Publications

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2018
Guillen-Ahlers H, Rao P.K, Perumalla D.S, Montoya M.J, Jadhav A.YL, Shortreed M.R, Smith L.M, Olivier M.  2018.  Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells. Journal of Visualized Experiments. (136)
Chen X.S, Lu L., Qian S.M, Scalf M., Smith L.M, Zhong X.H.  2018.  Canonical and Noncanonical Actions of Arabidopsis Histone Deacetylases in Ribosomal RNA Processing. Plant Cell. 30:134-152.
Zaidan N.Z, Walker K.J, Brown J.E, Schaffer L.V, Scalf M., Shortreed M.R, Iyer G., Smith L.M, Sridharan R..  2018.  Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports. 10:627-641.
Yang Z., Qian S., Scheid R.N, Lu L., Chen X., Liu R., Du X., Lv X., Boersma M.D, Scalf M. et al..  2018.  EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis. Nature genetics. 50(9)
Solntsev S.K, Shortreed M.R, Frey B.L, Smith L.M.  2018.  Enhanced Global Post-translational Modification Discovery with MetaMorpheus. Journal of Proteome Research. 17:1844-1851.
Schaffer L.V, Shortreed M.R, Cesnik A.J, Frey B.L, Solntsev S.K, Scalf M., Smith L.M.  2018.  Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families. Analytical Chemistry. 90:1325-1333.
Rolfs Z., Solntsev S.K, Shortreed M.R, Frey B.L, Smith L.M.  2018.  Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion. Journal of Proteome Research. 18(1):349-358.
Aebersold R., Agar J.N, Amster I.J, Baker M.S, Bertozzi C.R, Boja E.S, Costello C.E, Cravatt B.F, Fenselau C., Garcia B.A et al..  2018.  How many human proteoforms are there? Nature Chemical Biology. 14:206-214.
Spiniello M., Knoener R.A, Steinbrink M.I, Yang B., Cesnik A.J, Buxton K.E, Scalf M., Jarrard D.F, Smith L.M.  2018.  HyPR-MS for multiplexed discovery of MALAT1, NEAT1, and NORAD lncRNA protein interactomes. Journal of Proteome Research. 17(9):3022-3038.
Schaffer L.V, Rensvold J.W, Shortreed M.R, Cesnik A.J, Jochem A., Scalf M., Frey B.L, Pagliarini D.J, Smith L.M.  2018.  Identification and quantification of murine mitochondrial proteoforms using an integrated top-down and intact-mass strategy. Journal of Proteome Research. 17(10):3526-3536.
Lu L, Millikin RJ, Solntsev SK, Rolfs Z, Scalf M, Shortreed MR, Smith LM.  2018.  Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus. Journal of Proteome Research. 17(7):2370-2376.
Cesnik A.J, Yang B., Truong A., Etheridge T., Spiniello M., Steinbrink M.I, Shortreed M.L, Frey B.L, Jarrard D.F, Smith L.M.  2018.  Long noncoding RNAs AC009014. 3 and newly discovered XPLAID differentiate aggressive and indolent prostate cancers. Translational Oncology. 11(3):808-814.
Cesnik A.J, Yang B., Truong A., Etheridge T., Spiniello M., Steinbrink M.I, Shortreed M.R, Frey B.L, Jarrard D.F, Smith L.M.  2018.  Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers. Transl Oncol. 11:808-814.
Kim S.H, Stiles S.G, Feichtmeier J.M, Ramesh N., Zhan L.H, Scalf M.A, Smith L.M, Pandey U.B, Tibbetts R.S.  2018.  Mutation-dependent aggregation and toxicity in a Drosophila model for UBQLN2-associated ALS. Human Molecular Genetics. 27:322-337.
Leduc R.D, Schwammle V., Shortreed M.R, Cesnik A.J, Solntsev S.K, Shaw J.B, Martin M.J, Vizcaino J.A, Alpi E., Danis P. et al..  2018.  ProForma: A Standard Proteoform Notation. Journal of Proteome Research. 17:1321-1325.
Cesnik A.J, Shortreed M.R, Schaffer L.V, Knoener R.A, Frey B.L, Scalf M., Solntsev S.K, Dai Y.X, Gasch A.P, Smith L.M.  2018.  Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. Journal of Proteome Research. 17:568-578.
Smith L.M, Kelleher N.L.  2018.  Proteoforms as the next proteomics currency. Science. 359:1106-1107.
Rytz T.C, Miller M.J, McLoughlin F., Augustine R.C, Marshall R.S, Juan Y.T, Charng Y.Y, Scalf M., Smith L.M, Vierstra R.D.  2018.  SUMOylome Profiling Reveals a Diverse Array of Nuclear Targets Modified by the SUMO Ligase SIZ1 during Heat Stress. Plant Cell. 30:1077-1099.
Millikin R.J, Solntsev S.K, Shortreed M.R, Smith L.M.  2018.  Ultrafast Peptide Label-Free Quantification with FlashLFQ. Journal of Proteome Research. 17:386-391.

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