Publications

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Journal Article
Book A.J, Yang P.Z, Scalf M., Smith L.M, Vierstra R.D.  2005.  Tripeptidyl peptidase II. An oligomeric protease complex from Arabidopsis. Plant Physiology. 138:1046-1057.
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.
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.
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.
Pellitteri-Hahn M.C, Halligan B.D, Scalf M., Smith L.M, Hickey W.J.  2011.  Quantitative proteomic analysis of the chemolithoautotrophic bacterium Nitrosomonas europaea: Comparison of growing- and energy-starved cells. Journal of Proteomics. 74:411-419.
Li Q.Y, Uygun B.E, Geerts S., Ozer S., Scalf M., Gilpin S.E, Ott H.C, Yarmush M.L, Smith L.M, Welham N.V et al..  2016.  Proteomic analysis of naturally-sourced biological scaffolds. Biomaterials. 75:37-46.
Gemperline D.C, Marshall R.S, Lee K.H, Zhao Q.Z, Hu W.M, McLoughlin F., Scalf M., Smith L.M, Vierstra R.D.  2019.  Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in Arabidopsis. Journal of Biological Chemistry. 294:17570-17592.
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.
Chen X., Lu L., Mayer K.S, Scalf M., Qian S., Lomax A., Smith L.M, Zhong X..  2016.  POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis. Elife. 5
Gemperline D.C, Scalf M., Smith L.M, Vierstra R.D.  2016.  Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine. Proteomics. 16:920-924.
Lamos S.M, Krusemark C.J, McGee C.J, Scalf M., Smith L.M, Belshaw P.J.  2006.  Mixed isotope photoaffinity reagents for identification of small-molecule targets by mass spectrometry. Angewandte Chemie-International Edition. 45:4329-4333.
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.
Lu L., Scalf M., Shortreed M.R, Smith L.M.  2021.  Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics. 32:1319-1325.
Aguilar-Hernandez V., Kim D.Y, Stankey R.J, Scalf M., Smith L.M, Vierstra R.D.  2017.  Mass Spectrometric Analyses Reveal a Central Role for Ubiquitylation in Remodeling the Arabidopsis Proteome during Photomorphogenesis. Molecular Plant. 10:846-865.
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.
Zhang X., Scalf M., Berggren T.W, Westphall M.S, Smith L.M.  2006.  Identification of mammalian cell lines using MALDI-TOF and LC-ESI-MS/MS mass spectrometry. Journal of the American Society for Mass Spectrometry. 17:490-499.
Knoener R., Evans E., Becker J.T, Scalf M., Benner B., Sherer N.M, Smith L.M.  2021.  Identification of host proteins differentially associated with HIV-1 RNA splice variants. eLife. 10
Lee J.E, Mirza S.P, Didier D.N, Scalf M., Olivier M., Greene A.S, Smith L.M.  2008.  Identification of Cell Surface Markers to Differentiate Rat Endothelial and Fibroblast Cells Using Lectin Arrays and LC-ESI-MS/MS. Analytical Chemistry. 80:8269-8275.
Guillen-Ahlers H., Rao P.K, Levenstein M.E, Kennedy-Darling J., Perumalla D.S, Jadhav A.Y, Glenn J.P, Ludwig-Kubinski A., Drigalenko E., Montoya M.J et al..  2016.  HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics. 107:267-273.
Li Q., Shortreed M.R, Wenger C.D, Frey B.L, Schaffer L.V, Scalf M., Smith L.M.  2017.  Global Post-Translational Modification Discovery. J Proteome Res.
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.
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.
Knoener R.A, Becker J.T, Scalf M., Sherer N.M, Smith L.M.  2017.  Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry. Scientific Reports. 7
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.
Buxton K.E, Kennedy-Darling J., Shortreed M.R, Zaidan N.Z, Olivier M., Scalf M., Sridharan R., Smith L.M.  2017.  Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. Journal of Proteome Research. 16:3433-3442.

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