods. 2021. 18(6) p. 604-617 PubMed. 
• Santos Seckler HD, Park HM, Lloyd-Jones CM, Melani RD, Camarillo JM, Wilkins JT, Compton PD, Kelleher NL. “New Interface for Faster Proteoform Analysis: Immunoprecipitation Coupled with SampleStream-Mass Spectrometry” J Am Soc Mass Spectrom. 2021. 32(7) p. 1659-1670 PubMed.  
• Leon KE, Buj R, Lesko E, Dahl ES, Chen CW, Tangudu NK, Imamura-Kawasawa Y, Kossenkov AV, Hobbs RP, Aird KM. “DOT1L modulates the senescence-associated secretory phenotype through epigenetic regulation of IL1A” J Cell Biol. 2021. 220(8) PubMed. PubMedCentral.
• Adams LM, DeHart CJ, Kelleher NL. “Precise Characterization of KRAS4B Proteoforms by Combining Immunoprecipitation with Top-Down Mass Spectrometry” Methods Mol Biol. 2021. p. 47-64 PubMed. PubMedCentral.
• Ma W, Gil HJ, Liu X, Diebold LP, Morgan MA, Oxendine-Burns MJ, Gao P, Chandel NS, Oliver G. “Mitochondrial respiration controls the Prox1-Vegfr3 feedback loop during lymphatic endothelial cell fate specification and maintenance” Sci Adv. 2021. 7(18) PubMed. PubMedCentral.
• Gerbasi VR, Melani RD, Abbatiello SE, Belford MW, Huguet R, McGee JP, Dayhoff D, Thomas PM, Kelleher NL. “Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics” Anal Chem. 2021. 93(16) p. 6323-6328 PubMed.  
• Park SH, Fong KW, Kim J, Wang F, Lu X, Lee Y, Brea LT, Wadosky K, Guo C, Abdulkadir SA, Crispino JD, Fang D, Ntziachristos P, Liu X, Li X, Wan Y, Goodrich DW, Zhao JC, Yu J. “Posttranslational regulation of FOXA1 by Polycomb and BUB3/USP7 deubiquitin complex in prostate cancer” Sci Adv. 2021. 7(15) PubMed. PubMedCentral.
• Jooß K, Schachner LF, Watson R, Gillespie ZB, Howard SA, Cheek MA, Meiners MJ, Sobh A, Licht JD, Keogh MC, Kelleher NL. “Separation and Characterization of Endogenous Nucleosomes by Native Capillary Zone Electrophoresis-Top-Down Mass Spectrometry” Anal Chem. 2021. 93(12) p. 5151-5160 PubMed.  
• Choo P, Liu T, Odom TW. “Nanoparticle Shape Determines Dynamics of Targeting Nanoconstructs on Cell Membranes” J Am Chem Soc. 2021. 143(12) p. 4550-4555 PubMed.  
• Schachner LF, Jooß K, Morgan MA, Piunti A, Meiners MJ, Kafader JO, Lee AS, Iwanaszko M, Cheek MA, Burg JM, Howard SA, Keogh MC, Shilatifard A, Kelleher NL. “Decoding the protein composition of whole nucleosomes with Nuc-MS” Nat Methods. 2021. 18(3) p. 303-308 PubMed. PubMedCentral.
• Jung HJ, Sorbara MT, Pamer EG. “TAM mediates adaptation of carbapenem-resistant Klebsiella pneumoniae to antimicrobial stress during host colonization and infection” PLoS Pathog. 2021. 17(2) PubMed. PubMedCentral.
• Jooß K, McGee JP, Melani RD, Kelleher NL. “Standard procedures for native CZE-MS of proteins and protein complexes up to 800 kDa” Electrophoresis. 2021. 42(9-10) p. 1050-1059 PubMed.  
• Liu Y, Davis RG, Thomas PM, Kelleher NL, Jewett MC. “In vitro-Constructed Ribosomes Enable Multi-site Incorporation of Noncanonical Amino Acids into Proteins” Biochemistry. 2021. 60(3) p. 161-169 PubMed.  
• 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.
• McGee JP, Melani RD, Yip PF, Senko MW, Compton PD, Kafader JO, Kelleher NL. “Isotopic Resolution of Protein Complexes up to 466 kDa Using Individual Ion Mass Spectrometry” Anal Chem. 2021. 93(5) p. 2723-2727 PubMed.  
• 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.  
• Hilfenhaus G, Mompeón A, Freshman J, Prajapati DP, Hernandez G, Freitas VM, Ma F, Langenbacher AD, Mirkov S, Song D, Cho BK, Goo YA, Pellegrini M, Chen JN, Damoiseaux R, Iruela-Arispe ML. “A High-Content Screen Identifies Drugs That Restrict Tumor Cell Extravasation across the Endothelial Barrier” Cancer Res. 2021. 81(3) p. 619-633 PubMed. PubMedCentral.  
• Kula-Eversole E, Lee DH, Samba I, Yildirim E, Levine DC, Hong HK, Lear BC, Bass J, Rosbash M, Allada R. “Phosphatase of Regenerating Liver-1 Selectively Times Circadian Behavior in Darkness via Function in PDF Neurons and Dephosphorylation of TIMELESS” Curr Biol. 2021. 31(1) p. 138-149 PubMed.  

 

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.