Publications

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2022
Miller R.M, Knoener R.A, Benner B.E, Frey B.L, Scalf M., Shortreed M.R, Sherer N.M, Smith L.M.  2022.  Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1 br. Journal of Proteome Research. 21:993-1001.
Carr A.V, Frey B.L, Scalf M., Cesnik A.J, Rolfs Z., Pike K.A, Yang B., Keller M.P, Jarrard D.F, Shortreed M.R et al..  2022.  MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses. Journal of Proteome Research. 21:410-419.
Hansen S.R, White D.S, Scalf M., Correa I.R, Smith L.M, Hoskins A.A, Staley J.P.  2022.  Multi-step recognition of potential 5' splice sites by the Saccharomyces cerevisiae U1 snRNP. eLife. 11
Spiniello M., Scalf M., Casamassimi A., Abbondanza C., Smith L.M.  2022.  Towards an Ideal In Cell Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules. International Journal of Molecular Sciences. 23
2021
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
Lu L., Scalf M., Shortreed M.R, Smith L.M.  2021.  Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics. 32:1319-1325.
2020
Millikin R.J, Shortreed M.R, Scalf M., Smith L.M.  2020.  A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics. Journal of Proteome Research. 19:1975-1981.
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.
2019
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.
2018
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.
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.
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.
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.
2017
Dai Y.X, Shortreed M.R, Scalf M., Frey B.L, Cesnik A.J, Solntsev S., Schaffer L.V, Smith L.M.  2017.  Elucidating Escherichia coil Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database. Journal of Proteome Research. 16:4156-4165.
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.
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
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.
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.
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.
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.
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.
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
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.
2015
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.

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