Publications

2023

Caesar, L. K; Butun, F. A; Robey, M. T; Ayon, N. J; Gupta, R; Dainko, D; Bok, J. W; Nickles, G; Stankey, R. J; Johnson, D; Mead, D; Cank, K. B; Earp, C. E; Raja, H. A; Oberlies, N. H; Keller, N. P; Kelleher, N. L

Correlative metabologenomics of 110 fungi reveals metabolite-gene cluster pairs Journal Article

In: Nat Chem Biol., vol. 19, iss. 7, pp. 846-854, 2023.

Abstract | Links | BibTeX

Lloyd-Jones, C; Dos Santos Seckler, H; DiStefano, N; Sniderman, A; Compton, P. D; Kelleher, N. L; Wilkins, J. T

Preparative Electrophoresis for HDL Particle Size Separation and Intact-Mass Apolipoprotein Proteoform Analysis Journal Article

In: J Proteome Res. , vol. 22, iss. 5, pp. 1455-1465, 2023.

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Zhu, W; Butrin, A; Melani, R. D; Doubleday, P. F; Ferreira, G. M; Tavares, M. T; Habeeb Mohammad, T. S; Beaupre, B. A; Kelleher, N. L; Moran, G. R; Liu, D; Silverman, R. B

Correction to "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" Journal Article

In: J Am Chem Soc. , vol. 145, iss. 17, pp. 9895-9896, 2023.

Links | BibTeX

Shen, S; Butrin, A; Beaupre, B. A; Ferreira, G. M; Doubleday, P. F; Grass, D. H; Zhu, W; Kelleher, N. L; Moran, G. R; Liu, D; Silverman, R. B

Structural and Mechanistic Basis for the Inactivation of Human Ornithine Aminotransferase by (3 S,4 S)-3-Amino-4-fluorocyclopentenecarboxylic Acid Journal Article

In: Molecules, vol. 28, iss. 3, pp. 1133, 2023.

Abstract | Links | BibTeX

Adams, L. M; DeHart, C. J; Drown, B. S; Anderson, L. C; Bocik, W; Boja, E. S; Hiltke, T. M; Hendrickson, C. L; Rodriguez, H; Caldwell, M; Vafabakhsh, R; N.L., Kelleher.

Mapping the KRAS proteoform landscape in colorectal cancer identifies truncated KRAS4B that decreases MAPK signaling Journal Article

In: J Biol Chem. , vol. 299, iss. 1, 2023.

Abstract | Links | BibTeX

2022

Ives, A. N; Dunn, H. A; Afsari, H. S; Seckler, H. D. S; Foroutan, M. J; Chavez, E; Melani, R. D; Fellers, R. T; LeDuc, R. D; Thomas, P. M; Martemyanov, K. A; Kelleher, N. L; Vafabakhsh, R

Middle-Down Mass Spectrometry Reveals Activity-Modifying Phosphorylation Barcode in a Class C G Protein-Coupled Receptor Journal Article

In: J Am Chem Soc. , vol. 144, iss. 50, pp. 23104-23114, 2022.

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Ash, M. K; Bhimalli, P. P; Cho, B. K; Mattamana, B. B; Gambut, S; Tarhoni, I; Fhied, C. L; Reyes, A. F; Welninski, S. J; Arivalagan, J; Negrão, F; Goel, R; Beck, T. L; Hope, T. J; Sha, B. E; Goo, Y. A; Al-Harthi, L; Mamede, J. I; Borgia, J. A; Kelleher, N. L; Schneider, J. R

Bulk IgG glycosylation predicts COVID-19 severity and vaccine antibody response Journal Article

In: Cell Rep., vol. 41, iss. 11, pp. 111799, 2022.

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Rangel, D. L; Melani, R. D; Carvalho, E. L; Boldo, J. T; Gomes, Dos Santos T; Kelleher, N. L; Pinto, P. M

Venom characterization of the Brazilian Pampa snake Bothrops pubescens by top-down and bottom-up proteomics Journal Article

In: Toxicon, vol. 220, 2022.

Abstract | Links | BibTeX

P, McGee J.; Senko, M. W; Jooß, K; Des Soye, B. J; Compton, P. D; Kelleher, N. L; Kafader, J. O.

Automated Control of Injection Times for Unattended Acquisition of Multiplexed Individual Ion Mass Spectra Journal Article

In: Anal. Chem. , vol. 94, iss. 48, pp. 16543-16548, 2022.

Abstract | Links | BibTeX

Forte, E; Des Soye, B. J; Melani, R. D; Hollas, M. A. R; Kafader, J. O; Sha, B. E; Schneider, J. R; Kelleher, N. L

Divergent Antibody Repertoires Found for Omicron versus Wuhan SARS-CoV-2 Strains Using Ig-MS Journal Article

In: J Proteome Res., vol. 21, iss. 12, pp. 2987-2997, 2022.

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Schachner, L. F; Soye, B. D; Ro, S; Kenney, G. E; Ives, A. N; Su, T; Goo, Y. A; Jewett, M. C; Rosenzweig, A. C; Kelleher, N. L

Revving an Engine of Human Metabolism: Activity Enhancement of Triosephosphate Isomerase via Hemi-Phosphorylation Journal Article

In: ACS Chem Biol., vol. 17, no. 10, pp. 2769-2780, 2022.

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Aoi, Y; Shah, A. P; Ganesan, S; Soliman, S. H. A; Cho, B. K; Goo, Y. A; Kelleher, N. L; Shilatifard, A

SPT6 functions in transcriptional pause/release via PAF1C recruitment Journal Article

In: Mol Cell., vol. 82, no. 18, pp. 3412-3423.e5, 2022.

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Ranji Charna, A; Des Soye, B. J; Ntai, I; Kelleher, N. L; Jewett, M. C

An efficient cell-free protein synthesis platform for producing proteins with pyrrolysine-based noncanonical amino acids Journal Article

In: Biotechnol J., vol. 17, no. 9, 2022.

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Su, P; McGee, J. P; Durbin, K. R; Hollas, M. A. R; Yang, M; Neumann, E. K; Allen, J. L; Drown, B. S; Butun, F. A; Greer, J. B; Early, B. P; Fellers, R. T; Spraggins, J. M; Laskin, J; Camarillo, J. M; Kafader, J. O; Kelleher, N. L

Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry Journal Article

In: Sci Adv. , vol. 8, no. 32, 2022.

Abstract | Links | BibTeX

Jooß, K; McGee, J. P; Kelleher, N. L

Native Mass Spectrometry at the Convergence of Structural Biology and Compositional Proteomics Journal Article

In: Acc Chem Res., vol. 55, no. 14, pp. 1928-1937, 2022.

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Yang, M; Hu, H; Su, P; Thomas, P. M; Camarillo, J. M; Greer, J. B; Early, B. P; Fellers, R. T; Kelleher, N. L; Laskin, J

Proteoform-Selective Imaging of Tissues Using Mass Spectrometry Journal Article

In: Angew Chem Int Ed Engl., vol. 61, no. 29, 2022.

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Leung, W; Teater, M; Durmaz, C; Meydan, C; Chivu, A. G; Chadburn, A; Rice, E. J; Muley, A; Camarillo, J. M; Arivalagan, J; Li, Z; Flowers, C. R; Kelleher, N. L; Danko, C. G; Imielinski, M; Dave, S. S; Armstrong, S. A; Mason, C. E; Melnick, A. M

SETD2 Haploinsufficiency Enhances Germinal Center-Associated AICDA Somatic Hypermutation to Drive B-cell Lymphomagenesis Journal Article

In: Cancer Discov., vol. 12, no. 7, pp. 1782-1803, 2022.

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Amici, D. R; Ansel, D. J; Metz, K. A; Smith, R. S; Phoumyvong, C. M; Gayatri, S; Chamera, T; Edwards, S. L; O'Hara, B. P; Srivastava, S; Brockway, S; Takagishi, S. R; Cho, B. K; Goo, Y. A; Kelleher, N. L; Ben-Sahra, I; Foltz, D. R; Li, J; Mendillo, M. L

C16orf72/HAPSTR1 is a molecular rheostat in an integrated network of stress response pathways Journal Article

In: Proc Natl Acad Sci U S A., vol. 119, no. 27, 2022.

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Melani, R. D; Des Soye, B. J; Kafader, J. O; Forte, E; Hollas, M; Blagojevic, V; Negrão, F; McGee, J. P; Drown, B; Lloyd-Jones, C; Seckler, H. S; Camarillo, J. M; Compton, P. D; LeDuc, R. D; Early, B; Fellers, R. T; Cho, B. K; Mattamana, B. B; Goo, Y. A; Thomas, P. M; Ash, M. K; Bhimalli, P. P; Al-Harthi, L; Sha, B. E; Schneider, J. R; Kelleher, N. L

Next-Generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire Journal Article

In: J Proteome Res., vol. 21, no. 1, pp. 274-288, 2022.

Abstract | Links | BibTeX

Burnum-Johnson, K. E; Conrads, T. P; Drake, R. R; Herr, A. E; Iyengar, R; Kelly, R. T; Lundberg, E; MacCoss, M. J; Naba, A; Nolan, G. P; Pevzner, P. A; Rodland, K. D; Sechi, S; Slavov, N; Spraggins, J. M; Van Eyk, J. E; Vidal, M; Vogel, C; Walt, D. R; Kelleher, N. L

New Views of Old Proteins: Clarifying the Enigmatic Proteome Journal Article

In: Mol Cell Proteomics., vol. 21, no. 7, 2022.

Abstract | Links | BibTeX

Drown, B. S; Jooß, K; Melani, R. D; Lloyd-Jones, C; Camarillo, J. M; Kelleher, N. L

Mapping the Proteoform Landscape of Five Human Tissues Journal Article

In: J Proteome Res., vol. 21, no. 5, pp. 1299-1310, 2022.

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LeDuc, R. D; Deutsch, E. W; Binz, P. A; Fellers, R. T; Cesnik, A. J; Klein, J. A; Van Den Bossche, T; Gabriels, R; Yalavarthi, A; Perez-Riverol, Y; Carver, J; Bittremieux, W; Kawano, S; Pullman, B; Bandeira, N; Kelleher, N. L; Thomas, P. M; Vizcaíno, J. A

Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms Journal Article

In: J Proteome Res., vol. 21, no. 4, pp. 1189-1195, 2022.

Abstract | Links | BibTeX

Zhu, W; Butrin, A; Melani, R. D; Doubleday, P. F; Ferreira, G. M; Tavares, M. T; Habeeb Mohammad, T. S; Beaupre, B. A; Kelleher, N. L; Moran, G. R; Liu, D; Silverman, R. B

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 Journal Article

In: J Am Chem Soc., vol. 144, no. 12, pp. 5629-5642, 2022.

Abstract | Links | BibTeX

Park, Y. J; Jodts, R. J; Slater, J. W; Reyes, R. M; Winton, V. J; Montaser, R. A; Thomas, P. M; Dowdle, W. B; Ruiz, A; Kelleher, N. L; Bollinger, J. M. Jr; Krebs, C; Hoffman, B. M; Rosenzweig, A. C

A mixed-valent Fe(II)Fe(III) species converts cysteine to an oxazolone/thioamide pair in methanobactin biosynthesis Journal Article

In: Proc Natl Acad Sci U S A., vol. 119, no. 13, 2022.

Abstract | Links | BibTeX

Greer, J. B; Early, B. P; Durbin, K. R; Patrie, S. M; Thomas, P. M; Kelleher, N. L; LeDuc, R. D; Fellers, R. T

ProSight Annotator: Complete control and customization of protein entries in UniProt XML files Journal Article

In: Proteomics., vol. 22, no. 11-12, 2022.

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Plubell, D. L; Käll, L; Webb-Robertson, B. J; Bramer, L. M; Ives, A; Kelleher, N. L; Smith, L. M; Montine, T. J; Wu, C. C; MacCoss, M. J

Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics? Journal Article

In: J Proteome Res., vol. 21, no. 4, pp. 891-898, 2022.

Abstract | Links | BibTeX

Bartley, S. C; Proctor, M. T; Xia, H; Ho, E; Kang, D. S; Schuster, K; Bicca, M. A; Seckler, H. S; Viola, K. L; Patrie, S. M; Kelleher, N. L; De Mello, F. G; Klein, W. L

An Essential Role for Alzheimer's-Linked Amyloid Beta Oligomers in Neurodevelopment: Transient Expression of Multiple Proteoforms during Retina Histogenesis Journal Article

In: Int J Mol Sci., vol. 23, no. 4, pp. 2208, 2022.

Abstract | Links | BibTeX

Melani, R. D; Gerbasi, V. R; Anderson, L. C; Sikora, J. W; Toby, T. K; Hutton, J. E; Butcher, D. S; Negrão, F; Seckler, H. S; Srzentić, K; Fornelli, L; Camarillo, J. M; LeDuc, R. D; Cesnik, A. J; Lundberg, E; Greer, J. B; Fellers, R. T; Robey, M. T; DeHart, C. J; Forte, E; Hendrickson, C. L; Abbatiello, S. E; Thomas, P. M; Kokaji, A. I; Levitsky, J; Kelleher, N. L

The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells Journal Article

In: Science., vol. 375, no. 6579, pp. 411-418, 2022.

Abstract | Links | BibTeX

Hollas, M. A. R; Robey, M. T; Fellers, R. T; LeDuc, R. D; Thomas, P. M; Kelleher, N. L

The Human Proteoform Atlas: a FAIR community resource for experimentally derived proteoforms Journal Article

In: Nucleic Acids Res., vol. 50, no. D1, pp. D526-D533, 2022.

Abstract | Links | BibTeX

2021

Hickey, J. W; Neumann, E. K; Radtke, A. J; Camarillo, J. M; Beuschel, R. T; Albanese, A; McDonough, E; Hatler, J; Wiblin, A. E; Fisher, J; Croteau, J; Small, E. C; Sood, A; Caprioli, R. M; Angelo, R. M; Nolan, G. P; Chung, K; Hewitt, S. M; Germain, R. N; Spraggins, J. M; Lundberg, E; Snyder, M. P; Kelleher, N. L; Saka, S. K

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging Journal Article

In: Nat Methods., vol. 19, no. 3, pp. 284-295, 2021.

Abstract | Links | BibTeX

Caesar, L. K; Montaser, R; Keller, N. P; Kelleher, N. L

Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities Journal Article

In: Nat Prod Rep., vol. 38, no. 11, pp. 2041-2065, 2021.

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Smith, L. M; Agar, J. N; Chamot-Rooke, J; Danis, P. O; Ge, Y; Loo, J. A; Paša-Tolić, L; Tsybin, Y. O; Kelleher, N. L; for Top-Down Proteomics, Consortium

The Human Proteoform Project: Defining the human proteome Journal Article

In: Sci Adv., vol. 7, no. 46, 2021.

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Mandel-Brehm, C; Fichtner, M. L; Jiang, R; Winton, V. J; Vazquez, S. E; Pham, M. C; Hoehn, K. B; Kelleher, N. L; Nowak, R. J; Kleinstein, S. H; Wilson, M. R; DeRisi, J. L; O'Connor, K. C

Elevated N-Linked Glycosylation of IgG V Regions in Myasthenia Gravis Disease Subtypes Journal Article

In: J Immunol., vol. 207, no. 8, pp. 2005-2014, 2021.

Abstract | Links | BibTeX

Park, Y. J; Roberts, G. M; Montaser, R; Kenney, G. E; Thomas, P. M; Kelleher, N. L; Rosenzweig, A. C

Characterization of a Copper-Chelating Natural Product from the Methanotroph Methylosinus sp. LW3 Journal Article

In: Biochemistry., vol. 60, no. 38, pp. 2845-2850, 2021.

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Aoi, Y; Takahashi, Y. H; Shah, A. P; Iwanaszko, M; Rendleman, E. J; Khan, N. H; Cho, B. K; Goo, Y. A; Ganesan, S; Kelleher, N. L; Shilatifard, A

SPT5 stabilization of promoter-proximal RNA polymerase II Journal Article

In: Mol Cell., vol. 81, no. 21, pp. 4413-4424.e5, 2021.

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Wilkins, J. T; Seckler, H. S; Rink, J; Compton, P. D; Fornelli, L; Thaxton, C. S; LeDuc, R; Jacobs, D; Doubleday, P. F; Sniderman, A; Lloyd-Jones, D. M; Kelleher, N. L

Spectrum of Apolipoprotein AI and Apolipoprotein AII Proteoforms and Their Associations With Indices of Cardiometabolic Health: The CARDIA Study Journal Article

In: J Am Heart Assoc., vol. 10, no. 17, 2021.

Abstract | Links | BibTeX

Doubleday, P. F; Fornelli, L; Ntai, I; Kelleher, N. L

Oncogenic KRAS creates an aspartate metabolism signature in colorectal cancer cells Journal Article

In: FEBS J., vol. 288, no. 23, pp. 6683-6699, 2021.

Abstract | Links | BibTeX

Melani, R. D; Des Soye, B. J; Kafader, J. O; Forte, E; Hollas, M; Blagojevic, V; Negrão, F; McGee, J. P; Drown, B; Lloyd-Jones, C; Seckler, H. S; Camarillo, J. M; Compton, P. D; LeDuc, R. D; Early, B; Fellers, R. T; Cho, B. K; Mattamana, B. B; Goo, Y. A; Thomas, P. M; Ash, M. K; Bhimalli, P. P; Al-Harthi, L; Sha, B. E; Schneider, J. R; Kelleher, N. L

Next-generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire Journal Article

In: medRxiv., vol. 21, no. 1, pp. 274-288, 2021.

Abstract | Links | BibTeX

Santos Seckler, H. D; Park, H. M; Lloyd-Jones, C. M; Melani, R. D; Camarillo, J. M; Wilkins, J. T; Compton, P. D; Kelleher, N. L

New Interface for Faster Proteoform Analysis: Immunoprecipitation Coupled with SampleStream-Mass Spectrometry Journal Article

In: J Am Soc Mass Spectrom., vol. 32, no. 7, pp. 1659-1670, 2021.

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Shen, S; Butrin, A; Doubleday, P. F; Melani, R. D; Beaupre, B. A; Tavares, M. T; Ferreira, G. M; Kelleher, N. L; Moran, G. R; Liu, D; Silverman, R. B

Turnover and Inactivation Mechanisms for ( S)-3-Amino-4,4-difluorocyclopent-1-enecarboxylic Acid, a Selective Mechanism-Based Inactivator of Human Ornithine Aminotransferase Journal Article

In: J Am Chem Soc., vol. 143, no. 23, pp. 8689-8703, 2021.

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Zhu, W; Doubleday, P. F; Butrin, A; Weerawarna, P. M; Melani, R. D; Catlin, D. S; Dwight, T. A; Liu, D; Kelleher, N. L; Silverman, R. B

Remarkable and Unexpected Mechanism for ( S)-3-Amino-4-(difluoromethylenyl)cyclohex-1-ene-1-carboxylic Acid as a Selective Inactivator of Human Ornithine Aminotransferase Journal Article

In: J Am Chem Soc., vol. 143, no. 21, pp. 8193-8207, 2021.

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Alfaro, J. A; Bohländer, P; Dai, M; Filius, M; Howard, C. J; van Kooten, X. F; Ohayon, S; Pomorski, A; Schmid, S; Aksimentiev, A; Anslyn, E. V; Bedran, G; Cao, C; Chinappi, M; Coyaud, E; Dekker, C; Dittmar, G; Drachman, N; Eelkema, R; Goodlett, D; Hentz, S; Kalathiya, U; Kelleher, N. L; Kelly, R. T; Kelman, Z; Kim, S. H; Kuster, B; Rodriguez-Larrea, D; Lindsay, S; Maglia, G; Marcotte, E. M; Marino, J. P; 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 Journal Article

In: Nat Methods., vol. 18, no. 6, pp. 604-617, 2021.

Abstract | Links | BibTeX

Adams, L. M; DeHart, C. J; Kelleher, N. L

Precise Characterization of KRAS4B Proteoforms by Combining Immunoprecipitation with Top-Down Mass Spectrometry Journal Article

In: Methods Mol Biol., no. 2262, pp. 47-64, 2021.

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Robey, M. T; Caesar, L. K; Drott, M. T; Keller, N. P; Kelleher, N. L

An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes Journal Article

In: Proc Natl Acad Sci U S A., vol. 118, no. 19, 2021.

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Schachner, L. F; Tran, D. P; Lee, A; McGee, J. P; Jooss, K; Durbin, K; Seckler, H. D. S; Adams, L; Cline, E; Melani, R; Ives, A. N; Des Soye, B; Kelleher, N. L; Patrie, S. M

Reassembling protein complexes after controlled disassembly by top-down mass spectrometry in native mode Journal Article

In: Int J Mass Spectrom., vol. 465, 2021.

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McGee, J. P; Melani, R. D; Yip, P. F; Senko, M. W; Compton, P. D; Kafader, J. O; Kelleher, N. L

Isotopic Resolution of Protein Complexes up to 466 kDa Using Individual Ion Mass Spectrometry Journal Article

In: Anal Chem., vol. 93, no. 5, pp. 2723-2727, 2021.

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Liu, Y; Davis, R. G; Thomas, P. M; Kelleher, N. L; Jewett, M. C

In vitro-Constructed Ribosomes Enable Multi-site Incorporation of Noncanonical Amino Acids into Proteins Journal Article

In: Biochemistry., vol. 60, no. 3, pp. 161-169, 2021.

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Yusufova, N; Kloetgen, A; Teater, M; Osunsade, A; Camarillo, J. M; Chin, C. R; Doane, A. S; Venters, B. J; Portillo-Ledesma, S; Conway, J; Phillip, J. M; Elemento, O; Scott, D. W; Béguelin, W; Licht, J. D; Kelleher, N. L; Staudt, L. M; Skoultchi, A. I; Keogh, M. C; Apostolou, E; Mason, C. E; Imielinski, M; Schlick, T; David, Y; Tsirigos, A; Allis, C. D; Soshnev, A. A; Cesarman, E; Melnick, A. M

Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture Journal Article

In: Nature., vol. 589, no. 7841, pp. 299-305, 2021.

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2020

Hoofnagle, A. N; Cobbaert, C. M; Delatour, V; Kelleher, N. L; Lowenthal, M. S; Shuford, C. M

Should LC-MS/MS Be the Reference Measurement Procedure to Determine Protein Concentrations in Human Samples? Journal Article

In: Clin Chem., 2020.

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Hamm, P. S; Dunlap, C. A; Mullowney, M. W; Caimi, N. A; Kelleher, N. L; Thomson, R. J; Porras-Alfaro, A; Northup, D. E

Streptomyces buecherae sp. nov., an actinomycete isolated from multiple bat species Journal Article

In: Antonie Van Leeuwenhoek., vol. 113, no. 12, pp. 2213-2221, 2020.

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An, S; Camarillo, J. M; Huang, T. Y; Li, D; Morris, J. A; Zoltek, M. A; Qi, J; Behbahani, M; Kambhampati, M; Kelleher, N. L; Nazarian, J; Thomas, P. M; Saratsis, A. M

Histone tail analysis reveals H3K36me2 and H4K16ac as epigenetic signatures of diffuse intrinsic pontine glioma Journal Article

In: J Exp Clin Cancer Res., vol. 39, no. 1, pp. 261, 2020.

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Tryon, J. H; Rote, J. C; Chen, L; Robey, M. T; Vega, M. M; Phua, W. C; Metcalf, W. W; Ju, K. S; Kelleher, N. L; Thomson, R. J

Genome Mining and Metabolomics Uncover a Rare d-Capreomycidine Containing Natural Product and Its Biosynthetic Gene Cluster Journal Article

In: ACS Chem Biol. , vol. 15, no. 11, pp. 3013-3020, 2020.

Abstract | Links | BibTeX

Caesar, L. K; Kelleher, N. L; Keller, N. P.

In the fungus where it happens: History and future propelling Aspergillus nidulans as the archetype of natural products research Journal Article

In: Fungal Genet Biol., vol. 144, 2020.

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Abshiru, N. A; Sikora, J. W; Camarillo, J. M; Morris, J. A; Compton, P. D; Lee, T; Neelamraju, Y; Haddox, S; Sheridan, C; Carroll, M; Cripe, L. D; Tallman, M. S; Paietta, E. M; Melnick, A. M; Thomas, P. M; Garrett-Bakelman, F. E; Kelleher, N. L.

Targeted detection and quantitation of histone modifications from 1,000 cells Journal Article

In: PLoS One., vol. 15, no. 10, 2020.

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Deighan, W. I; Winton, V. J; Melani, R. D; Anderson, L. C; McGee, J. P; Schachner, L. F; Barnidge, D; Murray, D; Alexander, H. D; Gibson, D. S; Deery, M. J; McNicholl, F. P; McLaughlin, J; Kelleher, N. L; Thomas, P. M

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 Journal Article

In: Clin Chem Lab Med., 2020.

Abstract | Links | BibTeX

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Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry. Journal Article

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Heterologous Expression of the Unusual Terreazepine Biosynthetic Gene Cluster Reveals a Promising Approach for Identifying New Chemical Scaffolds. Journal Article

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Using 10,000 Fragment Ions to Inform Scoring in Native Top-down Proteomics. Journal Article

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Mutant EZH2 Induces a Pre-malignant Lymphoma Niche by Reprogramming the Immune Response. Journal Article

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Kafader, J. O; Melani, R. D; Durbin, K. R; Ikwuagwu, B; Early, B. P; Fellers, R. T; Beu, S. C; Zabrouskov, V; Makarov, A. A; Maze, J. T; Shinholt, D. L; Yip, P. F; Tullman-Ercek, D; Senko, M. W; Compton, P. D; Kelleher, N. L

Multiplexed mass spectrometry of individual ions improves measurement of proteoforms and their complexes. Journal Article

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Zhu, W; Doubleday, P. F; Catlin, D. S; Weerawarna, P. M; Butrin, A; Shen, S; Wawrzak, Z; Kelleher, N. L; Liu, D; Silverman, R. B

A Remarkable Difference That One Fluorine Atom Confers on the Mechanisms of Inactivation of Human Ornithine Aminotransferase by Two Cyclohexene Analogues of γ-Aminobutyric Acid. Journal Article

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Individual Ion Mass Spectrometry Enhances the Sensitivity and Sequence Coverage of Top-Down Mass Spectrometry. Journal Article

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Voltage Rollercoaster Filtering of Low-Mass Contaminants During Native Protein Analysis. Journal Article

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NMT1 and NMT2 are lysine myristoyltransferases regulating the ARF6 GTPase cycle. Journal Article

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Mechanism-Based Design of 3-Amino-4-Halocyclopentenecarboxylic Acids as Inactivators of GABA Aminotransferase Journal Article

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A MUC16 IgG Binding Activity Selects for a Restricted Subset of IgG Enriched for Certain Simian Immunodeficiency Virus Epitope Specificities. Journal Article

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Thorough Performance Evaluation of 213 nm Ultraviolet Photodissociation for Top-down Proteomics Journal Article

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Kafader, J. O; Melani, R. D; Schachner, L. F; Ives, A. N; Patrie, S. M; Kelleher, N. L; Compton, P. D

Native vs Denatured: An in Depth Investigation of Charge State and Isotope Distributions Journal Article

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A computational framework to explore large-scale biosynthetic diversity Journal Article

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Novel Interface for High-Throughput Analysis of Biotherapeutics by Electrospray Mass Spectrometry Journal Article

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Discovery of the Biosynthetic Machinery for Stravidins, Biotin Antimetabolites Journal Article

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Identification of Plasmodium falciparum proteoforms from liver stage models Journal Article

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Elucidating Proteoform Dynamics Underlying the Senescence Associated Secretory Phenotype Journal Article

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Navarro-Muñoz, J. C; Selem-Mojica, N; Mullowney, M. W; Kautsar, S. A; Tryon, J. H; Parkinson, E. I; De Los Santos, E. L. C; Yeong, M; Cruz-Morales, P; Abubucker, S; Roeters, A; Lokhorst, W; Fernandez-Guerra, A; Cappelini, L. T. D; Goering, A. W; Thomson, R. J; Metcalf, W. W; Kelleher, N. L; Barona-Gomez, F; Medema, M. H.

A computational framework to explore large-scale biosynthetic diversity Journal Article

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2019

Camarillo, J. M; Swaminathan, S; Abshiru, N. A; Sikora, J. W; Thomas, P. M; Kelleher, N. L

Coupling Fluorescence-Activated Cell Sorting and Targeted Analysis of Histone Modification Profiles in Primary Human Leukocytes Journal Article

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A Highly Productive, One-Pot Cell-Free Protein Synthesis Platform Based on Genomically Recoded Escherichia coli Journal Article

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Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms Journal Article

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Chromatin occupancy and epigenetic analysis reveal new insights into the function of the GATA1 N terminus in erythropoiesis Journal Article

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STORI Plots Enable Accurate Tracking of Individual Ion Signals Journal Article

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Multidimensional Top-Down Proteomics of Brain-Region-Specific Mouse Brain Proteoforms Responsive to Cocaine and Estradiol Journal Article

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A MUC16 IgG binding activity selects for a restricted subset of IgG enriched for certain SIV epitope specificities Journal Article

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A Mutation in Histone H2B Represents a New Class of Oncogenic Driver Journal Article

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A five-level classification system for proteoform identifications Journal Article

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Precision Targeting with EZH2 and HDAC Inhibitors in Epigenetically Dysregulated Lymphomas Journal Article

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Defining the NSD2 interactome: PARP1 PARylation reduces NSD2 histone methyltransferase activity and impedes chromatin binding Journal Article

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Standard Proteoforms and Their Complexes for Native Mass Spectrometry Journal Article

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Best practices and benchmarks for intact protein analysis for top-down mass spectrometry Journal Article

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Mechanism of Inactivation of Ornithine Aminotransferase by (1S,3S)-3-Amino-4-(hexafluoropropan-2-ylidenyl)cyclopentane-1-carboxylic Acid Journal Article

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Native top-down mass spectrometry provides insights into the copper centers of membrane-bound methane monooxygenase Journal Article

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Identification and Quantification of Proteoforms by Mass Spectrometry Journal Article

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

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

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

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

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

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

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

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

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

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

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

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

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Repurposed HisC Aminotransferases Complete the Biosynthesis of Some Methanobactins Journal Article

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

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

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

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

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

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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

In: Org Lett., vol. 20, no. 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

In: Proc Natl Acad Sci USA, vol. 115, no. 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.; Krebs Jr, C; Kelleher, N. L.; Rosenzweig, AC

The biosynthesis of methanobactin. Journal Article

In: Science, vol. 359, no. 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

In: Nat. Commun., vol. 9, no. 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

In: Anal Chem, vol. 90, no. 6, pp. 3802-3810, 2018.

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Smith, L. M.; Kelleher, N. L.

Proteoforms as the next proteomics currency. Journal Article

In: Science, vol. 359, no. 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

In: J Proteome Res., vol. 17, no. 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

In: Nat Chem Biol., vol. 14, no. 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

In: Biochemistry, vol. 57, no. 5, pp. 701-710, 2017.

Abstract | Links | BibTeX

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

In: Nat. Genet., vol. 49, no. 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

In: Nat. Genet., vol. 50, no. 1, pp. 62-72, 2017.

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Skinner, O. S.; Haverland, N. A.; Fornelli, L.; Melani, R. D.; Vale, L. H. F. Do; 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

In: Nat. Chem. Biol., vol. 14, no. 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

In: Biochemistry, vol. 56, no. 43, pp. 5844-5845, 2017.

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Skinner, O. S.; McAnally, M. O.; Duyne, R. P. Van; 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

In: Anal. Chem., vol. 89, no. 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

In: Proteomics, vol. 17, no. 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

In: Cell. Rep., vol. 21, no. 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

In: Nat Chem Biol, vol. 13, no. 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

In: Genes. Dev., vol. 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

In: eLife, no. 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

In: Biochemistry, vol. 56, no. 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

In: Sci. Rep., vol. 7, no. 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

In: 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

In: J Proteome Res, vol. 16, no. 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

In: J Proteome Res, vol. 16, no. 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

In: 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

In: ACS Chem Biol, vol. 12, no. 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

In: Methods Mol Biol, vol. 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

In: J Proteome Res, vol. 16, no. 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

In: 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

In: Biotechnol Bioeng, vol. 114, no. 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

In: ACS Synth Biol, vol. 6, no. 1, pp. 39-44, 2017, ISSN: 2161-5063 (Electronic) 2161-5063 (Linking).

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Greer, S. M.; Holden, D. D.; Fellers, R.; Kelleher, N. L.; Brodbelt, J. S.

Modulation of Protein Fragmentation Through Carbamylation of Primary Amines Journal Article

In: J Am Soc Mass Spectrom, vol. 28, no. 8, pp. 1587-1599, 2017, ISSN: 1879-1123 (Electronic) 1044-0305 (Linking).

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Haverland, N. A.; Skinner, O. S.; Fellers, R. T.; Tariq, A. A.; Early, B. P.; LeDuc, R. D.; Fornelli, L.; Compton, P. D.; Kelleher, N. L.

Defining Gas-Phase Fragmentation Propensities of Intact Proteins During Native Top-Down Mass Spectrometry Journal Article

In: J Am Soc Mass Spectrom, vol. 28, no. 6, pp. 1203-1215, 2017, ISSN: 1879-1123 (Electronic) 1044-0305 (Linking).

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Mandacaru, S. C.; do Vale, L. H.; Vahidi, S.; Xiao, Y.; Skinner, O. S.; Ricart, C. A.; Kelleher, N. L.; de Sousa, M. V.; Konermann, L.

Characterizing the Structure and Oligomerization of Major Royal Jelly Protein 1 (MRJP1) by Mass Spectrometry and Complementary Biophysical Tools Journal Article

In: Biochemistry, vol. 56, no. 11, pp. 1645-1655, 2017, ISSN: 1520-4995 (Electronic) 0006-2960 (Linking).

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Piunti, A.; Hashizume, R.; Morgan, M. A.; Bartom, E. T.; Horbinski, C. M.; Marshall, S. A.; Rendleman, E. J.; Ma, Q.; Takahashi, Y. H.; Woodfin, A. R.; Misharin, A. V.; Abshiru, N. A.; Lulla, R. R.; Saratsis, A. M.; Kelleher, N. L.; James, C. D.; Shilatifard, A.

Therapeutic targeting of polycomb and BET bromodomain proteins in diffuse intrinsic pontine gliomas Journal Article

In: Nat Med, vol. 23, no. 4, pp. 493-500, 2017, ISSN: 1546-170X (Electronic) 1078-8956 (Linking).

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Schroeter, E. R.; DeHart, C. J.; Cleland, T. P.; Zheng, W.; Thomas, P. M.; Kelleher, N. L.; Bern, M.; Schweitzer, M. H.

Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein Journal Article

In: J Proteome Res, vol. 16, no. 2, pp. 920-932, 2017, ISSN: 1535-3907 (Electronic) 1535-3893 (Linking).

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Toby, T. K.; Abecassis, M. M.; Kim, K.; Thomas, P. M.; Fellers, R. T.; LeDuc, R. D.; Kelleher, N. L.; Demetris, J.; Levitsky, J.

Proteoforms in Peripheral Blood Mononuclear Cells as Novel Rejection Biomarkers in Liver Transplant Recipients Journal Article

In: Am J Transplant, 2017, ISSN: 1600-6143 (Electronic) 1600-6135 (Linking).

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2016

Chen, Y.; McClure, R. A.; Kelleher, N. L.

Screening for Expressed Nonribosomal Peptide Synthetases and Polyketide Synthases Using LC-MS/MS-Based Proteomics Journal Article

In: Methods Mol Biol, vol. 1401, pp. 135-47, 2016, ISSN: 1940-6029 (Electronic) 1064-3745 (Linking).

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Durbin, K. R.; Fornelli, L.; Fellers, R. T.; Doubleday, P. F.; Narita, M.; Kelleher, N. L.

Quantitation and Identification of Thousands of Human Proteoforms below 30 kDa Journal Article

In: J Proteome Res, vol. 15, no. 3, pp. 976-82, 2016, ISSN: 1535-3907 (Electronic) 1535-3893 (Linking).

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Goering, A. W.; McClure, R. A.; Doroghazi, J. R.; Albright, J. C.; Haverland, N. A.; Zhang, Y.; Ju, K. S.; Thomson, R. J.; Metcalf, W. W.; Kelleher, N. L.

Metabologenomics: Correlation of Microbial Gene Clusters with Metabolites Drives Discovery of a Nonribosomal Peptide with an Unusual Amino Acid Monomer Journal Article

In: ACS Cent Sci, vol. 2, no. 2, pp. 99-108, 2016, ISSN: 2374-7943 (Print) 2374-7943 (Linking).

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Gunn, B.; Schneider, J.; Shansab, M.; Bastian, A. R.; Fahrbach, K.; th Smith, A.; Mahan, A.; Karim, M.; Licht, A.; Zvonar, I.; Tedesco, J.; Anderson, M.; Chapel, A.; Suscovich, T.; Malaspina, D.; Streeck, H.; Walker, B. D.; Kim, A.; Lauer, G.; Altfeld, M.; Pillai, S.; Szleifer, I.; Kelleher, N. L.; Kiser, P. F.; Hope, T. J.; Alter, G.

Enhanced binding of antibodies generated during chronic HIV infection to mucus component MUC16 Journal Article

In: Mucosal Immunol, vol. 9, no. 6, pp. 1549-1558, 2016, ISSN: 1935-3456 (Electronic) 1933-0219 (Linking).

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Hattori, T.; Lai, D.; Dementieva, I. S.; Montano, S. P.; Kurosawa, K.; Zheng, Y.; Akin, L. R.; Swist-Rosowska, K. M.; Grzybowski, A. T.; Koide, A.; Krajewski, K.; Strahl, B. D.; Kelleher, N. L.; Ruthenburg, A. J.; Koide, S.

Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation Journal Article

In: Proc Natl Acad Sci U S A, vol. 113, no. 8, pp. 2092-7, 2016, ISSN: 1091-6490 (Electronic) 0027-8424 (Linking).

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Henke, M. T.; Kelleher, N. L.

Modern mass spectrometry for synthetic biology and structure-based discovery of natural products Journal Article

In: Nat Prod Rep, vol. 33, no. 8, pp. 942-50, 2016, ISSN: 1460-4752 (Electronic) 0265-0568 (Linking).

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Henke, M. T.; Soukup, A. A.; Goering, A. W.; McClure, R. A.; Thomson, R. J.; Keller, N. P.; Kelleher, N. L.

New Aspercryptins, Lipopeptide Natural Products, Revealed by HDAC Inhibition in Aspergillus nidulans Journal Article

In: ACS Chem Biol, vol. 11, no. 8, pp. 2117-23, 2016, ISSN: 1554-8937 (Electronic) 1554-8929 (Linking).

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Kenney, G. E.; Goering, A. W.; Ross, M. O.; DeHart, C. J.; Thomas, P. M.; Hoffman, B. M.; Kelleher, N. L.; Rosenzweig, A. C.

Characterization of Methanobactin from Methylosinus sp. LW4 Journal Article

In: J Am Chem Soc, vol. 138, no. 35, pp. 11124-7, 2016, ISSN: 1520-5126 (Electronic) 0002-7863 (Linking).

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LaFave, L. M.; Beguelin, W.; Koche, R.; Teater, M.; Spitzer, B.; Chramiec, A.; Papalexi, E.; Keller, M. D.; Hricik, T.; Konstantinoff, K.; Micol, J. B.; Durham, B.; Knutson, S. K.; Campbell, J. E.; Blum, G.; Shi, X.; Doud, E. H.; Krivtsov, A. V.; Chung, Y. R.; Khodos, I.; de Stanchina, E.; Ouerfelli, O.; Adusumilli, P. S.; Thomas, P. M.; Kelleher, N. L.; Luo, M.; Keilhack, H.; Abdel-Wahab, O.; Melnick, A.; Armstrong, S. A.; Levine, R. L.

Reply to "Uveal melanoma cells are resistant to EZH2 inhibition regardless of BAP1 status" Journal Article

In: Nat Med, vol. 22, no. 6, pp. 578-9, 2016, ISSN: 1546-170X (Electronic) 1078-8956 (Linking).

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Liu, F.; Koval, M.; Ranganathan, S.; Fanayan, S.; Hancock, W. S.; Lundberg, E. K.; Beavis, R. C.; Lane, L.; Duek, P.; McQuade, L.; Kelleher, N. L.; Baker, M. S.

Systems Proteomics View of the Endogenous Human Claudin Protein Family Journal Article

In: J Proteome Res, vol. 15, no. 2, pp. 339-59, 2016, ISSN: 1535-3907 (Electronic) 1535-3893 (Linking).

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McClure, R. A.; Goering, A. W.; Ju, K. S.; Baccile, J. A.; Schroeder, F. C.; Metcalf, W. W.; Thomson, R. J.; Kelleher, N. L.

Elucidating the Rimosamide-Detoxin Natural Product Families and Their Biosynthesis Using Metabolite/Gene Cluster Correlations Journal Article

In: ACS Chem Biol, vol. 11, no. 12, pp. 3452-3460, 2016, ISSN: 1554-8937 (Electronic) 1554-8929 (Linking).

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Melani, R. D.; Seckler, H. S.; Skinner, O. S.; Vale, L. H. Do; Catherman, A. D.; Havugimana, P. C.; de Sousa, M. Valle; Domont, G. B.; Kelleher, N. L.; Compton, P. D.

CN-GELFrEE - Clear Native Gel-eluted Liquid Fraction Entrapment Electrophoresis Journal Article

In: J Vis Exp, no. 108, pp. 53597, 2016, ISSN: 1940-087X (Electronic) 1940-087X (Linking).

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Melani, R. D.; Skinner, O. S.; Fornelli, L.; Domont, G. B.; Compton, P. D.; Kelleher, N. L.

Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics Journal Article

In: Mol Cell Proteomics, vol. 15, no. 7, pp. 2423-34, 2016, ISSN: 1535-9484 (Electronic) 1535-9476 (Linking).

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Moussazadeh, N.; Berman, S. H.; Laufer, I.; Gounder, M.; Zheng, Y.; Sommer, J.; Bilsky, M. H.; Kelleher, N. L.; Brennan, C.

365 Epigenetic Profiling Reveals a Unique Histone Code in Chordoma Journal Article

In: Neurosurgery, vol. 63 Suppl 1, pp. 208, 2016, ISSN: 1524-4040 (Electronic) 0148-396X (Linking).

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Ntai, I.; LeDuc, R. D.; Fellers, R. T.; Erdmann-Gilmore, P.; Davies, S. R.; Rumsey, J.; Early, B. P.; Thomas, P. M.; Li, S.; Compton, P. D.; Ellis, M. J.; Ruggles, K. V.; Fenyo, D.; Boja, E. S.; Rodriguez, H.; Townsend, R. R.; Kelleher, N. L.

Integrated Bottom-Up and Top-Down Proteomics of Patient-Derived Breast Tumor Xenografts Journal Article

In: Mol Cell Proteomics, vol. 15, no. 1, pp. 45-56, 2016, ISSN: 1535-9484 (Electronic) 1535-9476 (Linking).

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Ntai, I.; Toby, T. K.; LeDuc, R. D.; Kelleher, N. L.

A Method for Label-Free, Differential Top-Down Proteomics Journal Article

In: Methods Mol Biol, vol. 1410, pp. 121-33, 2016, ISSN: 1940-6029 (Electronic) 1064-3745 (Linking).

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Ong, T. H.; Romanova, E. V.; Roberts-Galbraith, R. H.; Yang, N.; Zimmerman, T. A.; 3rd Collins, J. J.; Lee, J. E.; Kelleher, N. L.; Newmark, P. A.; Sweedler, J. V.

Mass Spectrometry Imaging and Identification of Peptides Associated with Cephalic Ganglia Regeneration in Schmidtea mediterranea Journal Article

In: J Biol Chem, vol. 291, no. 15, pp. 8109-20, 2016, ISSN: 1083-351X (Electronic) 0021-9258 (Linking).

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Savaryn, J. P.; Skinner, O. S.; Fornelli, L.; Fellers, R. T.; Compton, P. D.; Terhune, S. S.; Abecassis, M. M.; Kelleher, N. L.

Targeted analysis of recombinant NF kappa B (RelA/p65) by denaturing and native top down mass spectrometry Journal Article

In: J Proteomics, vol. 134, pp. 76-84, 2016, ISSN: 1876-7737 (Electronic) 1874-3919 (Linking).

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Savaryn, J. P.; Toby, T. K.; Catherman, A. D.; Fellers, R. T.; LeDuc, R. D.; Thomas, P. M.; Friedewald, J. J.; Salomon, D. R.; Abecassis, M. M.; Kelleher, N. L.

Comparative top down proteomics of peripheral blood mononuclear cells from kidney transplant recipients with normal kidney biopsies or acute rejection Journal Article

In: Proteomics, vol. 16, no. 14, pp. 2048-58, 2016, ISSN: 1615-9861 (Electronic) 1615-9853 (Linking).

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Savaryn, J. P.; Toby, T. K.; Kelleher, N. L.

A researcher's guide to mass spectrometry-based proteomics Journal Article

In: Proteomics, vol. 16, no. 18, pp. 2435-43, 2016, ISSN: 1615-9861 (Electronic) 1615-9853 (Linking).

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Schroeter, E. R.; DeHart, C. J.; Schweitzer, M. H.; Thomas, P. M.; Kelleher, N. L.

Bone protein "extractomics": comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics Journal Article

In: PeerJ, vol. 4, pp. e2603, 2016, ISSN: 2167-8359 (Print).

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Skinner, O. S.; Havugimana, P. C.; Haverland, N. A.; Fornelli, L.; Early, B. P.; Greer, J. B.; Fellers, R. T.; Durbin, K. R.; Vale, L. H. Do; Melani, R. D.; Seckler, H. S.; Nelp, M. T.; Belov, M. E.; Horning, S. R.; Makarov, A. A.; LeDuc, R. D.; Bandarian, V.; Compton, P. D.; Kelleher, N. L.

An informatic framework for decoding protein complexes by top-down mass spectrometry Journal Article

In: Nat Methods, vol. 13, no. 3, pp. 237-40, 2016, ISSN: 1548-7105 (Electronic) 1548-7091 (Linking).

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Skinner, O. S.; Schachner, L. F.; Kelleher, N. L.

The Search Engine for Multi-Proteoform Complexes: An Online Tool for the Identification and Stoichiometry Determination of Protein Complexes Journal Article

In: Curr Protoc Bioinformatics, vol. 56, pp. 13 30 1-13 30 11, 2016, ISSN: 1934-340X (Electronic) 1934-3396 (Linking).

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Toby, T. K.; Fornelli, L.; Kelleher, N. L.

Progress in Top-Down Proteomics and the Analysis of Proteoforms Journal Article

In: Annu Rev Anal Chem (Palo Alto Calif), vol. 9, no. 1, pp. 499-519, 2016, ISSN: 1936-1335 (Electronic) 1936-1327 (Linking).

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Zheng, Y.; Fornelli, L.; Compton, P. D.; Sharma, S.; Canterbury, J.; Mullen, C.; Zabrouskov, V.; Fellers, R. T.; Thomas, P. M.; Licht, J. D.; Senko, M. W.; Kelleher, N. L.

Unabridged Analysis of Human Histone H3 by Differential Top-Down Mass Spectrometry Reveals Hypermethylated Proteoforms from MMSET/NSD2 Overexpression Journal Article

In: Mol Cell Proteomics, vol. 15, no. 3, pp. 776-90, 2016, ISSN: 1535-9484 (Electronic) 1535-9476 (Linking).

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Zheng, Y.; Huang, X.; Kelleher, N. L.

Epiproteomics: quantitative analysis of histone marks and codes by mass spectrometry Journal Article

In: Curr Opin Chem Biol, vol. 33, pp. 142-50, 2016, ISSN: 1879-0402 (Electronic) 1367-5931 (Linking).

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2015

Albright, J. C.; Henke, M. T.; Soukup, A. A.; McClure, R. A.; Thomson, R. J.; Keller, N. P.; Kelleher, N. L.

Large-scale metabolomics reveals a complex response of Aspergillus nidulans to epigenetic perturbation Journal Article

In: ACS Chem Biol, vol. 10, no. 6, pp. 1535-41, 2015, ISSN: 1554-8937 (Electronic) 1554-8929 (Linking).

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Amiram, M.; Haimovich, A. D.; Fan, C.; Wang, Y. S.; Aerni, H. R.; Ntai, I.; Moonan, D. W.; Ma, N. J.; Rovner, A. J.; Hong, S. H.; Kelleher, N. L.; Goodman, A. L.; Jewett, M. C.; Soll, D.; Rinehart, J.; Isaacs, F. J.

Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids Journal Article

In: Nat Biotechnol, vol. 33, no. 12, pp. 1272-1279, 2015, ISSN: 1546-1696 (Electronic) 1087-0156 (Linking).

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Bok, J. W.; Ye, R.; Clevenger, K. D.; Mead, D.; Wagner, M.; Krerowicz, A.; Albright, J. C.; Goering, A. W.; Thomas, P. M.; Kelleher, N. L.; Keller, N. P.; Wu, C. C.

Fungal artificial chromosomes for mining of the fungal secondary metabolome Journal Article

In: BMC Genomics, vol. 16, pp. 343, 2015, ISSN: 1471-2164 (Electronic) 1471-2164 (Linking).

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Cleland, T. P.; Schroeter, E. R.; Zamdborg, L.; Zheng, W.; Lee, J. E.; Tran, J. C.; Bern, M.; Duncan, M. B.; Lebleu, V. S.; Ahlf, D. R.; Thomas, P. M.; Kalluri, R.; Kelleher, N. L.; Schweitzer, M. H.

Mass Spectrometry and Antibody-Based Characterization of Blood Vessels from Brachylophosaurus canadensis Journal Article

In: J Proteome Res, vol. 14, no. 12, pp. 5252-62, 2015, ISSN: 1535-3907 (Electronic) 1535-3893 (Linking).

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Compton, P. D.; Fornelli, L.; Kelleher, N. L.; Skinner, O. S.

Probing Asymmetric Charge Partitioning of Protein Oligomers during Tandem Mass Spectrometry Journal Article

In: Int J Mass Spectrom, vol. 390, pp. 132-136, 2015, ISSN: 1387-3806 (Print) 1387-3806 (Linking).

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Dam, D. H.; Lee, H.; Lee, R. C.; Kim, K. H.; Kelleher, N. L.; Odom, T. W.

Tunable loading of oligonucleotides with secondary structure on gold nanoparticles through a pH-driven method Journal Article

In: Bioconjug Chem, vol. 26, no. 2, pp. 279-85, 2015, ISSN: 1520-4812 (Electronic) 1043-1802 (Linking).

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Durbin, K. R.; Skinner, O. S.; Fellers, R. T.; Kelleher, N. L.

Analyzing internal fragmentation of electrosprayed ubiquitin ions during beam-type collisional dissociation Journal Article

In: J Am Soc Mass Spectrom, vol. 26, no. 5, pp. 782-7, 2015, ISSN: 1879-1123 (Electronic) 1044-0305 (Linking).

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Fellers, R. T.; Greer, J. B.; Early, B. P.; Yu, X.; LeDuc, R. D.; Kelleher, N. L.; Thomas, P. M.

ProSight Lite: graphical software to analyze top-down mass spectrometry data Journal Article

In: Proteomics, vol. 15, no. 7, pp. 1235-8, 2015, ISSN: 1615-9861 (Electronic) 1615-9853 (Linking).

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Hong, S. H.; Kwon, Y. C.; Martin, R. W.; Soye, B. J. Des; de Paz, A. M.; Swonger, K. N.; Ntai, I.; Kelleher, N. L.; Jewett, M. C.

Improving cell-free protein synthesis through genome engineering of Escherichia coli lacking release factor 1 Journal Article

In: Chembiochem, vol. 16, no. 5, pp. 844-53, 2015, ISSN: 1439-7633 (Electronic) 1439-4227 (Linking).

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Kim, K.; Compton, P. D.; Toby, T. K.; Thomas, P. M.; Wilkins, J. T.; Mutharasan, R. K.; Kelleher, N. L.

Reducing protein oxidation in low-flow electrospray enables deeper investigation of proteoforms by top down proteomics Journal Article

In: EuPA Open Proteom, vol. 8, pp. 40-47, 2015, ISSN: 2212-9685 (Print) 2212-9685 (Linking).

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Kim, K. H.; Compton, P. D.; Tran, J. C.; Kelleher, N. L.

Online matrix removal platform for coupling gel-based separations to whole protein electrospray ionization mass spectrometry Journal Article

In: J Proteome Res, vol. 14, no. 5, pp. 2199-206, 2015, ISSN: 1535-3907 (Electronic) 1535-3893 (Linking).

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LaFave, L. M.; Beguelin, W.; Koche, R.; Teater, M.; Spitzer, B.; Chramiec, A.; Papalexi, E.; Keller, M. D.; Hricik, T.; Konstantinoff, K.; Micol, J. B.; Durham, B.; Knutson, S. K.; Campbell, J. E.; Blum, G.; Shi, X.; Doud, E. H.; Krivtsov, A. V.; Chung, Y. R.; Khodos, I.; de Stanchina, E.; Ouerfelli, O.; Adusumilli, P. S.; Thomas, P. M.; Kelleher, N. L.; Luo, M.; Keilhack, H.; Abdel-Wahab, O.; Melnick, A.; Armstrong, S. A.; Levine, R. L.

Loss of BAP1 function leads to EZH2-dependent transformation Journal Article

In: Nat Med, vol. 21, no. 11, pp. 1344-9, 2015, ISSN: 1546-170X (Electronic) 1078-8956 (Linking).

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Le, H. V.; Hawker, D. D.; Wu, R.; Doud, E.; Widom, J.; Sanishvili, R.; Liu, D.; Kelleher, N. L.; Silverman, R. B.

Design and mechanism of tetrahydrothiophene-based gamma-aminobutyric acid aminotransferase inactivators Journal Article

In: J Am Chem Soc, vol. 137, no. 13, pp. 4525-33, 2015, ISSN: 1520-5126 (Electronic) 0002-7863 (Linking).

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Lee, H.; Doud, E. H.; Wu, R.; Sanishvili, R.; Juncosa, J. I.; Liu, D.; Kelleher, N. L.; Silverman, R. B.

Mechanism of inactivation of gamma-aminobutyric acid aminotransferase by (1S,3S)-3-amino-4-difluoromethylene-1-cyclopentanoic acid (CPP-115) Journal Article

In: J Am Chem Soc, vol. 137, no. 7, pp. 2628-40, 2015, ISSN: 1520-5126 (Electronic) 0002-7863 (Linking).

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Lee, H.; Le, H. V.; Wu, R.; Doud, E.; Sanishvili, R.; Kellie, J. F.; Compton, P. D.; Pachaiyappan, B.; Liu, D.; Kelleher, N. L.; Silverman, R. B.

Mechanism of Inactivation of GABA Aminotransferase by (E)- and (Z)-(1S,3S)-3-Amino-4-fluoromethylenyl-1-cyclopentanoic Acid Journal Article

In: ACS Chem Biol, vol. 10, no. 9, pp. 2087-98, 2015, ISSN: 1554-8937 (Electronic) 1554-8929 (Linking).

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Lorenzatto, K. R.; Kim, K.; Ntai, I.; Paludo, G. P.; de Lima, J. Camargo; Thomas, P. M.; Kelleher, N. L.; Ferreira, H. B.

Top Down Proteomics Reveals Mature Proteoforms Expressed in Subcellular Fractions of the Echinococcus granulosus Preadult Stage Journal Article

In: J Proteome Res, vol. 14, no. 11, pp. 4805-14, 2015, ISSN: 1535-3907 (Electronic) 1535-3893 (Linking).

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Skinner, O. S.; Vale, L. H. Do; Catherman, A. D.; Havugimana, P. C.; de Sousa, M. V.; Compton, P. D.; Kelleher, N. L.

Native GELFrEE: a new separation technique for biomolecular assemblies Journal Article

In: Anal Chem, vol. 87, no. 5, pp. 3032-8, 2015, ISSN: 1520-6882 (Electronic) 0003-2700 (Linking).

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Skinner, O. S.; Kelleher, N. L.

Illuminating the dark matter of shotgun proteomics Journal Article

In: Nat Biotechnol, vol. 33, no. 7, pp. 717-8, 2015, ISSN: 1546-1696 (Electronic) 1087-0156 (Linking).

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Tang, W.; Li, H.; Doud, E. H.; Chen, Y.; Choing, S.; Plaza, C.; Kelleher, N. L.; Poulos, T. L.; Silverman, R. B.

Mechanism of Inactivation of Neuronal Nitric Oxide Synthase by (S)-2-Amino-5-(2-(methylthio)acetimidamido)pentanoic Acid Journal Article

In: J Am Chem Soc, vol. 137, no. 18, pp. 5980-9, 2015, ISSN: 1520-5126 (Electronic) 0002-7863 (Linking).

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Ye, H.; Wang, J.; Zhang, Z.; Jia, C.; Schmerberg, C.; Catherman, A. D.; Thomas, P. M.; Kelleher, N. L.; Li, L.

Defining the Neuropeptidome of the Spiny Lobster Panulirus interruptus Brain Using a Multidimensional Mass Spectrometry-Based Platform Journal Article

In: J Proteome Res, vol. 14, no. 11, pp. 4776-91, 2015, ISSN: 1535-3907 (Electronic) 1535-3893 (Linking).

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Zheng, H.; Kim, J.; Liew, M.; Yan, J. K.; Herrera, O.; Bok, J. W.; Kelleher, N. L.; Keller, N. P.; Wang, Y.

Redox metabolites signal polymicrobial biofilm development via the NapA oxidative stress cascade in Aspergillus Journal Article

In: Curr Biol, vol. 25, no. 1, pp. 29-37, 2015, ISSN: 1879-0445 (Electronic) 0960-9822 (Linking).

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2014

Albright, J. C.; Goering, A. W.; Doroghazi, J. R.; Metcalf, W. W.; Kelleher, N. L.

Strain-specific proteogenomics accelerates the discovery of natural products via their biosynthetic pathways Journal Article

In: J Ind Microbiol Biotechnol, vol. 41, no. 2, pp. 451-9, 2014, ISSN: 1476-5535 (Electronic) 1367-5435 (Linking).

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Cannon, J. R.; Cammarata, M. B.; Robotham, S. A.; Cotham, V. C.; Shaw, J. B.; Fellers, R. T.; Early, B. P.; Thomas, P. M.; Kelleher, N. L.; Brodbelt, J. S.

Ultraviolet photodissociation for characterization of whole proteins on a chromatographic time scale Journal Article

In: Anal Chem, vol. 86, no. 4, pp. 2185-92, 2014, ISSN: 1520-6882 (Electronic) 0003-2700 (Linking).

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Catherman, A. D.; Skinner, O. S.; Kelleher, N. L.

Top Down proteomics: facts and perspectives Journal Article

In: Biochem Biophys Res Commun, vol. 445, no. 4, pp. 683-93, 2014, ISSN: 1090-2104 (Electronic) 0006-291X (Linking).

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Dang, X.; Scotcher, J.; Wu, S.; Chu, R. K.; Tolic, N.; Ntai, I.; Thomas, P. M.; Fellers, R. T.; Early, B. P.; Zheng, Y.; Durbin, K. R.; Leduc, R. D.; Wolff, J. J.; Thompson, C. J.; Pan, J.; Han, J.; Shaw, J. B.; Salisbury, J. P.; Easterling, M.; Borchers, C. H.; Brodbelt, J. S.; Agar, J. N.; Pasa-Tolic, L.; Kelleher, N. L.; Young, N. L.

The first pilot project of the consortium for top-down proteomics: a status report Journal Article

In: Proteomics, vol. 14, no. 10, pp. 1130-40, 2014, ISSN: 1615-9861 (Electronic) 1615-9853 (Linking).

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Doroghazi, J. R.; Albright, J. C.; Goering, A. W.; Ju, K. S.; Haines, R. R.; Tchalukov, K. A.; Labeda, D. P.; Kelleher, N. L.; Metcalf, W. W.

A roadmap for natural product discovery based on large-scale genomics and metabolomics Journal Article

In: Nat Chem Biol, vol. 10, no. 11, pp. 963-8, 2014, ISSN: 1552-4469 (Electronic) 1552-4450 (Linking).

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Durbin, K. R.; Fellers, R. T.; Ntai, I.; Kelleher, N. L.; Compton, P. D.

Autopilot: an online data acquisition control system for the enhanced high-throughput characterization of intact proteins Journal Article

In: Anal Chem, vol. 86, no. 3, pp. 1485-92, 2014, ISSN: 1520-6882 (Electronic) 0003-2700 (Linking).

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Hong, S. H.; Ntai, I.; Haimovich, A. D.; Kelleher, N. L.; Isaacs, F. J.; Jewett, M. C.

Cell-free protein synthesis from a release factor 1 deficient Escherichia coli activates efficient and multiple site-specific nonstandard amino acid incorporation Journal Article

In: ACS Synth Biol, vol. 3, no. 6, pp. 398-409, 2014, ISSN: 2161-5063 (Electronic) 2161-5063 (Linking).

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Kelleher, N. L.; Thomas, P. M.; Ntai, I.; Compton, P. D.; LeDuc, R. D.

Deep and quantitative top-down proteomics in clinical and translational research Journal Article

In: Expert Rev Proteomics, vol. 11, no. 6, pp. 649-51, 2014, ISSN: 1744-8387 (Electronic) 1478-9450 (Linking).

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

The C-score: a Bayesian framework to sharply improve proteoform scoring in high-throughput top down proteomics Journal Article

In: J Proteome Res, vol. 13, no. 7, pp. 3231-40, 2014, ISSN: 1535-3907 (Electronic) 1535-3893 (Linking).

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Li, Y.; Compton, P. D.; Tran, J. C.; Ntai, I.; Kelleher, N. L.

Optimizing capillary electrophoresis for top-down proteomics of 30-80 kDa proteins Journal Article

In: Proteomics, vol. 14, no. 10, pp. 1158-64, 2014, ISSN: 1615-9861 (Electronic) 1615-9853 (Linking).

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Ntai, I.; Kim, K.; Fellers, R. T.; Skinner, O. S.; th Smith, A. D.; Early, B. P.; Savaryn, J. P.; LeDuc, R. D.; Thomas, P. M.; Kelleher, N. L.

Applying label-free quantitation to top down proteomics Journal Article

In: Anal Chem, vol. 86, no. 10, pp. 4961-8, 2014, ISSN: 1520-6882 (Electronic) 0003-2700 (Linking).

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Oyer, J. A.; Huang, X.; Zheng, Y.; Shim, J.; Ezponda, T.; Carpenter, Z.; Allegretta, M.; Okot-Kotber, C. I.; Patel, J. P.; Melnick, A.; Levine, R. L.; Ferrando, A.; Mackerell, A. D. Jr.; Kelleher, N. L.; Licht, J. D.; Popovic, R.

Point mutation E1099K in MMSET/NSD2 enhances its methyltranferase activity and leads to altered global chromatin methylation in lymphoid malignancies Journal Article

In: Leukemia, vol. 28, no. 1, pp. 198-201, 2014, ISSN: 1476-5551 (Electronic) 0887-6924 (Linking).

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Popovic, R.; Martinez-Garcia, E.; Giannopoulou, E. G.; Zhang, Q.; Zhang, Q.; Ezponda, T.; Shah, M. Y.; Zheng, Y.; Will, C. M.; Small, E. C.; Hua, Y.; Bulic, M.; Jiang, Y.; Carrara, M.; Calogero, R. A.; Kath, W. L.; Kelleher, N. L.; Wang, J. P.; Elemento, O.; Licht, J. D.

Histone methyltransferase MMSET/NSD2 alters EZH2 binding and reprograms the myeloma epigenome through global and focal changes in H3K36 and H3K27 methylation Journal Article

In: PLoS Genet, vol. 10, no. 9, pp. e1004566, 2014, ISSN: 1553-7404 (Electronic) 1553-7390 (Linking).

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Skinner, O. S.; Catherman, A. D.; Early, B. P.; Thomas, P. M.; Compton, P. D.; Kelleher, N. L.

Fragmentation of integral membrane proteins in the gas phase Journal Article

In: Anal Chem, vol. 86, no. 9, pp. 4627-34, 2014, ISSN: 1520-6882 (Electronic) 0003-2700 (Linking).

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Southey, B. R.; Lee, J. E.; Zamdborg, L.; Atkins, N. Jr.; Mitchell, J. W.; Li, M.; Gillette, M. U.; Kelleher, N. L.; Sweedler, J. V.

Comparing label-free quantitative peptidomics approaches to characterize diurnal variation of peptides in the rat suprachiasmatic nucleus Journal Article

In: Anal Chem, vol. 86, no. 1, pp. 443-52, 2014, ISSN: 1520-6882 (Electronic) 0003-2700 (Linking).

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Ye, H.; Mandal, R.; Catherman, A.; Thomas, P. M.; Kelleher, N. L.; Ikonomidou, C.; Li, L.

Top-down proteomics with mass spectrometry imaging: a pilot study towards discovery of biomarkers for neurodevelopmental disorders Journal Article

In: PLoS One, vol. 9, no. 4, pp. e92831, 2014, ISSN: 1932-6203 (Electronic) 1932-6203 (Linking).

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Zheng, Y.; Tipton, J. D.; Thomas, P. M.; Kelleher, N. L.; Sweet, S. M.

Site-specific human histone H3 methylation stability: fast K4me3 turnover Journal Article

In: Proteomics, vol. 14, no. 19,