All Faculty and Research Staff Publications

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2016
Shortreed MR, Frey BL, Scalf M, Knoener RA, Cesnik AJ, Smith LM. Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements. Journal of Proteome Research. 2016 ;15:1213-1221.
Cesnik AJ, Shortreed MR, Sheynkman GM, Frey BL, Smith LM. Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy. Journal of Proteome Research. 2016 ;15:800-808.
Chen XS, Lu L, Mayer KS, Scalf M, Qian SM, Lomax A, Smith LM, Zhong XH. POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis. eLife. 2016 ;5.
Li QY, Chang Z, Oliveira G, Xiong M, Smith LM, Frey BL, Welham NV. Protein turnover during in vitro tissue engineering. Biomaterials. 2016 ;81:104-113.
Sheynkman GM, Shortreed MR, Cesnik AJ, Smith LM. Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. In: Bohn PW, Pemberton JE Vol. 9. Palo Alto: Annual Reviews; 2016. pp. 521-545.
Li QY, Uygun BE, Geerts S, Ozer S, Scalf M, Gilpin SE, Ott HC, Yarmush ML, Smith LM, Welham NV, et al. Proteomic analysis of naturally-sourced biological scaffolds. Biomaterials. 2016 ;75:37-46.
Keller MP, Paul PK, Rabaglia ME, Stapleton DS, Schueler KL, Broman AT, Ye SI, Leng N, Brandon CJ, Neto EC, et al. The Transcription Factor Nfatc2 Regulates beta-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets. Plos Genetics. 2016 ;12.
2014
Guillen-Ahlers H, Shortreed MR, Smith LM, Olivier M. Advanced methods for the analysis of chromatin-associated proteins. Physiological Genomics. 2014 ;46:441-447.
Liu RR, Li QY, Smith LM. Detection of Large Ions in Time-of-Flight Mass Spectrometry: Effects of Ion Mass and Acceleration Voltage on Microchannel Plate Detector Response. Journal of the American Society for Mass Spectrometry. 2014 ;25:1374-1383.
Kennedy-Darling J, Guillen-Ahlers H, Shortreed MR, Scalf M, Frey BL, Kendziorski C, Olivier M, Gasch AP, Smith LM. Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae. Journal of Proteome Research. 2014 ;13:3810-3825.
Wu CH, Holden MT, Smith LM. Enzymatic Fabrication of High-Density RNA Arrays. Angewandte Chemie-International Edition. 2014 ;53:13514-13517.
Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang YB, Shenykrnan GM, Bandhakavi S, Smith LM, Griffin TJ. Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework. Journal of Proteome Research. 2014 ;13:5898-5908.
Cesnik AJ, Shortreed MR, Sheynkman GM, Frey BL, Smith LM. In-Depth Identification of Protein Sequence Variants and Posttranslational Modifications in 10 Human Cell Lines. Molecular & Cellular Proteomics. 2014 ;13:S49-S49.
Sheynkman GM, Shortreed MR, Frey BL, Scalf M, Smith LM. Large-Scale Mass Spectrometric Detection of Variant Peptides Resulting from Nonsynonymous Nucleotide Differences. Journal of Proteome Research. 2014 ;13:228-240.
Kennedy-Darling J, Smith LM. Measuring the Formaldehyde Protein-DNA Cross-Link Reversal Rate. Analytical Chemistry. 2014 ;86:5678-5681.
Ladror DT, Frey BL, Scalf M, Levenstein ME, Artymiuk JM, Smith LM. Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions. Biochemical and Biophysical Research Communications. 2014 ;445:535-541.
Kennedy-Darling J, Holden MT, Shortreed MR, Smith LM. Multiplexed Programmable Release of Captured DNA. Chembiochem. 2014 ;15:2353-2356.
Rhoads TW, Rose CM, Bailey DJ, Riley NM, Molden RC, Nestler AJ, Merrill AE, Smith LM, Hebert AS, Westphall MS, et al. Neutron-Encoded Mass Signatures for Quantitative Top-Down Proteomics. Analytical Chemistry. 2014 ;86:2314-2319.
2013
Kim DY, Scalf M, Smith LM, Vierstra RD. Advanced Proteomic Analyses Yield a Deep Catalog of Ubiquitylation Targets in Arabidopsis. Plant Cell. 2013 ;25:1523-1540.
Russell JD, Scalf M, Book AJ, Ladror DT, Vierstra RD, Smith LM, Coon JJ. Characterization and Quantification of Intact 26S Proteasome Proteins by Real-Time Measurement of Intrinsic Fluorescence Prior to Top-down Mass Spectrometry. Plos One. 2013 ;8.
Frey BL, Ladror DT, Sondalle SB, Krusemark CJ, Jue AL, Coon JJ, Smith LM. Chemical Derivatization of Peptide Carboxyl Groups for Highly Efficient Electron Transfer Dissociation. Journal of the American Society for Mass Spectrometry. 2013 ;24:1710-1721.
Sheynkman GM, Shortreed MR, Frey BL, Smith LM. Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq. Molecular & Cellular Proteomics. 2013 ;12:2341-2353.
Broderick AH, Carter MCD, Lockett MR, Smith LM, Lynn DM. Fabrication of Oligonucleotide and Protein Arrays on Rigid and Flexible Substrates Coated with Reactive Polymer Multilayers. ACS Applied Materials & Interfaces. 2013 ;5:351-359.
Torde RG, Therrien AJ, Shortreed MR, Smith LM, Lamos SM. Multiplexed Analysis of Cage and Cage Free Chicken Egg Fatty Acids Using Stable Isotope Labeling and Mass Spectrometry. Molecules. 2013 ;18:14977-14988.
Smith LM, Kelleher NL, Down PConsortium. Proteoform: a single term describing protein complexity. Nature Methods. 2013 ;10:186-187.
Welham NV, Chang Z, Smith LM, Frey BL. Proteomic analysis of a decellularized human vocal fold mucosa scaffold using 2D electrophoresis and high-resolution mass spectrometry. Biomaterials. 2013 ;34:669-676.
Miller MJ, Scalf M, Rytz TC, Hubler SL, Smith LM, Vierstra RD. Quantitative Proteomics Reveals Factors Regulating RNA Biology as Dynamic Targets of Stress-induced SUMOylation in Arabidopsis. Molecular & Cellular Proteomics. 2013 ;12:449-463.
2011
Krusemark CJ, Frey BL, Smith LM, Belshaw PJ. Complete Chemical Modification of Amine and Acid Functional Groups of Peptides and Small Proteins Gevaert K, Vandekerckhove J. Methods Mol Biol. 2011 ;753:77-91.
Jarecki JL, Frey BL, Smith LM, Stretton AO. Discovery of Neuropeptides in the Nematode Ascaris suum by Database Mining and Tandem Mass Spectrometry. Journal of Proteome Research. 2011 ;10:3098-3106.
Olson CN, Galloway MM, Yu G, Hedman CJ, Lockett MR, Yoon TP, Stone EA, Smith LM, Keutsch FN. Hydroxycarboxylic Acid-Derived Organosulfates: Synthesis, Stability, and Quantification in Ambient Aerosol. Environmental Science & Technology. 2011 ;45:6468-6474.
Park J, Qin H, Scalf M, Hilger RT, Westphall MS, Smith LM, Blick RH. A Mechanical Nanomembrane Detector for Time-of-Flight Mass Spectrometry. Nano Letters. 2011 ;11:3681-3684.
Russell JD, Hilger RT, Ladror DT, Tervo MA, Scalf M, Shortreed MR, Coon JJ, Smith LM. Parallel Detection of Intrinsic Fluorescence from Peptides and Proteins for Quantification during Mass Spectrometric Analysis. Analytical Chemistry. 2011 ;83:2187-2193.
Pellitteri-Hahn MC, Halligan BD, Scalf M, Smith LM, Hickey WJ. Quantitative proteomic analysis of the chemolithoautotrophic bacterium Nitrosomonas europaea: Comparison of growing- and energy-starved cells. Journal of Proteomics. 2011 ;74:411-419.
Wu CH, Chen SY, Shortreed MR, Kreitinger GM, Yuan Y, Frey BL, Zhang Y, Mirza S, Cirillo LA, Olivier M, et al. Sequence-Specific Capture of Protein-DNA Complexes for Mass Spectrometric Protein Identification. Plos One. 2011 ;6.
Hallows WC, Yu W, Smith BC, Devires MK, Ellinger JJ, Someya S, Shortreed MR, Prolla T, Markley JL, Smith LM, et al. Sirt3 Promotes the Urea Cycle and Fatty Acid Oxidation during Dietary Restriction. Molecular Cell. 2011 ;41:139-149.
Smith LM, Shortreed MR, Olivier M. To understand the whole, you must know the parts: unraveling the roles of protein-DNA interactions in genome regulation. Analyst. 2011 ;136:3060-3065.

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