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Items: 1 to 50 of 299

1.

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

LeDuc RD, Fellers RT, Early BP, Greer JB, Shams DP, Thomas P, Kelleher NL.

Mol Cell Proteomics. 2019 Jan 15. pii: mcp.RA118.000993. doi: 10.1074/mcp.RA118.000993. [Epub ahead of print]

PMID:
30647073
2.

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

Kafader JO, Melani RD, Senko MW, Makarov AA, Kelleher NL, Compton PD.

Anal Chem. 2019 Jan 4. doi: 10.1021/acs.analchem.8b04519. [Epub ahead of print]

PMID:
30609364
3.

A Novel Crosslinking Protocol Stabilizes Amyloid β Oligomers Capable of Inducing Alzheimer's-Associated Pathologies.

Cline EN, Das A, Bicca MA, Mohammad SN, Schachner LF, Kamel JM, DiNunno N, Weng A, Paschall JD, Lo Bu R, Khan FM, Rollins MG, Ives AN, Shekhawat G, Nunes-Tavares N, de Mello FG, Compton PD, Kelleher NL, Klein WL.

J Neurochem. 2018 Dec 18. doi: 10.1111/jnc.14647. [Epub ahead of print]

PMID:
30565253
4.

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

Toby TK, Fornelli L, Srzentić K, DeHart CJ, Levitsky J, Friedewald J, Kelleher NL.

Nat Protoc. 2019 Jan;14(1):119-152. doi: 10.1038/s41596-018-0085-7.

PMID:
30518910
5.

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

Fisher OS, Kenney GE, Ross MO, Ro SY, Lemma BE, Batelu S, Thomas PM, Sosnowski VC, DeHart CJ, Kelleher NL, Stemmler TL, Hoffman BM, Rosenzweig AC.

Nat Commun. 2018 Oct 15;9(1):4276. doi: 10.1038/s41467-018-06681-5.

6.

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

Jin Q, Martinez CA, Arcipowski KM, Zhu Y, Gutierrez-Diaz BT, Wang KK, Johnson MR, Volk AG, Wang F, Wu J, Grove C, Wang H, Sokirniy I, Thomas PM, Goo YA, Abshiru NA, Hijiya N, Peirs S, Vandamme N, Berx G, Goosens S, Marshall SA, Rendleman EJ, Takahashi YH, Wang L, Rawat R, Bartom ET, Collings CK, Van Vlierberghe P, Strikoudis A, Kelly S, Ueberheide B, Mantis C, Kandela I, Bourquin JP, Bornhauser B, Serafin V, Bresolin S, Paganin M, Accordi B, Basso G, Kelleher NL, Weinstock J, Kumar S, Crispino JD, Shilatifard A, Ntziachristos P.

Clin Cancer Res. 2019 Jan 1;25(1):222-239. doi: 10.1158/1078-0432.CCR-18-1740. Epub 2018 Sep 17.

PMID:
30224337
7.

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

Gruppuso PA, Boylan JM, Zabala V, Neretti N, Abshiru NA, Sikora JW, Doud EH, Camarillo JM, Thomas PM, Kelleher NL, Sanders JA.

PLoS One. 2018 Sep 7;13(9):e0203351. doi: 10.1371/journal.pone.0203351. eCollection 2018.

8.

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

Swaroop A, Oyer JA, Will CM, Huang X, Yu W, Troche C, Bulic M, Durham BH, Wen QJ, Crispino JD, MacKerell AD Jr, Bennett RL, Kelleher NL, Licht JD.

Oncogene. 2018 Aug 31. doi: 10.1038/s41388-018-0474-y. [Epub ahead of print]

PMID:
30171259
9.

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

Compton PD, Kelleher NL, Gunawardena J.

J Proteome Res. 2018 Aug 3;17(8):2727-2734. doi: 10.1021/acs.jproteome.8b00150. Epub 2018 Jul 10.

PMID:
29945451
10.

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

Riley NM, Sikora JW, Seckler HS, Greer JB, Fellers RT, LeDuc RD, Westphall MS, Thomas PM, Kelleher NL, Coon JJ.

Anal Chem. 2018 Jul 17;90(14):8553-8560. doi: 10.1021/acs.analchem.8b01638. Epub 2018 Jul 5.

PMID:
29924586
11.

Natural products from thioester reductase containing biosynthetic pathways.

Mullowney MW, McClure RA, Robey MT, Kelleher NL, Thomson RJ.

Nat Prod Rep. 2018 Sep 19;35(9):847-878. doi: 10.1039/c8np00013a. Review.

PMID:
29916519
12.

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

Fornelli L, Srzentić K, Huguet R, Mullen C, Sharma S, Zabrouskov V, Fellers RT, Durbin KR, Compton PD, Kelleher NL.

Anal Chem. 2018 Jul 17;90(14):8421-8429. doi: 10.1021/acs.analchem.8b00984. Epub 2018 Jun 28.

PMID:
29894161
13.

The unique biomineralization transcriptome and proteome of Lytechinus variegatus teeth.

Alvares K, DeHart CJ, Thomas PM, Kelleher NL, Veis A.

Connect Tissue Res. 2018 Dec;59(sup1):20-29. doi: 10.1080/03008207.2017.1408605.

PMID:
29745816
14.

Repurposed HisC Aminotransferases Complete the Biosynthesis of Some Methanobactins.

Park YJ, Kenney GE, Schachner LF, Kelleher NL, Rosenzweig AC.

Biochemistry. 2018 Jun 26;57(25):3515-3523. doi: 10.1021/acs.biochem.8b00296. Epub 2018 May 10.

PMID:
29694778
15.

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

Zheng J, Chen L, Skinner OS, Ysselstein D, Remis J, Lansbury P, Skerlj R, Mrosek M, Heunisch U, Krapp S, Charrow J, Schwake M, Kelleher NL, Silverman RB, Krainc D.

J Am Chem Soc. 2018 May 9;140(18):5914-5924. doi: 10.1021/jacs.7b13003. Epub 2018 Apr 30.

PMID:
29676907
16.

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

Seckler HDS, Fornelli L, Mutharasan RK, Thaxton CS, Fellers R, Daviglus M, Sniderman A, Rader D, Kelleher NL, Lloyd-Jones DM, Compton PD, Wilkins JT.

J Proteome Res. 2018 Jun 1;17(6):2156-2164. doi: 10.1021/acs.jproteome.8b00100. Epub 2018 Apr 27.

17.

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

Robey MT, Ye R, Bok JW, Clevenger KD, Islam MN, Chen C, Gupta R, Swyers M, Wu E, Gao P, Thomas PM, Wu CC, Keller NP, Kelleher NL.

ACS Chem Biol. 2018 May 18;13(5):1142-1147. doi: 10.1021/acschembio.8b00024. Epub 2018 Apr 17.

PMID:
29631395
18.

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

Ntai I, Fornelli L, DeHart CJ, Hutton JE, Doubleday PF, LeDuc RD, van Nispen AJ, Fellers RT, Whiteley G, Boja ES, Rodriguez H, Kelleher NL.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4140-4145. doi: 10.1073/pnas.1716122115. Epub 2018 Apr 2.

19.

Proteoforms as the next proteomics currency.

Smith LM, Kelleher NL.

Science. 2018 Mar 9;359(6380):1106-1107. doi: 10.1126/science.aat1884. Epub 2018 Mar 8. No abstract available.

PMID:
29590032
20.

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

Miley GP, Rote JC, Silverman RB, Kelleher NL, Thomson RJ.

Org Lett. 2018 Apr 20;20(8):2369-2373. doi: 10.1021/acs.orglett.8b00700. Epub 2018 Mar 27.

PMID:
29584440
21.

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

Martin RW, Des Soye BJ, Kwon YC, Kay J, Davis RG, Thomas PM, Majewska NI, Chen CX, Marcum RD, Weiss MG, Stoddart AE, Amiram M, Ranji Charna AK, Patel JR, Isaacs FJ, Kelleher NL, Hong SH, Jewett MC.

Nat Commun. 2018 Mar 23;9(1):1203. doi: 10.1038/s41467-018-03469-5.

22.

The biosynthesis of methanobactin.

Kenney GE, Dassama LMK, Pandelia ME, Gizzi AS, Martinie RJ, Gao P, DeHart CJ, Schachner LF, Skinner OS, Ro SY, Zhu X, Sadek M, Thomas PM, Almo SC, Bollinger JM Jr, Krebs C, Kelleher NL, Rosenzweig AC.

Science. 2018 Mar 23;359(6382):1411-1416. doi: 10.1126/science.aap9437.

PMID:
29567715
23.

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

Clevenger KD, Ye R, Bok JW, Thomas PM, Islam MN, Miley GP, Robey MT, Chen C, Yang K, Swyers M, Wu E, Gao P, Wu CC, Keller NP, Kelleher NL.

Biochemistry. 2018 Jun 12;57(23):3237-3243. doi: 10.1021/acs.biochem.8b00076. Epub 2018 Mar 20.

24.

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

Parkinson EI, Tryon JH, Goering AW, Ju KS, McClure RA, Kemball JD, Zhukovsky S, Labeda DP, Thomson RJ, Kelleher NL, Metcalf WW.

ACS Chem Biol. 2018 Apr 20;13(4):1029-1037. doi: 10.1021/acschembio.7b01089. Epub 2018 Mar 13.

PMID:
29510029
25.

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

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.

Anal Chem. 2018 Mar 20;90(6):3802-3810. doi: 10.1021/acs.analchem.7b04108. Epub 2018 Feb 26.

PMID:
29481055
26.

How many human proteoforms are there?

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.

Nat Chem Biol. 2018 Feb 14;14(3):206-214. doi: 10.1038/nchembio.2576.

PMID:
29443976
27.

ProForma: A Standard Proteoform Notation.

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.

J Proteome Res. 2018 Mar 2;17(3):1321-1325. doi: 10.1021/acs.jproteome.7b00851. Epub 2018 Feb 14.

PMID:
29397739
28.

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

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.

Nat Genet. 2018 Jan;50(1):62-72. doi: 10.1038/s41588-017-0001-z. Epub 2017 Nov 27.

29.

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

Skinner OS, Haverland NA, Fornelli L, Melani RD, Do Vale LHF, Seckler HS, Doubleday PF, Schachner LF, Srzentić K, Kelleher NL, Compton PD.

Nat Chem Biol. 2018 Jan;14(1):36-41. doi: 10.1038/nchembio.2515. Epub 2017 Nov 13.

30.

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

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.

Genes Dev. 2017 Oct 1;31(19):2003-2014. doi: 10.1101/gad.305201.117.

31.

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

Mascarenhas R, Le HV, Clevenger KD, Lehrer HJ, Ringe D, Kelleher NL, Silverman RB, Liu D.

Biochemistry. 2017 Oct 31;56(43):5844-5845. doi: 10.1021/acs.biochem.7b00961. Epub 2017 Oct 18. No abstract available.

PMID:
29045130
32.

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

Rickels R, Herz HM, Sze CC, Cao K, Morgan MA, Collings CK, Gause M, Takahashi YH, Wang L, Rendleman EJ, Marshall SA, Krueger A, Bartom ET, Piunti A, Smith ER, Abshiru NA, Kelleher NL, Dorsett D, Shilatifard A.

Nat Genet. 2017 Nov;49(11):1647-1653. doi: 10.1038/ng.3965. Epub 2017 Oct 2.

33.

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

Skinner OS, McAnally MO, Van Duyne RP, Schatz GC, Breuker K, Compton PD, Kelleher NL.

Anal Chem. 2017 Oct 17;89(20):10711-10716. doi: 10.1021/acs.analchem.7b01581. Epub 2017 Oct 4.

34.

A synthetic biology approach to probing nucleosome symmetry.

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.

Elife. 2017 Sep 12;6. pii: e28836. doi: 10.7554/eLife.28836.

35.

Diversity of Amyloid-beta Proteoforms in the Alzheimer's Disease Brain.

Wildburger NC, Esparza TJ, LeDuc RD, Fellers RT, Thomas PM, Cairns NJ, Kelleher NL, Bateman RJ, Brody DL.

Sci Rep. 2017 Aug 25;7(1):9520. doi: 10.1038/s41598-017-10422-x.

36.

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

Haverland NA, Waas M, Ntai I, Keppel T, Gundry RL, Kelleher NL.

Proteomics. 2017 Oct;17(19). doi: 10.1002/pmic.201700156.

37.

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

Mascarenhas R, Le HV, Clevenger KD, Lehrer HJ, Ringe D, Kelleher NL, Silverman RB, Liu D.

Biochemistry. 2017 Sep 19;56(37):4951-4961. doi: 10.1021/acs.biochem.7b00499. Epub 2017 Sep 6. Erratum in: Biochemistry. 2017 Oct 31;56(43):5844-5845.

38.

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

Zha L, Jiang Y, Henke MT, Wilson MR, Wang JX, Kelleher NL, Balskus EP.

Nat Chem Biol. 2017 Oct;13(10):1063-1065. doi: 10.1038/nchembio.2448. Epub 2017 Aug 7.

39.

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

Clevenger KD, Bok JW, Ye R, Miley GP, Verdan MH, Velk T, Chen C, Yang K, Robey MT, Gao P, Lamprecht M, Thomas PM, Islam MN, Palmer JM, Wu CC, Keller NP, Kelleher NL.

Nat Chem Biol. 2017 Aug;13(8):895-901. doi: 10.1038/nchembio.2408. Epub 2017 Jun 12.

40.

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

Toby TK, Abecassis M, Kim K, Thomas PM, Fellers RT, LeDuc RD, Kelleher NL, Demetris J, Levitsky J.

Am J Transplant. 2017 Sep;17(9):2458-2467. doi: 10.1111/ajt.14359. Epub 2017 Jun 27.

41.

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

Cleland TP, DeHart CJ, Fellers RT, VanNispen AJ, Greer JB, LeDuc RD, Parker WR, Thomas PM, Kelleher NL, Brodbelt JS.

J Proteome Res. 2017 May 5;16(5):2072-2079. doi: 10.1021/acs.jproteome.7b00043. Epub 2017 Apr 19.

42.

Modulation of Protein Fragmentation Through Carbamylation of Primary Amines.

Greer SM, Holden DD, Fellers R, Kelleher NL, Brodbelt JS.

J Am Soc Mass Spectrom. 2017 Aug;28(8):1587-1599. doi: 10.1007/s13361-017-1648-5. Epub 2017 Apr 3.

43.

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

Haverland NA, Skinner OS, Fellers RT, Tariq AA, Early BP, LeDuc RD, Fornelli L, Compton PD, Kelleher NL.

J Am Soc Mass Spectrom. 2017 Jun;28(6):1203-1215. doi: 10.1007/s13361-017-1635-x. Epub 2017 Apr 3.

44.

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

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.

Nat Med. 2017 Apr;23(4):493-500. doi: 10.1038/nm.4296. Epub 2017 Feb 27.

45.

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

Mandacaru SC, do Vale LH, Vahidi S, Xiao Y, Skinner OS, Ricart CA, Kelleher NL, de Sousa MV, Konermann L.

Biochemistry. 2017 Mar 21;56(11):1645-1655. doi: 10.1021/acs.biochem.7b00020. Epub 2017 Mar 7.

46.

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

Fornelli L, Toby TK, Schachner LF, Doubleday PF, Srzentić K, DeHart CJ, Kelleher NL.

J Proteomics. 2018 Mar 20;175:3-4. doi: 10.1016/j.jprot.2017.02.002. Epub 2017 Feb 7. No abstract available.

PMID:
28188863
47.

Substrate Trapping in the Siderophore Tailoring Enzyme PvdQ.

Clevenger KD, Mascarenhas R, Catlin D, Wu R, Kelleher NL, Drake EJ, Gulick AM, Liu D, Fast W.

ACS Chem Biol. 2017 Mar 17;12(3):643-647. doi: 10.1021/acschembio.7b00031. Epub 2017 Feb 15.

48.

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

Fornelli L, Durbin KR, Fellers RT, Early BP, Greer JB, LeDuc RD, Compton PD, Kelleher NL.

J Proteome Res. 2017 Feb 3;16(2):609-618. doi: 10.1021/acs.jproteome.6b00698. Epub 2016 Dec 2.

49.

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

DeHart CJ, Fellers RT, Fornelli L, Kelleher NL, Thomas PM.

Methods Mol Biol. 2017;1558:381-394. doi: 10.1007/978-1-4939-6783-4_18.

50.

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

Schroeter ER, DeHart CJ, Cleland TP, Zheng W, Thomas PM, Kelleher NL, Bern M, Schweitzer MH.

J Proteome Res. 2017 Feb 3;16(2):920-932. doi: 10.1021/acs.jproteome.6b00873. Epub 2017 Jan 23.

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