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2013

Kim D.Y, Scalf M., Smith L.M, Vierstra R.D. 2013. Advanced Proteomic Analyses Yield a Deep Catalog of Ubiquitylation Targets in Arabidopsis. Plant Cell. 25:1523-1540.

Russell J.D, Scalf M., Book A.J, Ladror D.T, Vierstra R.D, Smith L.M, Coon J.J. 2013. Characterization and Quantification of Intact 26S Proteasome Proteins by Real-Time Measurement of Intrinsic Fluorescence Prior to Top-down Mass Spectrometry. Plos One. 8

Frey B.L, Ladror D.T, Sondalle S.B, Krusemark C.J, Jue A.L, Coon J.J, Smith L.M. 2013. Chemical Derivatization of Peptide Carboxyl Groups for Highly Efficient Electron Transfer Dissociation. Journal of the American Society for Mass Spectrometry. 24:1710-1721.

Sheynkman G.M, Shortreed M.R, Frey B.L, Smith L.M. 2013. Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq. Molecular & Cellular Proteomics. 12:2341-2353.

Broderick A.H, Carter M.CD, Lockett M.R, Smith L.M, Lynn D.M. 2013. Fabrication of Oligonucleotide and Protein Arrays on Rigid and Flexible Substrates Coated with Reactive Polymer Multilayers. ACS Applied Materials & Interfaces. 5:351-359.

Torde R.G, Therrien A.J, Shortreed M.R, Smith L.M, Lamos S.M. 2013. Multiplexed Analysis of Cage and Cage Free Chicken Egg Fatty Acids Using Stable Isotope Labeling and Mass Spectrometry. Molecules. 18:14977-14988.

Smith L.M, Kelleher N.L, Ge Y., Down PConsortium. 2013. Proteoform: a single term describing protein complexity. Nature Methods. 10:186-187.

Welham N.V, Chang Z., Smith L.M, Frey B.L. 2013. Proteomic analysis of a decellularized human vocal fold mucosa scaffold using 2D electrophoresis and high-resolution mass spectrometry. Biomaterials. 34:669-676.

Miller M.J, Scalf M., Rytz T.C, Hubler S.L, Smith L.M, Vierstra R.D. 2013. Quantitative Proteomics Reveals Factors Regulating RNA Biology as Dynamic Targets of Stress-induced SUMOylation in Arabidopsis. Molecular & Cellular Proteomics. 12:449-463.

2014

Guillen-Ahlers H., Shortreed M.R, Smith L.M, Olivier M.. 2014. Advanced methods for the analysis of chromatin-associated proteins. Physiological Genomics. 46:441-447.

Liu R.R, Li Q.Y, Smith L.M. 2014. 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. 25:1374-1383.

Kennedy-Darling J., Guillen-Ahlers H., Shortreed M.R, Scalf M., Frey B.L, Kendziorski C., Olivier M., Gasch A.P, Smith L.M. 2014. Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae. Journal of Proteome Research. 13:3810-3825.

Jagtap P.D, Johnson J.E, Onsongo G., Sadler F.W, Murray K., Wang Y.B, Shenykrnan G.M, Bandhakavi S., Smith L.M, Griffin T.J. 2014. Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework. Journal of Proteome Research. 13:5898-5908.

Sheynkman GM, Shortreed MR, Frey BL, Scalf M, Smith L.M. 2014. Large-Scale Mass Spectrometric Detection of Variant Peptides Resulting from Nonsynonymous Nucleotide Differences. Journal of Proteome Research. 13:228-240.

Kennedy-Darling J, Smith L.M. 2014. Measuring the Formaldehyde Protein-DNA Cross-Link Reversal Rate. Analytical Chemistry. 86:5678-5681.

Ladror D.T, Frey B.L, Scalf M., Levenstein M.E, Artymiuk J.M, Smith L.M. 2014. Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions. Biochemical and Biophysical Research Communications. 445:535-541.

Kennedy-Darling J., Holden M.T, Shortreed M.R, Smith L.M. 2014. Multiplexed Programmable Release of Captured DNA. Chembiochem. 15:2353-2356.

Rhoads T.W, Rose C.M, Bailey D.J, Riley N.M, Molden R.C, Nestler A.J, Merrill A.E, Smith L.M, Hebert A.S, Westphall M.S et al.. 2014. Neutron-Encoded Mass Signatures for Quantitative Top-Down Proteomics. Analytical Chemistry. 86:2314-2319.

2015

Ling C.Y, Li Q.Y, Brown M.E, Kishimoto Y., Toya Y., Devine E.E, Choi K.O, Nishimoto K., Norman I.G, Tsegyal T. et al.. 2015. Bioengineered vocal fold mucosa for voice restoration. Science Translational Medicine. 7

Lockett MR, Smith L.M. 2015. Carbon Substrates: A Stable Foundation for Biomolecular Arrays. Annu. Rev. Anal. Chem.. 8:263-285.

Hoffman E.A, Frey B.L, Smith L.M, Auble D.T. 2015. Formaldehyde Crosslinking: A Tool for the Study of Chromatin Complexes. Journal of Biological Chemistry. 290:26404-26411.

Shortreed M.R, Wenger C.D, Frey B.L, Sheynkman G.M, Scalf M., Keller M.P, Attie A.D, Smith L.M. 2015. Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search. Journal of Proteome Research. 14:4714-4720.

Holden M.T, Carter M.CD, Wu C.H, Wolfer J., Codner E., Sussman M.R, Lynn D.M, Smith L.M. 2015. Photolithographic Synthesis of High-Density DNA and RNA Arrays on Flexible, Transparent, and Easily Subdivided Plastic Substrates. Analytical Chemistry. 87:11420-11428.

2016

Shortreed M.R, Frey B.L, Scalf M., Knoener R.A, Cesnik A.J, Smith L.M. 2016. Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements. Journal of Proteome Research. 15:1213-1221.

Cesnik A.J, Shortreed M.R, Sheynkman G.M, Frey B.L, Smith L.M. 2016. Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy. Journal of Proteome Research. 15:800-808.

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