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Nicolas Young Lab

Publications

Master
Content

Holt MV, Wang T, Young, NL*. One-Pot Quantitative Top- and Middle-Down Analysis of GluC-Digested Histone H4. Holt, M.V., Wang, T. & Young, N.L. J. Am. Soc. Mass Spectrom. 2019 PMID: 31147891

Graham BW, Bougoulias ME, Dodge KL, Thaxton CT, Olaso D, Tao Y, Young NL, Marshall AG, and Trakselis MA. Control of Hexamerization, Assembly, and Excluded Strand Specificity for the Sulfolobus solfataricus MCM Helicase. Biochemistry. 2018 Sep 10. PMID: 30199238

Wang T, Holt MV, Young, NL*. The Histone H4 Proteoform Dynamics in Response to SUV4-20 Inhibition Reveals Single Molecule Mechanisms of Inhibitor Resistance. Epigenetics & Chromatin 2018 11:29 PMID: 29880017

Wang T, Holt MV, Young, NL*. Early Butyrate Induced Acetylation of Histone H4 is Proteoform Specific and Linked to Methylation State. Epigenetics. 2018 Aug 7:1-17. PMID: 29940793

Jiang T, Hoover ME, Holt MV, Freitas MA, Marshall AG, and Young NL*. Middle-Down Characterization of Histone H4 Combinatorial Post-Translational Modification Codes for Breast Cancer Invasion. Proteomics, Proteomics. 2018 Apr 17:e1700442. PMID: 29667342

Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL*, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL & Zhang B. How Many Human Proteoforms are There? Nat Chem Biol. 2018 Feb 14;14(3):206-214 PMID: 29443976

Tao Y, Fang P, Kim S, Guo M, Young NL, and Marshall AG. Mapping the contact surfaces in the Lamin A:AIMP3 complex by hydrogen/deuterium exchange FT-ICR mass spectrometry. PLoS ONE12(8): e0181869. PMID: 28797100

Fan Y, Guo YR, Yuan W, Zhou Y, Holt MV, Wang T, Demeler B, Young NL, Zhong W, Tao YT. Structure of a pentameric virion-associated fiber with a potential role in Orsay virus entry to host cells. PLoS Pathog. 2017 Feb 27;13(2):e1006231. PMID: 28241071

Holt MV, Wang T, Young NL*. Recent Advances in Understanding Histone Modification Events. Curr Mol Bio Rep (2017) 3: 11.

Guan X, Brownstein NC, Young NL, Marshall AG. Ultrahigh Resolution FT-ICR MS and MS/MS for Peptide de Novo Amino Acid Sequencing for a Seven-Protein Mixture by Paired Single-Residue Transposed Lys-N and Lys-C Digestion. Rapid Commun Mass Spectrom. 2017 Jan 30;31(2):207-217. PMID: 27813191

Dang X, Singh A, Spetman BD, Nolan KD, Isaacs JS, Dennis JH, Dalton S, Marshall AG, Young NL*. Label-Free Relative Quantitation of Isobaric and Isomeric Human Histone H2A and H2B Variants by Fourier Transform Ion Cyclotron Resonance Top-Down MS/MS. J. Proteome Res., 2016, 15 (9), pp 3196–3203 PMID: 27431976

Graham BW, Tao Y, Dodge KL, Thaxton CT, Olaso D, Young NL, Marshall AG, Trakselis MA. DNA Interactions Probed by Hydrogen-Deuterium Exchange (HDX) Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Confirm External Binding Sites on the Minichromosomal Maintenance (MCM) Helicase. J Biol Chem. 2016 Jun 10;291(24):12467-80.

Chen Y, Hoover ME, Dang X, Shomo AA, Guan X, Marshall AG, Freitas MA,* & Young NL*. Quantitative Mass Spectrometry Reveals that Intact Histone H1 Phosphorylations are Variant Specific and Exhibit Single Molecule Hierarchical Dependence. Mol Cell Proteomics. 2016 Mar;15(3):818-33.

Askenasy I, Pennington JM, Tao Y, Marshall AG, Young NL, Shang W, Stroupe ME. The N-terminal Domain of Escherichia coli Assimilatory NADPH-Sulfite Reductase Hemoprotein Is an Oligomerization Domain That Mediates Holoenzyme Assembly. J Biol Chem. 2015 Jul 31;290(31):19319-33.

Guan X, Noble KA, Tao Y, Roux KH, Sathe SK, Young NL*, Marshall AG*. Epitope Mapping of 7S Cashew Antigen in Complex with Antibody by Solution-Phase H/D Exchange Monitored by FT-ICR Mass Spectrometry. J. of Mass Spec. 50(6) 812-9 (2015)

Brownstein NC, Guan X, Mao Y, Zhang Q, DiMaggio PA, Xia Q, Zhang L, Marshall AG, & Young NL*. Paired Single Residue-Transposed Lys-N and Lys-C Digestions Combined with Ultrahigh Resolution FT-ICR MS and MS/MS for Peptide De Novo Sequencing. Rapid Commun. Mass Spectrom, 29(7), 659-66 (2015)

Dang X, Scotcher J, Wu S, Chu RK, Tolic N, Ntai I, Thomas PM, Fellers RT, Early BP, Zheng Y, Durbin KR, Leduc RD, Wolff JJ, Thompson CJ, Pan J, Han J, Shaw JB, Salisbury JP, Easterling M, Borchers CH, Brodbelt JS, Agar JN, Paša-Tolic L, Kelleher NL, & Young NL*. The first pilot project of the consortium for top-down proteomics: A status report, Proteomics 14, 1130-40 (2014). PMID: 24644084 *Featured Cover Article, May 2014 Issue of Proteomics

Dang X & Young NL*. Ultraviolet photodissociation enhances top-down mass spectrometry as demonstrated on green fluorescent protein variants. Proteomics, 14, 1128-9 (2014) PMID: 24723542

Ficarro SB, Biagi JM, Wang J, Scotcher J, Koleva RI, Card JD, Adelmant G, He H, Askenazi M, Marshall AG, Young NL, Gray NS, & Marto JA. Protected amine labels: a versatile molecular scaffold for multiplexed nominal mass and sub-Da isotopologue quantitative proteomic reagents. J Am Soc Mass Spectrom, 25, 636-50 (2014) PMID: 24496597

Kim DG, Lee JY, Kwon NH, Fang P, Zhang Q, Wang J, Young NL, Guo M, Cho HY, Mushtaq H, Jeon YH, Choi JW, Han JM, Kang HW, Joo JE, Hur Y, Kang W, Yang H, Nam DH, Lee MS, Lee JW, Kim ES, Moon A, Kim K, Kim D, Kang EJ, Moon Y, Rhee KH, Han BW, Yang JS, Han G, Yand WS, Lee C, Wang MW & Kim S. Chemical inhibition of prometastatic lysyl-tRNA synthetase-laminin receptor interaction. Nat Chem Biol. 2014 Jan;10(1):29-34 PMID: 24212136

Harshman SW, Young NL, Parthun MR, Freitas MA. Histone H1: Current Perspectives and Challenges. Nucleic Acids Res, 2013, 1–17 PMID: 23945933

Smith LM, Kelleher NL & The Consortium for Top Down Proteomics. Proteoform: a single term describing protein complexity. Nature Methods 10, 186–187 (2013) Includes Young NL PMID: 23443629

Zhang Q, Noble KA, Mao Y, Young NL, Sathe SK, Roux KH, Marshall AG. Rapid Screening for Potential Epitopes Reactive with a Polycolonal Antibody by Solution-Phase H/D Exchange Monitored by FT-ICR Mass Spectrometry. J. Am. Soc. Mass Spectr., 24, 1016-1025 (2013) PMID: 23681851

Zhang Q, Chen J, Kuwajima K, Zhang HM, Xian F, Young NL, Marshall AG. Nucleotide-induced conformational changes of tetradecameric GroEL mapped by H/D exchange monitored by FT-ICR mass spectrometry. Sci Rep. 2013;3:1247 PMID: 23409238

Voigt P, LeRoy G, Drury III WJ, Zee BM, Son J, Beck D, Young NL, Garcia BA & Reinberg D. Asymmetrically Modified Nucleosomes. Cell, Volume 151, Issue 1, 181-193, 28 Sept 2012

Barber MF, Michishita-Kioi E, Xi Y, Tasselli L, Kioi M, Moqtaderi Z, Tennen RI, Paredes S, Young NL, Chen K, Struhl K, Garcia BA, Gozani O, Li W, and Chua KF. SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. Nature. 2012 Jul 5;487(7405):114-8

Green EM, Mas G, Young NL, Garcia BA, Gozani O. Methylation of H4 lysines 5, 8 and 12 by yeast Set5 calibrates chromatin stress responses. Nat Struct Mol Biol. 19, 361–363 (2012) PMID: 22343720

Zee BM, Young NL, Garcia BA. Quantitative proteomic approaches to studying histone modifications. Curr Chem Genomics. 2011;5(Suppl 1):106-14. PMID: 21966350

Torrente MP, Zee BM, Young NL, Baliban RC, LeRoy G, Floudas CA, Hake SB and Garcia BA. Proteomic Interrogation of Human Chromatin. PloS ONE, 2011, 6(9): e24747 PMID: 21935452

Waldmann T, Izzo A, Kamieniarz K, Richter F, Voger C, Sarg B, Lindner H, Young NL, Mittler G, Garcia BA and Schneider R. Methylation of H2AR29 is a novel repressive PRMT6 target. Epigenetics & Chromatin, 2011, 4:11. PMID: 21774791

Yan K, Cao Q, Reilly CM, Young NL, Garcia BA and Mishra N. Histone deacetylase 9 deficiency protects against effector T cell-mediated systemic autoimmunity. J Biol Chem. 2011 Aug 19;286(33):28833-43. PMID: 21708950

Young NL, DiMaggio PA and Garcia BA. The Significance, Development and Progress of High-Throughput Combinatorial Histone Code Analysis. Cell Mol Life Sciences, 2010 Dec;67(23):3983-4000. PMID: 20683756

Plazas-Mayorca MD, Bloom JS, Zeissler U, Leroy G, Young NL, DiMaggio PA, Krugylak L, Schneider R and Garcia BA. Quantitative proteomics reveals direct and indirect alterations in the histone code following methyltransferase knockdown. Mol Biosyst. 2010 Sep;6(9):1719-29. PMID: 20577673

Young NL, Plazas-Mayorca MD, Dimaggio PA, Flaniken IZ, Beltran AJ, Mishra N, Leroy G, Floudas CA, Garcia BA. Collective Mass Spectrometry Approaches Reveal Broad and Combinatorial Modification of High Mobility Group Protein A1a. J Am Soc Mass Spectrom. 2010 Jun;21(6):960-70. PMID: 20202861

Young NL, Plazas-Mayorca MD, Garcia BA. Systems-wide proteomic characterization of combinatorial post-translational modification patterns. Expert Rev Proteomics. 2010 Feb;7(1):79-92. PMID: 20121478

Baliban RC, Dimaggio PA, Plazas-Mayorca MD, Young NL, Garcia BA, Floudas CA. A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry. Mol Cell Proteomics. 2010 May;9(5):764-79. PMID: 20103568

Plazas-Mayorca MD, Zee BM, Young NL, Fingerman IM, Leroy G, Briggs SD, Garcia BA. One-Pot Shotgun Quantitative Mass Spectrometry Characterization of Histones J Proteome Res. 2009 Nov;8(11):5367-74

Young NL, DiMaggio PA, Plazas-Mayorca MD, Baliban RC, Floudas CA, Garcia BA. High-Throughput Characterization of Combinatorial Histone Codes. Mol Cell Proteomics. 8:2266-2284, 2009. PMID: 19654425

DiMaggio PA Jr, Young NL, Baliban RC, Garcia BA, Floudas CA. A Mixed-Integer Linear Optimization Framework for the Identification of Post-translational Modifications in Histone H3 using ETD and ECD Tandem Mass Spectrometry. Mol Cell Proteomics 2009 8:2527-2543. PMID: 19666874

LeRoy G, Weston JT, Zee BM, Young NL, Plazas-Mayorca MD, Garcia BA. Heterochromatin Protein 1 is Extensively Decorated with Histone Code-like Post-translational Modifications. Mol Cell Proteomics. 8:2432-2442, 2009.

El Gazzar M, Yoza BK, Chen X, Garcia BA, Young NL, McCall CE. Chromatin-Specific Remodeling by HMGB1 and Linker Histone H1 Silences Proinflammatory Genes during Endotoxin Tolerance. Mol Cell Biol. 2009 Apr;29(7):1959-71. PMID: 19158276

Xie W, Song C, Young NL, Sperling AS, Xu F, Sridharan R, Conway AE, Garcia BA, Plath K, Clark AT, Grunstein M. Histone H3 K56 acetylation is linked to the core transcriptional network in human embryonic stem cells. Mol Cell. 2009 Feb;33(4):417-27. PMID: 19250903

Leroy G, Plazas-Mayorca MD; Young NL, Garcia, BA. “Decoding the histone code by quantitative proteomics.” Mol Cell Proteomics 2009 Aug; 8(8), Supplement 1, S11.

Plazas-Mayorca MD, Young NL, Garcia BA, “Identification of Differentially Expressed Histone Codes Using HILIC Chromatography and Mass Spectrometry”, Am. Biotechnol. Lab. 2009; 27(2); 10-12.

Young NL, Plazas-Mayorca MD, Garcia BA, “A Method to Separate and Characterize Modified Forms of Histones Using HILIC Chromatography and Electron Transfer Dissociation-Mass Spectrometry”, Am. Biotechnol. Lab. 2009; 27(1); 23-25.

Young NL, Sisto MC, Young MN, Grant PG, Killilea DW, LaMotte L, Wu KJ, Lebrilla CB. A Novel Steady-State Asymmetric Nanospray Dual Ion Source for Accurate Mass Determination within a Chromatographic Separation. Anal. Chem. 2007; 79 (15); 5711 -5718. PMID: 17614364

Young NL, Lee S, Whetstone PA, Cheal SM, Benner WH, Lebrilla CB, Meares C. A Method to Site-Specifically Identify and Quantitate Carbonyl End Products of Protein Oxidation Using Oxidation-Dependent Element Coded Affinity Tags (O-ECAT) and NanoLiquid Chromatography Fourier Transform Mass Spectrometry. J. Proteome Research 2006; 5(3); 539-547. PMID: 16512668

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Book Chapters

Content

Young NL, Garcia BA (2011). Chapter 4: LC-MS of Intact Proteins. In Thomas Letzel (Editor), Protein and Peptide Analysis by LC-MS: Experimental Strategies (pp.38-55). Cambridge, UK: Royal Society of Chemistry Press, ISBN 978-1-84973-182-9