Publications

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

    2018

  • 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.  [Epub ahead of print] PubMed.
  • 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.
  •  

    2017

  • 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.
  • 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.
  • 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.
  • 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.
  • Whitney JC, Peterson SB, Kim J, Pazos M, Verster AJ, Radey MC, Kulasekara HD, Ching MQ, Bullen NP, Bryant D, Goo YA, Surette MG, Borenstein E, Vollmer W, Mougous JD, “A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria.” Elife. 2017PubMed. PubMedCentral.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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. 7. 2017. 9520. PubMed. PubMedCentral.
  • “Open Science Cyber Risk Profile.” Open Science Cyber Risk Profile. Web. 15 Feb. 2017. Github
  • 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.
  • Schroeter ER., Dehart CJ, Cleland TP, Zheng W, Thomas PM, Kelleher NL, Bern M, Schweitzer MH. “Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein.” Journal of Proteome Research. 2017. 16(2) p. 920-32. PubMedPubMedCentral.
  • 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. 2017. 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 . 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

  • Rui G, 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.” Biotechnology and Bioengineering. 2016. PubMed. PubMedCentral.
  • Skinner OS, Schachner LF, Kelleher NL. “The Search Engine for Multi-Proteoform Complexes: An Online Tool for the Identification and Stoichiometry Determination of Protein Complexes.” Current Protocols in Bioinformatics. 2016. 56:13.30.1-13.30.11. PubMed. PubMedCentral.
  • Savaryn JP, Toby TK, Kelleher NL. “A researcher’s guide to mass spectrometry-based proteomics.” Proteomics2016. 16(18) p.435-443. PubMed. PubMedCentral.
  • Toby TK, Fornelli L, Kelleher NL. “Progress in Top-Down Proteomics and the Analysis of Proteoforms.” Annu. Rev. Anal. 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. 11124-1127. 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 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):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):4805-14 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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