Publications

319 entries « 1 of 7 »

2019

LeDuc, R D; Fellers, R T; Early, B P; Greer, J B; Shams, D P; Thomas, P; Kelleher, N L

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

Mol Cell Proteomics., 18 (4), pp. 796-805, 2019.

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Cline, E N; Das, A; Bicca, M A; Mohammad, S N; Schachner, L F; Kamel, J M; DiNunno, N; Weng, A; Paschall, J D; Bu, R L; Khan, F M; Rollins, M G; Ives, A N; Shekhawat, G; Nunes-Tavares, N; de Mello, F G; Compton, P D; Kelleher, N L; Klein, W L

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

J Neurochem., 148 (6), pp. 822-836, 2019.

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Kafader, J O; Melani, R D; Senko, M W; Makarov, A A; Kelleher, N L; Compton, P D

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

Anal Chem., 91 (4), pp. 2776-2783, 2019.

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Swaroop, A; Oyer, J A; Will, C M; Huang, X; Yu, W; Troche, C; Bulic, M; Durham, B H; Wen, Q J; Crispino, J D; MacKerell, Jr A D; Bennett, R L; Kelleher, N L; Licht, J D

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

Oncogene., 38 (5), pp. 671-686, 2019.

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Jin, Q; Martinez, C A; Arcipowski, K M; Zhu, Y; Gutierrez-Diaz, B T; Wang, K K; Johnson, M R; Volk, A G; Wang, F; Wu, J; Grove, C; Wang, H; Sokirniy, I; Thomas, P M; Goo, Y A; Abshiru, N A; Hijiya, N; Peirs, S; Vandamme, N; Berx, G; Goosens, S; Marshall, S A; Rendleman, E J; Takahashi, Y H; Wang, L; Rawat, R; Bartom, E T; Collings, C K; Van Vlierberghe, P; Strikoudis, A; Kelly, S; Ueberheide, B; Mantis, C; Kandela, I; Bourquin, J P; Bornhauser, B; Serafin, V; Bresolin, S; Paganin, M; Accordi, B; Basso, G; Kelleher, N L; Weinstock, J; Kumar, S; Crispino, J D; Shilatifard, A; Ntziachristos, P

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

Clin Cancer Res., 25 (1), pp. 222-239, 2019.

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Toby, T K; Fornelli, L; Srzentić, K; DeHart, C J; Levitsky, J; Friedewald, J; Kelleher, N L

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

Nat Protoc., 14 (1), pp. 119-152, 2019.

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2018

Alvares, K; DeHart, C J; Thomas, P M; Kelleher, N L; Veis, A

The unique biomineralization transcriptome and proteome of Lytechinus variegatus teeth Journal Article

Connect Tissue Res., 59 (sup1), pp. 20-29, 2018.

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Fisher, O S; Kenney, G E; Ross, M O; Ro, S Y; Lemma, B E; Batelu, S; Thomas, P M; Sosnowski, V C; DeHart, C J; Kelleher, N L; Stemmler, T L; Hoffman, B M; Rosenzweig, A C

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

Nat Commun., 9 (1), pp. 4276, 2018.

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Mullowney, M W; McClure, R A; Robey, M T; Kelleher, N L; Thomson, R J

Natural products from thioester reductase containing biosynthetic pathways Journal Article

Nat Prod Rep., 35 (9), pp. 847-878, 2018.

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Gruppuso, P A; Boylan, J M; Zabala, V; Neretti, N; Abshiru, N A; Sikora, J W; Doud, E H; Camarillo, J M; Thomas, P M; Kelleher, N L; Sanders, J A

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

PLoS One., 13 (9), 2018.

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Compton, P D; Kelleher, N L; Gunawardena, J

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

J Proteome Res., 17 (8), pp. 2727-2734, 2018.

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Fornelli, L; Srzentić, K; Huguet, R; Mullen, C; Sharma, S; Zabrouskov, V; Fellers, R T; Durbin, K R; Compton, P D; Kelleher, N L

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

Anal Chem., 90 (14), pp. 8421-8429, 2018.

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Riley, N M; Sikora, J W; Seckler, H S; Greer, J B; Fellers, R T; LeDuc, R D; Westphall, M S; Thomas, P M; Kelleher, N L; Coon, J J

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

Anal Chem., 90 (14), pp. 8553-8560, 2018.

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Park, Y J; Kenney, G E; Schachner, L F; Kelleher, N L; Rosenzweig, A C

Repurposed HisC Aminotransferases Complete the Biosynthesis of Some Methanobactins Journal Article

Biochemistry, 57 (25), pp. 3515-3523, 2018.

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Clevenger, K D; Ye, R; Bok, J W; Thomas, P M; Islam, M N; Miley, G P; Robey, M T; Chen, C; Yang, K; Swyers, M; Wu, E; Gao, P; Wu, C C; Keller, N P; Kelleher, N L

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

Biochemistry, 57 (23), pp. 3237-3243, 2018.

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Seckler, H D S; Fornelli, L; Mutharasan, R K; Thaxton, C S; Fellers, R; Daviglus, M; Sniderman, A; Rader, D; Kelleher, N L; Lloyd-Jones, D M; Compton, P D; Wilkins, J T

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

J Proteome Res., 17 (6), pp. 2156-2164, 2018.

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Robey, M T; Ye, R; Bok, J W; Clevenger, K D; Islam, M N; Chen, C; Gupta, R; Swyers, M; Wu, E; Gao, P; Thomas, P M; Wu, C C; Keller, N P; Kelleher, N L

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

ACS Chem Biol., 13 (5), pp. 1142-1147, 2018.

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Zheng, J; L, Chen.; Skinner, O S; Ysselstein, D; Remis, J; Lansbury, P; Skerlj, R; Mrosek, M; Heunisch, U; Krapp, S; Charrow, J; Schwake, M; Kelleher, N L; Silverman, R B; Krainc, D

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

J Am Chem Soc., 140 (18), pp. 5914-5924, 2018.

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Parkinson, E I; Tryon, J H; Goering, A W; Ju, K S; McClure, R A; Kemball, J D; Zhukovsky, S; Labeda, D P; Thomson, R J; Kelleher, N L; Metcalf, W W

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

ACS Chem Biol., 13 (4), pp. 1029-1037, 2018.

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Miley, G P; Rote, J C; Silverman, R B; Kelleher, N L; Thomson, R J

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

Org Lett., 20 (8), pp. 2369-2373, 2018.

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Ntai, I; Fornelli, L; DeHart, C J; Hutton, J E; Doubleday, P F; LeDuc, R D; van Nispen, A J; Fellers, R T; Whiteley, G; Boja, E S; Rodriguez, H; Kelleher, N L

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

Proc Natl Acad Sci USA, 115 (16), pp. 4140-4145, 2018.

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Kenney, G E; Dassama, L M K; Pandelia, M E; Gizzi, A S; Martinie, R J; Gao, P; DeHart, C J; Schachner, L F; Skinner, O S; Ro, S Y; Zhu, X; Sadek, M; Thomas, P M; Almo, S C; Bollinger, J M; Jr Krebs, C; Kelleher, N L; Rosenzweig, AC

The biosynthesis of methanobactin. Journal Article

Science, 359 (6382), pp. 1411-1416, 2018.

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Martin, R W; Des Soye, B J; Kwon, Y C; Kay, J; Davis, R G; Thomas, P M; Majewska, N I; Chen, C X; Marcum, R D; Weiss, M G; Stoddart, A E; Amiram, M; Ranji Charna, A K; Patel, J R; Isaacs, F J; Kelleher, N L; Hong, S H; Jewett, MC

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

Nat. Commun., 9 (1), pp. 1203, 2018.

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Davis, R G; Park, H M; Kim, K; Greer, J B; Fellers, R T; LeDuc, R D; Romanova, E V; Rubakhin, S S; Zombeck, J A; Wu, C; Yau, P M; Gao, P; van Nispen, A J; Patrie, S M; Thomas, P M; Sweedler, J V; Rhodes, J S; Kelleher, N L

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

Anal Chem, 90 (6), pp. 3802-3810, 2018.

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Smith, L M; Kelleher, N L

Proteoforms as the next proteomics currency. Journal Article

Science, 359 (6380), pp. 1106-1107, 2018.

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LeDuc, R; Schwammle, V; Shortreed, MR ; Cesnick, 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. Journal Article

J Proteome Res., 17 (3), pp. 1321-1325, 2018.

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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? Journal Article

Nat Chem Biol., 14 (3), pp. 206-214, 2018.

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2017

Harris, D; Lukoyanov, D; Shaw, S; Compton, P D; Tokmina-Lukaszewska, M; Bothner, B; Kelleher, N L; Dean, D R; Hoffman, B M; Seefeldt, L C

The Mechanism of N2 Reduction Catalyzed by Fe-Nitrogenase Involves Reductive Elimination of H2 Journal Article

Biochemistry, 57 (5), pp. 701-710, 2017.

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Rickels, R; Herz, H M; Sze, C C; Cao, K; Morgan, M A; Collings, C K; Gause, M; Takahashi, Y H; Wang, L; Rendleman, E J; Marshall, S A; Krueger, A; Bartom, E T; Piunti, A; Smith, E R; Abshiru, N A; Kelleher, N L; Dorsett, D; Shilatifard, A

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

Nat. Genet., 49 (11), pp. 1647-1653, 2017.

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Turcan, S; Makarov, V; Taranda, J; Wang, Y; Fabius, A W M; Wu, W; Zheng, Y; El-Amine, N; Haddock, S; Nanjangud, G; LeKaye, H C; Brennan, C; Cross, J; Huse, J T; Kelleher, N L; Osten, P; Thompson, C B; Chan, T A

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

Nat. Genet., 50 (1), pp. 62-72, 2017.

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Skinner, O S; Haverland, N A; Fornelli, L; Melani, R D; Vale, Do L H F; Seckler, H S; Doubleday, P F; Schachner, L F; Srzentić, K; Kelleher, N L; Compton, P D

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

Nat. Chem. Biol., 14 (1), pp. 36-41, 2017.

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Mascarenhas, R; Le, H V; Clevenger, K D; Lehrer, H J; Ringe, D; Kelleher, N L; Silverman, R B; Liu, D

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

Biochemistry, 56 (43), pp. 5844-5845, 2017.

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Skinner, O S; McAnally, M O; Duyne, Van R P; Schatz, G C; Breuker, K; Compton, P D; Kelleher, N L

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

Anal. Chem., 89 (20), pp. 10711-10716, 2017.

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Haverland, N A; Wass, M; Ntai, I; Keppel, T; Gundry, R L; Kelleher, N L

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

Proteomics, 17 (19), 2017.

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Ezponda, T; Dupéré-Richer, D; Will, C M; Small, E C; Varghese, N; Patel, T; Nabet, B; Popovic, R; Oyer, J; Bulic, M; Zheng, Y; Huang, X; Shah, M Y; Maji, S; Riva, A; Occhionorelli, M; Tonon, G; Kelleher, N; Keats, J; Licht, J D

UTX/KDM6A Loss Enhances the Malignant Phenotype of Multiple Myeloma and Sensitizes Cells to EZH2 inhibition Journal Article

Cell. Rep., 21 (3), pp. 628-640, 2017.

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Zha, L; Jiang, Y; Henke, M T; Wilson, M R; Wang, J X; Kelleher, N L; Balskus, E P

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

Nat Chem Biol, 13 (10), pp. 1063-1065, 2017.

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Morgan, M A J; Rickels, R A; Collings, C K; He, X; Cao, K; Herz, H M; Cozzolino, K A; Abshiru, N A; Marshall, S A; Rendleman, E J; Sze, C C; Piunti, A; Kelleher, N L; Savas, J N; Shilatifard, A

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

Genes. Dev., 19 , pp. 2003-2014, 2017.

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Ichikawa, Y; Connelly, C F; Appleboim, A; Miller, T C; Jacobi, H; Abshiru, N A; Chou, H J; Chen, Y; Sharma, U; Zheng, Y; Thomas, P M; Chen, H V; Bajaj, V; Müller, C W; Kelleher, N L; Friedman, N; Bolon, D N; Rando, O J; Kaufman, P D

A synthetic biology approach to probing nucleosome symmetry Journal Article

eLife, (6), 2017.

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Mascarenhas, R; Le, H V; Clevenger, K D; Lehrer, H J; Ringe, D; Kelleher, N L; Silverman, R B; Liu, D

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

Biochemistry, 56 (37), pp. 4951-4961, 2017.

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Wildburger, N C; Esparza, T J; LeDuc, R D; Fellers, R T; Thomas, P M; Cairns, N J; Kelleher, N L; Bateman, R J; Brody, D L

Diversity of Amyloid-beta Proteoforms in the Alzheimer’s Disease Brain Journal Article

Sci. Rep., 7 (1), pp. 9520, 2017.

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Zhou, Y; Zhang, X; Fornelli, L; Compton, P D; Kelleher, N; Wirth, M J

Chromatographic efficiency and selectivity in top-down proteomics of histones. Journal Article

J Chromatogr B Analyt Technol Biomed Life Sci, pp. 47-53, 2017.

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Anderson, L C; DeHart, C J; Kaiser, N K; Fellers, R T; Smith, D F; Greer, J B; LeDuc, R D; Blakney, G T; Thomas, P M; Kelleher, N L; Hendrickson, C L

Identification and Characterization of Human Proteoforms by Top-Down LC-21 Tesla FT-ICR Mass Spectrometry Journal Article

J Proteome Res, 16 (2), pp. 1087-1096, 2017, ISSN: 1535-3907 (Electronic) 1535-3893 (Linking).

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Cleland, T P; DeHart, C J; Fellers, R T; VanNispen, A J; Greer, J B; LeDuc, R D; Parker, W R; Thomas, P M; Kelleher, N L; Brodbelt, J S

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

J Proteome Res, 16 (5), pp. 2072-2079, 2017, ISSN: 1535-3907 (Electronic) 1535-3893 (Linking).

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Clevenger, K D; Bok, J W; Ye, R; Miley, G P; Verdan, M H; Velk, T; Chen, C; Yang, K; Robey, M T; Gao, P; Lamprecht, M; Thomas, P M; Islam, M N; Palmer, J M; Wu, C C; Keller, N P; Kelleher, N L

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

Nat Chem Biol, 2017, ISSN: 1552-4469 (Electronic) 1552-4450 (Linking).

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Clevenger, K D; Mascarenhas, R; Catlin, D; Wu, R; Kelleher, N L; Drake, E J; Gulick, A M; Liu, D; Fast, W

Substrate Trapping in the Siderophore Tailoring Enzyme PvdQ Journal Article

ACS Chem Biol, 12 (3), pp. 643-647, 2017, ISSN: 1554-8937 (Electronic) 1554-8929 (Linking).

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DeHart, C J; Fellers, R T; Fornelli, L; Kelleher, N L; Thomas, P M

Bioinformatics Analysis of Top-Down Mass Spectrometry Data with ProSight Lite Journal Article

Methods Mol Biol, 1558 , pp. 381-394, 2017, ISSN: 1940-6029 (Electronic) 1064-3745 (Linking).

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Fornelli, L; Durbin, K R; Fellers, R T; Early, B P; Greer, J B; LeDuc, R D; Compton, P D; Kelleher, N L

Advancing Top-down Analysis of the Human Proteome Using a Benchtop Quadrupole-Orbitrap Mass Spectrometer Journal Article

J Proteome Res, 16 (2), pp. 609-618, 2017, ISSN: 1535-3907 (Electronic) 1535-3893 (Linking).

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Fornelli, L; Toby, T K; Schachner, L F; Doubleday, P F; Srzentic, K; DeHart, C J; Kelleher, N L

Top-down proteomics: Where we are, where we are going? Journal Article

J Proteomics, 2017, ISSN: 1876-7737 (Electronic) 1874-3919 (Linking).

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Gan, R; Perez, J G; Carlson, E D; Ntai, I; Isaacs, F J; Kelleher, N L; Jewett, M C

Translation system engineering in Escherichia coli enhances non-canonical amino acid incorporation into proteins Journal Article

Biotechnol Bioeng, 114 (5), pp. 1074-1086, 2017, ISSN: 1097-0290 (Electronic) 0006-3592 (Linking).

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Goering, A W; Li, J; McClure, R A; Thomson, R J; Jewett, M C; Kelleher, N L

In Vitro Reconstruction of Nonribosomal Peptide Biosynthesis Directly from DNA Using Cell-Free Protein Synthesis Journal Article

ACS Synth Biol, 6 (1), pp. 39-44, 2017, ISSN: 2161-5063 (Electronic) 2161-5063 (Linking).

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319 entries « 1 of 7 »