Publications

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Rolfs Z., Millikin R.J, Smith L.M.  2020.  An Algorithm to Improve the Speed of Semi and Non-specific Enzyme Searches in Proteomics. Current Bioinformatics. 15:1065-1074.
Rolfs Z., Solntsev S.K, Shortreed M.R, Frey B.L, Smith L.M.  2019.  Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion. Journal of Proteome Research. 18:349-358.
Rolfs Z., Frey B.L, Shi X.D, Kawai Y., Smith L.M, Welham N.V.  2021.  An atlas of protein turnover rates in mouse tissues. Nature Communications. 12
Rolfs Z., Smith L.M.  2021.  Internal Fragment Ions Disambiguate and Increase Identifications in Top-Down Proteomics. Journal of Proteome Research. 20:5412-5418.
Russell J.N, Butler J.E, Hamers R.J, Smith L.M, Bent S.F.  2003.  Creating Chemical and Biological Diamond Interfaces.
Russell JD, Hilger RT, Ladror DT, Tervo MA, Scalf M, Shortreed MR, Coon J.J, Smith L.M.  2011.  Parallel Detection of Intrinsic Fluorescence from Peptides and Proteins for Quantification during Mass Spectrometric Analysis. Analytical Chemistry. 83:2187-2193.
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
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.
S
Sanders JZ, MacKellar SL, Otto BJ, Dodd CT, Heiner C, Hood LE, Smith L.M.  1990.  Peak height variability and accuracy in automated DNA sequencing. Struct. Methods, Proc. Conversation Discip. Biomol. Stereodyn., 6th. 1:89-102.
Saracco S.A, Hansson M., Scalf M., Walker J.M, Smith L.M, Vierstra R.D.  2009.  Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis. Plant Journal. 59:344-358.
Scalf M., Westphall M.S, Krause J., Kaufman S.L, Smith L.M.  1999.  Controlling charge states of large ions. Science. 283:194-197.
Scalf M., Westphall M.S, Smith L.M.  2000.  Charge reduction electrospray mass spectrometry. Analytical Chemistry. 72:52-60.
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.
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.
Schaffer L.V, Millikin R.J, Miller R.M, Anderson L.C, Fellers R.T, Ge Y., Kelleher N.L, LeDuc R.D, Liu X., Payne S.H et al..  2019.  Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics.
Schaffer L.V, Tucholski T., Shortreed M.R, Ge Y., Smith L.M.  2019.  Intact-Mass Analysis Facilitating the Identification of Large Human Heart Proteoforms. Analytical Chemistry. 91(17)
Schaffer L.V, Anderson L.C, Butcher D.S, Shortreed M.R, Miller R.M, Pavelec C., Smith L.M.  2021.  Construction of Human Proteoform Families from 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Top-Down Proteomic Data. Journal of Proteome Research. 20:317-325.
Schaffer L.V, Millikin R.J, Shortreed M.R, Scalf M., Smith L.M.  2020.  Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data. Journal of Proteome Research. 19:3510-3517.
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.
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.
Sheynkman G.M, Shortreed M.R, Cesnik A.J, Smith L.M.  2016.  Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. 9:521-545.
Shortreed M.R, Chang S.B, Hong D.G, Phillips M., Campion B., Tulpan D.C, Andronescu M., Condon A., Hoos H.H, Smith L.M.  2005.  A thermodynamic approach to designing structure-free combinatorial DNA word sets. Nucleic Acids Research. 33:4965-4977.
Shortreed M.R, Lamos S.M, Frey B.L, Phillips M.F, Patel M., Belshaw P.J, Smith L.M.  2006.  Ionizable isotopic labeling reagent for relative quantification of amine metabolites by mass spectrometry. Analytical Chemistry. 78:6398-6403.
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.
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.

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