All Faculty and Research Staff Publications

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2018
Chen XS, Lu L, Qian SM, Scalf M, Smith LM, Zhong XH. Canonical and Noncanonical Actions of Arabidopsis Histone Deacetylases in Ribosomal RNA Processing. Plant Cell. 2018 ;30:134-152.
Zaidan NZ, Walker KJ, Brown JE, Schaffer LV, Scalf M, Shortreed MR, Iyer G, Smith LM, Sridharan R. Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports. 2018 ;10:627-641.
Solntsev SK, Shortreed MR, Frey BL, Smith LM. Enhanced Global Post-translational Modification Discovery with MetaMorpheus. Journal of Proteome Research. 2018 ;17:1844-1851.
Schaffer LV, Shortreed MR, Cesnik AJ, Frey BL, Solntsev SK, Scalf M, Smith LM. Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families. Analytical Chemistry. 2018 ;90:1325-1333.
Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, et al. How many human proteoforms are there?. Nature Chemical Biology. 2018 ;14:206-214.
Cesnik AJ, Yang B, Truong A, Etheridge T, Spiniello M, Steinbrink MI, Shortreed MR, Frey BL, Jarrard DF, Smith LM. Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers. Transl Oncol. 2018 ;11:808-814.
Kim SH, Stiles SG, Feichtmeier JM, Ramesh N, Zhan L, Scalf MA, Smith LM, U. Pandey B, Tibbetts RS. Mutation-dependent aggregation and toxicity in a Drosophila model for UBQLN2-associated ALS. Human Molecular Genetics. 2018 ;27:322-337.
Leduc RD, Schwammle V, Shortreed MR, Cesnik AJ, Solntsev SK, Shaw JB, Martin MJ, Vizcaino JA, Alpi E, Danis P, et al. ProForma: A Standard Proteoform Notation. Journal of Proteome Research. 2018 ;17:1321-1325.
Cesnik AJ, Shortreed MR, Schaffer LV, Knoener RA, Frey BL, Scalf M, Solntsev SK, Dai YX, Gasch AP, Smith LM. Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. Journal of Proteome Research. 2018 ;17:568-578.
Smith LM, Kelleher NL. Proteoforms as the next proteomics currency. Science. 2018 ;359:1106-1107.
2017
Dai YX, Shortreed MR, Scalf M, Frey BL, Cesnik AJ, Solntsev S, Schaffer LV, Smith LM. Elucidating Escherichia coil Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database. Journal of Proteome Research. 2017 ;16:4156-4165.
Buxton KE, Kennedy-Darling J, Shortreed MR, Zaidan NZ, Olivier M, Scalf M, Sridharan R, Smith LM. Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. Journal of Proteome Research. 2017 ;16:3433-3442.
Knoener RA, Becker JT, Scalf M, Sherer NM, Smith LM. Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry. Scientific Reports. 2017 ;7.
Li QY, Shortreed MR, Wenger CD, Frey BL, Schaffer LV, Scalf M, Smith LM. Global Post-Translational Modification Discovery. Journal of Proteome Research. 2017 ;16:1383-1390.
Aguilar-Hernandez V, Kim DY, Stankey RJ, Scalf M, Smith LM, Vierstra RD. Mass Spectrometric Analyses Reveal a Central Role for Ubiquitylation in Remodeling the Arabidopsis Proteome during Photomorphogenesis. Molecular Plant. 2017 ;10:846-865.
Dai Y, Kennedy-Darling J, Shortreed MR, Scalf M, Gasch AP, Smith LM. Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins. Analytical Chemistry. 2017 ;89:7841-7846.
Holden MT, Carter MCD, Ting SK, Lynn DM, Smith LM. Parallel DNA Synthesis on Poly(ethylene terephthalate). Chembiochem. 2017 ;18:1914-1916.
Proffitt JM, Glenn J, Cesnik AJ, Jadhav A, Shortreed MR, Smith LM, Kavanagh K, Cox LA, Olivier M. Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys. Bmc Genomics. 2017 ;18.
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.

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